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SP-1 sites; AP-1 sites, Ap-2 sites; motifs 1-4; CCATT sites; exon 1 start
>rat D50092 http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6&dopt=g&db=n&uid=01235732
tcttcctctttaccaatttcttgttaccaaagttccacgatggcctttttctttccgttaggtaacctttcattttctcgactacccattatgtaacgggagcgctgggttctggatcagtcttccattaaagatgacttttatagtctgtgagcgtcgtcacagagtgctgacactggggtggggaggggagtacggggggagggggttaaacagataacaagcatttaagccagtacggagcggtgactcatcccaccgcgagaagccattggtgagcatcacgctccgcccctcgccccgcccagcccccggcctgtcgggtccctcaccacgccccgctcccccgcgttgtcagagcagcagacggagtctgagtctgagcgtcgcg-----tcggtggcag
>mouse2 U29186 Lee http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6&dopt=g&db=n&uid=02865214
tcttcgttaccaatttcttgttaccaaagttcaacgatggcttcctcgctccgttaggtaacctttcattttctcaactacccattatgtaacgggagcattgggtactggatcagtcttccattaaagatgatttttatagttgctgagcgtcgtcagggagtgctgacactgggggcggtttaaacagatacaagcatttaagccagtccggagcggtgactcattcccccaccccccacccccccgcgagagacgcggcgcggccattggtgagcatcacgccccgcccctcgcccagcctagctcccgcctgccccgcccctttccactcccggctcccccgcgttgtcggatcagcagaccgattctgggcgctgcgtccgatcggtggcag
>hamster M14055 Basler http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6&dopt=g&db=n&uid=00191424
tctccctctttagcaatttcttgctcctagagtttcagcaattgctttctcgctccattaggcaacctttcattttctcaccttccccattatgtaacgggagcaatgggttctggaccagtcttccattaaagatgatttttatagtcggtgagcgccgtcagggagtgatgacacctgggggcggtttaaaccgtacaatcccttaaaccagtctggagcggtgactcatggcgcggccattggtgagcacgacgcaagccccgccccacccagcccggccccgccctgctacccctcctgactcactgccccgcccgctcccccgcggcgtccgagcagcagaccgagaaggcacatcgagtccactcgtcgcgtcggtggcag
>human U29185 Lee http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6&dopt=g&db=n&uid=02865216
tctcctctttagaaatttctggttgccaaagttccagaaattgcttcctcattcctgagcctttcattttctcgatttctccattatgtaacggggagctggagctttgggccgaatttccaattaaagatgatttttacagtcaatgagccacgtcagggagcgatggcacccgcaggcggtatcaactgatgcaagtgttcaagcgaatctcaactcgttttttccggtgactcattcccggccctgcttggcagcgctgcaccctttaacttaaacctcggccggccgcccgccgggggcacagagtgtgcgccgggccgcgcggcaattggtccccgcgccgacctccgcccgcgagcgccgccgcttcccttccccgccccgcgtccctccccctcggccccgc
>sheep1 U67922=X79914 Lee http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6&dopt=g&db=n&uid=01778172
tgtccttttcagaaatttctggttaccagagttcccgaaattgctttctcattccctaatctttcattttctccattacgtaacgagaagctggggctttggccgattttccctctaaagatgatttttatcgtcaacaagcaatttcagggagtgatgagccagggaggcggtgttagttgatgctagcgtttatgctagtctcaactcgtttttcccagggacttagattcctgggtctgccggtaaaccccgggcgcccgcagcgggcgcgcctgagcgtgcgcgcgccgtcgcctccccccccccgcagctcctcctctgcacggcgactcaccagccctagttgccagtcgctgacagccgcagagctgagagcgtcttctctcccagaggcaggt
>cow D26150 Yoshimoto http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6&dopt=g&db=n&uid=00442463
tgtcccttttagaaatttctggttaccaaagttccagaaattgctttctcattccctaatctttcattttctccattacgtaacgagaagctggggctttggccgattttccctttaaagatgatttttatcgtcaacaagcaatttcagggagtgatgagccggggaggcggtattagctgatgctagcgtttaagctagtctcaactcgtttttcccagggacttagattcctgggtctgccagtaaaccccgggcgccggcagcgggtgcgcctgagcgtcgcgcgcgccgtcgcctccccgcccctgcccctcctcctccgcccggcgacttacccgccctagttgccagtcgctgacagccgcagagctgagagcgtcttctctctcgcagaagca
>mouse1 X79932 Saeki http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6&dopt=g&db=n&uid=00517361
cttcctcgctccgttaggtaacctttcattttctcaactacccattatgtaacgggagcattgggtactggatcagtcttccattaaagatgatttttatagttgctgagcgtcgtcagggagtgctgacactgggggcggtttaaacagatacaagcatttaagccagtccggagcggtgactcattccccccaccccccacccccccgcgagagacgcggcgcggccattggtgagcatcacgccccgcccctcgcccagcctagctcccgcctgccccgcccctttccactcccggctcccccgcgttgtcggatcagcagaccgattct
>mouse3 U52821 Baybutt http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6&dopt=g&db=n&uid=01297087
aatgtcgaaaatcttcgttaccaatttcttgttaccaaagttcaacgatggcttcctcgctccgttaggtaacctttcattttctcaactacccattatgtaacgggagcattgggtactggatcagtcttccattaaagatgatttttatagttgctgagcgtcgtcagggagtgctgacactgggggcggtttaaacagatacaagcatttaagccagtccggagcggtgactcatccccccccacccccacccccccgcgagagacgcggcgcggccattggtgagcatcacgccccgcccctcgccccgcctagctcccgcctgccccgcccctttccactcccggctcccccgcgttgtcggatcagcagaccgattct
>ra tcttcct-ctttaccaatttcttgttaccaaagttccacga-tggcctttttctttccgttaggtaacctttcattttctc
>mo tcttc--g-tt-accaatttcttgttaccaaagttcaacga--tggcttcctcgctccgttaggtaacctttcattttctc
>ha tctccctgctttac-aatttcttgctcctagagtttca-gcaattgctttctcgctccattaggcaacctttcattttctc
>hu tctcct--ctttagaaatttctggttgccaaagttcca-gaaattgcttcctcattcc-t--g--agcctttcattttctc
>sh tgtcctt--ttcagaaatttctggttaccagagttccc-gaaattgctttctcattccct-----aatctttcattttctc
>co tgtccct--tttagaaatttctggttaccaaagttcca-gaaattgctttctcattccct-----aatctttcattttctc
....o.o.o....oo.o..ooooooo.o:o.o:o.oooo:o:.o:..:..ooo..oo..ooo.o.....o:.ooooooooooooo
>ra ctttcattttctcgacta-cccattatgtaacgg-gagcgctgggttctggatcagtcttccattaaagatgacttttatagtctgtgagcgtcgtcacagagt
>mo ctttcattttctcaacta-cccattatgtaacgg-gagcattgggtactggatcagtcttccattaaagatgatttttatagttgctgagcgtcgtcagggagt
>ha ctttcattttctcaccttccccattatgtaacgg-gagcaatgggttctggaccagtcttccattaaagatgatttttatagtcggtgagcgccgtcagggagt
>hu ctttcattttctcgatttctccattatgtaacggggagctggagctttgggccgaatttccaattaaagatgatttttacagtcaatgagccacgtcagggagc
>sh ctttcattttct--------ccattacgtaacgagaagctggggcttt-ggccgattttccctctaaagatgatttttatcgtcaacaagcaatttcagggagt
>co ctttcattttct--------ccattacgtaacgagaagctggggcttt-ggccgattttccctttaaagatgatttttatcgtcaacaagcaatttcagggagt
>ra tcacagagtgctgacac-tggggtggggaggggagtacggggggagggggttaaacagataacaagcatttaagccagtacggagcggtgactca
>mo tcagggagtgctgacac-tgggggcggt-----------------------ttaaacagatacaagcatttaagccagtccggagcggtgactca
>hu tcagggagcgatggcacccgcaggcggt-------------atcaactgatgcaagtgttcaagcgaatctcaactcgttttttccggtgactca
>sh tcagggagtgatgagccagggaggcggt-------------gttagttgatgctagcgtttatgctagtctcaactcgtttttcccagggactta
>co tcagggagtgatgagccggggaggcggt-------------attagctgatgctagcgtttaagctagtctcaactcgtttttcccagggactta
>ra gtgactcat---cccacc------------gcgagaa----------gccattggtgagca----tcacgctccgcccctc--------gccccgcccagcccccgg-cctgtcgggtccctcaccacgcccc------------gctccccc_gcgttgtcagagcagcagacggagtctgag----------------cgtcgcgtcggtggcag
>mo gtgactcattcccccaccccccacccccccgcgagagacgcggcgcggccattggtgagca----tcacgccccgcccctc--------gcccagcctagct-cccg-cct------------gccccgcccctttccactcccggctccccc_gcgttgtcggatcagcagaccgattctgggcg-----------ctgcgtcgcatcggtggcag
>ha gtgactcat--------------------------------ggcgcggccattggtgagcacgacgcaagccccgccccacccagcccggccccgccctgctacccctcctgactca----ctgccccgcccg-------------ctccccc_gcggcgtccgagcagcagaccgag--aaggcacatcgagtccact-cgtcgcgtcggtggcag
>hu gtgactca--ttcccggccctgc--ttggc-agcgctgcaccctttaacttaaacctcggccggccgcccgccgggggcacagagtgtgcgccgggccgcgcggcaattggtccccgcgccgacctccgcccgcgagcg_ccgccgcttcccttccccgccccgcccgcgtccctccccctcggccccgcgcgtcgcctgtcctccga------_gccagtcgctgacagccgcggcgccgcgagcttcc
>sh gggacttagattcctgggtctgccggtaaaccccgggcgcccgcagcgggcgcgcctgagcgt-----------------------------------gcgcgcgccgt--------cgcc--tccccccccccgcagctcctcctctgcacggcgactcaccagc-----------------------------------cct------_agttgccagtcgctgacagccgcagagctgagagcgtct
>co gggacttagattcctgggtctgccagtaaaccccgggcgccggcagcgggtgcgcctgagcgt----------------------------------cgcgcgcgccgt--------cgcc--tccccgcccctgcccctcctcctccgcccggcgacttacccgccct-----------------------------------------_agttgccagtcgctgacagccgcagagctgagagcgtct
exon 1
gcgttgtcagagcagcagacggagtctgag----------------cgtcgcgtcggtggcag gtaagcgggctgctgaagcc D50092 Rattus norvegicus Saeki,K 1997
gcgttgtcggatcagcagaccgattctgggcg-----------ctgcgtcgcatcggtggcag gtaagcgggctgctgaagcc U29186 Mus musculus Lee,I.Y 1998
gcggcgtccgagcagcagaccgag--aaggcacatcgagtccact-cgtcgcgtcggtggcag gtaagcgg-cttctgaaggt M14055 Mesocricetus auratus Basler,K 1987
------gccagtcgctgacagccgcggcgccgcgagcttctcctctcctcacgaccgaggcag gtaaac-gcccggggtggga U29185 Homo sapiens Lee,IY 1998
ctagttgccagtcgctgacagccgcagagctgagagcgtcttctctcc------cagaggcag gtaaatagccacgtagtcct U67922 Ovis aries Lee,IY 1998
--agttgccagtcgctgacagccgcagagctgagagcgtcttctctc-t--cg-cagaagcag gtaaatagccgcgtagtcct D26150 Bos taurus Yoshimoto,J 1994
exon1b
>hu gtaaac-gcccggggtgggaggaacgcgggcgggggcaggggagagcgc
>co gtaaatagccgcgtagtcctttaaactcccagcggaggacgccaaccctgggtcttgcggccgaggccc-aggg-acccagccgaatcggattgg-tgggaggcagaccttgacc_gtgagtagggctgggggcttgcggcgggcgcggggaacgtcgggcctgttg
>sh gtaaatagccacgtagtcctttaaacccccagcggaggccgcc---cccgg--cttgcggccgaggccctagggcactcagccggatcggactggctgggaggcagaccttgacc_gtgaggaggactgggggcttccggcgggcgcggggaacgtcgggcctgttt
--
>ra 2832 2878 5109 5206
>mo 8612 8658 10849 10946 28680 30687
>ha 333 342 349 351 354 410
>hu 12634 12767 15390 15488 25464 27817)
>sh 5666 5717 8139 8236 22268 26295
>co 803 855 3298 3395
exon 1 intron 1 exon 2
>rat 47 2230 98 83% identical to mouse over intron 1
>mouse 47 2190 98 539 bp in 3 retrotransposons in intron 1
>hamster 57 - 98
>human 134 2622 99 only last 180 bp related to cow in intron 1, 353 bp in 3 retrotransposons
>sheep 52 2421 98 91% identical to cow over intron 1
>cow 53 2442 98
Though the prion gene is chock-full of retrotransposons, there are no recognizable ones here except for 3 each in human and mouse intron 1:
>mouse intervening repeats in region of exon 1-2
repeat_region 7980..8069 PB1D7
exon 1 8612..8658
repeat_region 9619..9844 B3 = 226 bp
repeat_region 10044..10163 B1-F = 120 bp
repeat_region 10070..10163 PB1D7 = 193 bp
exon 2 10849..10946
>human intervening repeats in region of exon 1-2
repeat_region 11478..11800 AluJo
exon 1 12634..12767
repeat_region 14413..14498 L1MC1 = 86 bp
repeat_region 14583..14653 MIR = 71 bp
repeat_region 14752..14947 L1ME3 = 196 bp
exon 2 15390..15488
>sheep intervening repeats in region of exon 1-2
repeat_region 3756..4215 MLT1F
exon 1 5666..5717
exon 2 8139..8236
>ra intron 1
gt2881 aagcgggctg ctgaagccag gcgtcagcga gcattcagcc ttcctcccgt cgacaagctc
2941 ggcttactgt gcctctccgg gacttgaggc cgcggggctg ggactggggt tgagcttggc
3001 taggaggtgg ctgtgcaccc gctgtgcgcg actcctggag ggaccgaatc ccagggcagc
3061 gaggccggga gccgagcctg attcacagct caacatcgct gtgggggatg gggggttggg
3121 ggggtggcat cttttaactg ccctgtgctg ttttcttctc tcgttgtaat agctacagcg
3181 aacataattt caccccgtga ttccaccacg gtctcatccg tcctcagcac cacactcatt
3241 gctccccttg ctcagtttca tactcagcgc agccgttcgc cttcactgcc ctgcctaggc
3301 gttttcatgg ttgtcttata ttcttttact ttgaatatcg tggtttaata gcagttgccg
3361 gtgtgctaaa ttcctcattt ccttaagaga aactcctggg aggatggaat taaagacgtt
3421 gcaaatttaa ttataccaca aacaggaatc aaaattttgc attaaaatgc cagacatctt
3481 gaaaaattta actattcaat aaaaaaaaaa aaggaactac tttacctaca cacacatccg
3541 agtgcttcaa agagtccaag gaaatagaaa gctaagggat gatttgggtt gtatttgaat
3601 ctgacacgag ctttccatat tatttatagc agggactgaa ggatgagtca ttttctgaat
3661 aagatgcaaa ttaaagcaag tttgttgtct ttacatcgat taaacagaca gagatgatga
3721 cagcagcaac cctaacctag aggttgtctg aaaccaccgt gttcaagttt ggggagcagg
3781 tggccctcct taagagctcg attgattgct ttacaaccaa cgttatgact tggcattgcc
3841 tggggttcct tttatttatt cctttcttta aaagactact atctatttta tgagcatgag
3901 tgtttcgctc cacagaagca tgtatacaag cctggttctg cggaggtcag aagagacagg
3961 gtgttggaag ccctggaact agagctaggg atgattctgt gagcccctgc cacaggggag
4021 ctcagatccc caatccaggc tgtctggaag agcagccaga gctcttaact accgaacacc
4081 ccccccccca tcccctctca ttcacattta gaaaggagaa aactgctacc catgtctggc
4141 atttatttca gagattaact gtgcaaaact cgatgtgaaa gtatactatt ctgtttccca
4201 gtcacactta gttgacagtg taagtcagta agggctttgg ttggttggtt tggttggttg
4261 gttcctgggt tagtctggat gtgcttgttg agagctcaat aacaggcttt caatatggat
4321 atgtagctgg gaattcgcta tgtagaccag gcaggcctca aatttgtggc aatcctccct
4381 gtgattcccc agaatgccct ggtacaggca taagccactg tgcccagccg taaaacaatc
4441 tggtgaggta ttattagttg catgctgtga cccagaaacc ccacttctgg caattcacct
4501 gccgtggtgg aaccaacaaa gggctagggg agccatatgg ccaacagtta cagaaaatta
4561 gatccaaggg aaaagcaacc taaatgttta acaggcgagc agctaagaaa ctgacaggct
4621 cgtgagggag ctgtagcaat cccgaagaac actcttcatt ttagactcca tgtatccctg
4681 ggaaaaacag agtcaaagta caggttagga gaccgggact cctctggacc catgctgtcc
4741 tctgaaaagc ccagaagagc tataatgaaa gagctcagaa gatgtctgat cttggctttc
4801 tttatgtttg ttgctgtatt gtttccacta acaaacaact aaaaaaaaaa aaaaagttca
4861 caggcttctt tccttaaaat actggggatt gaacccaggg atagtttttt agtgtctaaa
4921 ttaacatgac catgccctgt ttgccttttt ggagtatgtt tgaatctgcc cttatttcca
4981 ttctcaaata ctgctccatt ttatatgact atttagtttt ggcttgataa tttgcatatg
5041 agattagatc atctttcagt tctcagactt atttatcaat tctagttttt ctttttgttg
5101 ttttaaag
>mou intron 1
gt aagcgggctg ctgaagccag gccttggcga gcactcagcc
8701 ttccgtcgtc aagctcggct cactgcgcct ctcggggcct tgaggccacg gggactagga
8761 ctgggactgg gactggggct gagtctggct gggaggtgac tgtacacccc ctgtgcgcga
8821 ctcctggagg aaccgaatcc cagggcagcc aggccgggag ccagcctttc cttcccgagc
8881 cagattcaca gctcagcatc gctggggatg ggggtggcat cttttgactg tccttggctg
8941 ttttcttctc tctttgtagt agctacagcg aacataattt tacctcgtta ttccaccaca
9001 gtcattactc ccttgcacag tttcattctc aacgtcgccg tgcgccttca ctgccctgtc
9061 taggcgtttt catgattgtc tattttcttg tactttgaat accgtggttt aatagcagtt
9121 gcgggtgcgc agaattctcc atttccttaa gagaaactcc tgggagaatg ggactaaaga
9181 cgtgcaaatt taattatatc gcaaacagga atcaaaattt tgcattaaaa tgccaaacat
9241 cttgaaaaat taactattca atgaagaaaa ggaactactt tacctacaca cacatccgag
9301 agcttcgagg aggcgaagga aatagaaagc taagggatga tttgggttgt atttgaatct
9361 gacacaagct ttccatatta tttatagcag ggactaaacg atgagtcatt ttctgaataa
9421 gatgcaaatt aaagcaagtt tgtttgttgt ctttacatct attaaataga cagagacaat
9481 ggcaacagca accctaacct agaggttgcc tgaaagtgtc aggtttggga acaagtggcc
9541 ctgcttaagg gctagaaaga ttgctttaca accaacaatc atgacttgac attgcctggg
9601 gttccttttg tctattcctt ttttaaaaga ctagtgttta ttttatgtgc atgagtgttt
9661 tgcatccaca ttcgcctgta tacacacctg gttctgtgga ggtcaggaga gggtgctgga
9721 tgccctggca ctagagccgt gaatggttat gtgagcccct gccacagggg agctcagaac
9781 caaatccagg tcctctggaa gagcaaccag agctcttaaa acttctaagt atccctccat
9841 cccctttcca tcatatttgg aaaggagaaa actgctaccc atgcctggca tttatttcag
9901 agattaactg tctgtgtaaa acttgacatt gaaagtgcac tattctgttt cccattcata
9961 cttagttgag actactgtaa gtcagttagg gctttttttg tttggttcct tggttagttt
10021 ggagtgtgtt tgtgagctca ttaacaggct ttcagtatgt agctgaaatt tgctgtgtag
10081 accagacagg cctcaaattt gtggcaatcc tccctgcatc ttcccagaat gccctggtac
10141 aggcataaac caccgtgccc agcagtaaaa caatctggtg aggtattatt agtcgtgtgc
10201 tgtgacccag aaaccccact cctggcaatt tactgggaag gaacaaacaa agggctaggg
10261 gagccatatg gcctgcagtt agagaaaatt agatccaact gaaaaatcaa cctaaaggtg
10321 taaaagccaa gcagttaaga aactgacagg ctcatgatgg aagccgaggc catcgtgaac
10381 actcttcatt ttaggcccca cgtatcactg gggacaactg agagtcaaag tacaggtaag
10441 gagaccaagg cttttcagga ctcaggctgt ctcagtgaaa agcccagaag agcagtaatt
10501 gaaagagctc agacgatgtg tctgatctcc tctgtttgtt tgttgctgta ttatttccac
10561 taacttattt gggaggaaaa aaaacagttc acaggcttct tttcttgaaa tactggggat
10621 tgctgggatc gaacccaggg ataggttttt agtttctaaa ataacataga tcatgccctg
10681 tttgcttttt ggaatatgtt tgcgctgccc ttattttcat gttcaaatac tgctccattt
10741 tgcgtgactc tttagtattg gtttgatgat ttgcatatta gattagattg tatttcagtt
10801 ctcagactta tttatcaatt ctagttttct ctttttgttg ttttaaag
>ha partial intron 1
gtaagcggct
421 tctgaagcct ggccccggga agggtgctgg agccaggcct cggtaagcct tcggcttccc
481 agagccaagc ccggcttact ccggctctcg gggcgctgag gccgcggggc tgaggttgag
541 tctggctggg aggtgaccgc gcacccgcag ccgcgcgtct ccttgaggga ccgaacccca
601 ggagaggcca ggagccatcc cttcctcccg agcccggctc acccccagag tcgctcgggg
661 atgggggatg ggggatgggg tggcatcttt tgactgtcgt ttgctgtttt cttctctctt
721 tgtaatagct acagcgaaca taattttacc cagggttcca ccgtggtctc gtccgtcctc
781 ggcatctctc agtccagtac atacccaagg
>hu intron 1
ccc cctcggcccc gcgcgtcgcc tgtcctccga gccagtcgct
12721 gacagccgcg gcgccgcgag cttctcctct cctcacgacc gaggcaggta aacgcccggg
12781 gtgggaggaa cgcgggcggg ggcaggggag ccgcgggggc cgagtgagga ccccgggcct
12841 cgggtcccag gcgcaagggt gcccggccgg gcggggtcgg gaccccagtg aggaggggcc
12901 gggggctgcc ccgcgggcgc gtgacggtct cgggcctgcc cggctgcgct ggtctccgct
12961 cgggtgaggc ggcttggctt cgcttttcag gttaggaaag ctccctttac tgcgcgttgg
13021 ggggctgggg gagctggcgg agccacgtta gggaggtcgg tggcgccggg gtgtctcagc
13081 gccccctgca ccccgcgcgg gtccggccca gcgggcgatc gctggcgccc agggaactcc
13141 gggagggccg ccagcgggct ccgcaggcgc ggggcgggga ggggcgcctg ggggccgcgg
13201 ggctcgcgct ccccgcccgt tggccgcccc tcggaggccg agatcggggc ccagaacgcc
13261 ccttggcaaa gcctggcgct tccgcgatgc ccagagggtg cttgggggga tggagagagg
13321 ggcgcccgcc ggggtagttc cgggagcctc ggtgcctccc gccgcagctg cagcgttcct
13381 cccgggaggc ggcccagccc ttcatcctcg ccgcctgagc ttctccgagg ggggctgcag
13441 ccttgcggcc gttgccaccg cctggagaag cggcccacgc ggactgacgg gcgggggcgg
13501 ggcctcgggc ctcggcgggg gcggggtccg gggaggcccc accctctgtt ctccaggggc
13561 ggggagagag gagctgcagg tctgcggcct ggccccaggt gcgatggcgg accccagctt
13621 ggccagtcac attcctccca gtccccctgg agggagaacg ctggccatgg ggggctccaa
13681 ggaacaacca gcctcggatg acgacccttg ggtcaccggt ctccccacct gtgcggcagg
13741 cgccttcacg tttcattatt aaacaatggg gagaaatcca tgtttactgt cctttttagg
13801 aattttttgc tcttctcttt gaggtggctg taggaaatag attttttttt taacctcgca
13861 attccaccac ggtcacatcc atcctcgcca tcgcagagcc acagctctcc gtttttgttt
13921 cctagcctcc agattctcac acaacacagt gcagtttcac tgctgtaatg atgaggatct
13981 tcatggccgc gttattttct tgttctgaga gcatcacggt ttaattagca gttccccata
14041 tgatttgaag tgtttcccgt ttccttaggg aaaactcctg gtagaatagg attaaggatt
14101 tttacaaata taattatcaa aaacatagga acagggaatt ggataaatat gttaaacttc
14161 tggaaaaatc aacaacgctc ttagatttgt agaagaaagg aaaaaatcac cagtggaaag
14221 gagcaatttt acttacacaa acacagagaa ggtcttacag tgaaaaaaag ctaaccagta
14281 aggggaaaag caggcagagg ggtaggatgt gatttgtatg ttatttatat ctaacacaag
14341 tcttccacac cgaaaggaaa atattaagat tataatagat aaatggcaaa atgatgagtc
14401 atttacacaa taaaatgcaa attagagcat gtttgggtta tcattttaca tctattaaaa
14461 taaccaaaat aattaatagt aacagcaacc cttgctggaa ggttgcccaa aacttggcat
14521 tttcaagtgt ctggggaggt ggcagggctt tggggtcaca aagatggttc tgcagtcaat
14581 tttgtgacct tggacaggct acctaatttc ctgatcctcc ttttgtccat tcatagaatg
14641 gaggaaatga tagctacttt ctgcgtctgt atgtatgagt tattgggggc atttcgaacc
14701 agtgacaaac attttgttaa gcaatctggt gatgcattaa gaagctggaa gctgtgaccc
14761 agaaacccca ctcctgagaa cttacctgca atggaagaaa caaacaaaca aaaacaggca
14821 tgtattccta gcagaatgat ctaaaattag aacacctgga aaagagccta aatgtataac
14881 accagggcag tagctaagaa aattatgaca cattaactga aatgaacatt atgtaaccac
14941 taaaaatcat gattttggag cctgtgatat gtggggaaaa actgacaagt aaaaaagtgg
15001 gttattaact gcacctgctt actctaacgt gaacgcatat gtgaaaaatc tgaaaggaaa
15061 agcacagaaa atggacgttt tcattgaaat tgtcggtgat cttaattttc ctttggtgaa
15121 tatattgctc tcactaaggg cgtttaaaaa atagttcaca ggttttaatt ttttagatga
15181 aatggaccca cagttttctg taagagaaag gagagattgt tatatttgct acttagaata
15241 aaagattttt agccaacgtt gtttcctttt tcaaatattt ttccattttt ttagttgatt
15301 aatgatttag taatttgtgt attgggtttt tttaagaatc agttcttaga ttcatttatc
15361 aattctagtt ttttgttgtt gtttttaag
>cow intron 1
gtaaa tagccgcgta gtcctttaaa ctcccagcgg aggacgccaa
901 ccctgggtct tgcggccgag gcccagggac ccagccgaat cggattggtg ggaggcagac
961 cttgaccgtg agtagggctg ggggcttgcg gcgggcgcgg ggaacgtcgg gcctgttgag
1021 cgtgctcgtt ggtttttgcc agccgccgct cggttttacc ctcctggtta ggagagctcc
1081 atttactcgg aatgtgggcg ggggccgcgg ctggctggtc cccctcccga ggtatgtggg
1141 tggtgtgtag gaatctagcc ccctcccacg ctcgtccact gcgggagtgg gatgggcgaa
1201 tcgcaccggt agaggggccg cagtcgagga accgctgggg acctcagaag aacaagggcg
1261 agcccgggat ttgggccctc ccgaagccca gaggagtcgc ggaattgggg gtgggggtgg
1321 tggggaagaa acgggcgcca acggggcccg acctcggcgg tgaggagtgc cggagcatcc
1381 gtgggccccc agccgctgct gccgaactcc tcccgagagg cggccctgcc tgccatcacg
1441 cggctgggag gtacctgggt agccgcagcg ggtgggtctc tggcaacccc ccggggatcg
1501 gctctggcgg gcgtacgtgg cctgggcttc agcctcggcg cggggaatca tgggccacct
1561 ggcgctctct ccgggccaga gaaatccagg taccgggaac agtgtttcct gggagctctg
1621 atgtggtgga cccaaaagca aagcgaaatt ttccctgtct cgactgatcc tccagaagga
1681 gggaactcgg ccgtcaggag actgagggga ggggattcag gcgcctctca gagaaccacc
1741 ctcatctgcc agtaagggtg gcaccttcac gcttgatttt tttttttttt tcccctcaca
1801 cgtttgatta ttaaacaacg agaagtccgt tttttgctgt cctttttcgt ttttgttttt
1861 tttttttcct tttcttttgg taccatatgt agcaaataga ttttttaaaa tcataagccc
1921 accaccctca ccatcttttt ttcagtttcc tcgtctccag attcttaaca acaaagcagt
1981 ttcacctccc tgatcatggt tatccttatc tcatggccgg gttattttct tgtacttaag
2041 agcaatcacg ttttattaag cagttccccg aatgctgaac ctttgaagtg ttacctttcc
2101 ttacaaaaga taccacatag aataggatta aaaattttca caagttgtca gagaaaaata
2161 ggaacagaaa attgtataaa aatgtcagac ctctggaaaa tgaacagctc tctcagattt
2221 gaaaattaac ctatgaaaag gaacagtttt cctacggaaa cattgaggtg ctctaacaat
2281 gaaaaagaat cagaaaagga aaaaaacaga gttaggatgt gatttgtata tgatttgtat
2341 ctgatgcaaa tttttcatac ttgtgaaaga aaaatatcaa gattataaaa agataaatgg
2401 tgaaatgaac aatcatttat gaaataaaat acaaatcaaa gcaagtctgg atttacaact
2461 actagtaaaa acaacagtaa cagcaaccac ttctggaaag ttacctagaa atttgcatat
2521 tcagtatgtg aggtggcaag gctttggagt tagaaatatg gtctgcaact aattttacaa
2581 tttgggacct aatttcctca tccccctttt ggacattcat aaaatagagg aaattatacc
2641 tacttcagag tttgccaaga ttaactgtgt aaaactgacc tttagtgtgt atacttttat
2701 tcttttccta gtcacactgc actgggggac gttgtgaatc tgtatgaaat ttgtgaaaaa
2761 cagtcaggtg atcctttaag ccatgaccct aaaacccact cctgggaact tacctgtaat
2821 ggaggaaacc aggaaagaag aagaaaagct gcattcaccc acagaactca gaatgatcta
2881 aaattagatc cagtccggag tcaacctaaa tgtattaata aaatagcagg gcagcagcta
2941 agaaaatcat agcactttaa ctgaaaggaa cattgtgtaa ccatcacgag tcataatttt
3001 agagcctctc tgtgatatac aggaaaaaac tgacaggtca aagtaagatt actcagacat
3061 ggatgcgttt gtggaaaatc tgaatgaaaa atgaatccac agtttgctgt gtatgggagg
3121 agagttcagt gtcacgtttg ctgctttttt taagttagca tcatctcttt tttaaaaata
3181 ctatcatatt ttttccctga gtagattcat tagtggttta ataatttata tactgttatt
3241 ctgttaaata atccgttctt agatttatca attatagttt tttctttttt ttttaag
>sheep intron 1
gta aatagccacg tagtccttta aacccccagc ggaggccgcc
5761 cccggcttgc ggccgaggcc ctagggcact cagccggatc ggactggctg ggaggcagac
5821 cttgaccgtg aggaggactg ggggcttccg gcgggcgcgg ggaacgtcgg gcctgtttag
5881 cgtgctcgtt ggtttttgcc agccaccgct cggttttgcc ctcctggtta ggagagctcc
5941 atttactcgg aatgtgggcg ggggccgcgg ctggctggtc cccctcctga agtatgtggg
6001 tggtgtgtag gaatctagcc ccctcccacg ctcgtccact gcgggagtgg catgggcgga
6061 tcgcaccggt agaggggccg cagtccgagg aaccgctggg gagatcagaa gaacaagcga
6121 gaggccccgg gctctgggcc ctcccgaagc ccagcggaga cgcggaattg ggggtggggg
6181 gtggggaaga agcgggcgcc caacggggcc agacctcggc cgtgaggagt gccggagcga
6241 ccgtgggccc ccagccgctg ctgccgaact cctcccgaga ggcggccctg cttgccatca
6301 cgcggctggg aggtacctgg gtagccgcag cgggtgggtc tctggcagcc ccctggggat
6361 cggctcgggc gggcgtgcgt ggcctgggct tcagcctcgg cgaggggagt catgggcgac
6421 ccggccctct ctccagagaa atccaggtac cgggagcagt gtttcctggg agctctgatg
6481 tggtcgaccc aaaagcaaag cgatattttc gctgtctcga ctgaaggagg gaactcggcc
6541 ctcaggagac tgaggggagg ggatcaggcg cctcttggag aaccaccctc atctgccagt
6601 aagggtggca ccttcacgtt tttttttttg ttgttgttgt tttctcacac gtttgattat
6661 taaacaacga ggagaagtcc gttttttgct gttctttttc gttttttccc ccctctcttt
6721 tcttttggta ccatatgtag caaatagatt ttttaaaatc ataagaccac catcctcacc
6781 atcttgtttt tcagtttcct cgtctccaga ttcttaacaa agcagtttca cttccctgat
6841 gatggttatc ctcatctcat ggccaggtta ttttcttgta cttaagagca atcactgttt
6901 attaagcagt ttcccgaatg ctgaaccttt gaagtgttac ctttccttgc aaaagattcc
6961 gtatagaata ggattaaaaa ttttcacaag ttgtcagaga aaaataagaa cagaaaattg
7021 aataaaatgt cagacctctg gaaaatgaac agctttctca aatttgaaaa ttaactataa
7081 aaaggaacag ttttcctacg gagacactga ggcgctctca gtgaaaaaga acgatgaaaa
7141 agaaccagaa aaggaaagaa aacggagtta tgtatatgat ttgtatctga tgcaaatttt
7201 tcatacttgt gaaagaaaaa tatcaagatt ataaaaagat aaatggtgaa atgaagaatc
7261 atttatggaa taaaatacaa atcaaagcaa gtctggatta tcgttttaca actactagta
7321 aaaacagtaa cagcaaccac tcctggaagg ttacctagaa atttgcatat tcgtttatgt
7381 gaggtggcaa ggctttggag ttagaaatat ggctctgcag ctaattttac aatttgggac
7441 ctaatttcgt catcgtcctt ttgtccattt ataaaataga ggaaattata cctacttcag
7501 gagtttgcca agattaactg tgtaaaactg acctttagca tgtatacatt tattctttcc
7561 ctagtcacac tgcactgggg gacatttgtg aatctatgaa atttgtgaaa aatggatcct
7621 ttaagccatg accctgaaac cccactcctg ggaacttacc tgcaatggaa gaaattcgga
7681 aagaagaaaa gctgcattca cccacagggc tcagaatgat ctaaaattag atccagtcca
7741 gagacaacct aaaggtatta agaaaatagc agggcagcag ctaagaaaat catagcactt
7801 taactgaaag gaacattgtg taacccatca cgtggcataa ttttagagcc tctctgtgat
7861 atataggaaa aaagtgacag gtcaaagtaa gattactcag acatggatgc atatgtggaa
7921 aatctgaata aaaaatggac ccacagtttt ctgtgtatgg gaggagagtt cagtgtcatg
7981 tttgctgctt ttttttagtc agcgtcatct cttttaaaaa tactatcata tttttttcct
8041 tgagtagatt cattagtggt ttaataattt atatactgtt attctattaa ataatccgtt
8101 cttagattta tcaattatag tttgtttttt tttttaag
>ra 300 bp above exon 1
2281 tacatcagtg atgctgcctt tcaccactga aaggcattta cggtggttta tgtatgatat
2341 caaataaaga gtatttaaca cttctttata gttgaaaaag aaaggaaaga agggaatcaa
2401 ccgagaatga taaaccaaca ttcaatggcc aatatacttt ctaagcctct aattctttta
2461 tagtttatgg ggaaatgtca aaaatcttcc tctttaccaa tttcttgtta ccaaagttcc
2521 acgatggctt tttctttccg ttaggtaacc tttcattttc tcgactaccc attatgtaac
2581 gggagcgctg ggttctggat cagtcttcca ttaaagatga cttttatagt ctgtgagcgt
2641 cgtcacagag tgctgacact ggggtgggga ggggagtacg gggggagggg gttaaacaga
2701 taacaagcat ttaagccagt acggagcggt gactcatccc accgcgagaa gccattggtg
2761 agcatcacgc tccgcccctc gccccgccca gcccccggcc tgtcgggtcc ctcaccacgc
2821 cccgctcccc c
>mo 300 bp above exon 1
8041 tgagtttgag gtcagcttaa attacttagt aggaacacca ggccaaattg ggctatggga
8101 ttgtctccaa agataaagaa aaaagggaag gagagaaaag aaaaagaaag gaaagaaggg
8161 gaaaagaagg aatcagcaga gaataaataa gtcaacatgc aatggccaat atactttcta
8221 ggcctctaat tcttttatag tttgtgggaa aatgtcgaaa atcttcgtta ccaatttctt
8281 gttaccaaag ttcaacgatg gcttcctcgc tccgttaggt aacctttcat tttctcaact
8341 acccattatg taacgggagc attgggtact ggatcagtct tccattaaag atgattttta
8401 tagttgctga gcgtcgtcag ggagtgctga cactgggggc ggtttaaaca gatacaagca
8461 tttaagccag tccggagcgg tgactcattc ccccaccccc cacccccccg cgagagacgc
8521 ggcgcggcca ttggtgagca tcacgccccg cccctcgccc agcctagctc ccgcctgccc
8581 cgcccctttc cactcccggc tcccccgcgt t
>ha 300+ above exon 1
1 tcgaaaatct ccctctttag caatttcttg ctcctagagt ttcagcaatt gctttctcgc
61 tccattaggc aacctttcat tttctcacct tccccattat gtaacgggag caatgggttc
121 tggaccagtc ttccattaaa gatgattttt atagtcggtg agcgccgtca gggagtgatg
181 acacctgggg gcggtttaaa ccgtacaatc ccttaaacca gtctggagcg gtgactcatt
241 tccccaggga gaagtggcgc ggccattggt gagcacgacg caagccccgc cccacccagc
301 ccggccccgc cctgctaccc ctcctgactc actgccccgc ccgctccccc gcg
>hu above exon 1
attcctg agcctttcat tttctcgatt
12361 tctccattat gtaacgggga gctggagctt tgggccgaat ttccaattaa agatgatttt
12421 tacagtcaat gagccacgtc agggagcgat ggcacccgca ggcggtatca actgatgcaa
12481 gtgttcaagc gaatctcaac tcgttttttc cggtgactca ttcccggccc tgcttggcag
12541 cgctgcaccc tttaacttaa acctcggccg gccgcccgcc gggggcacag agtgtgcgcc
12601 gggccgcgcg gcaattggtc cccgcgccga cct
>co 300 above exon 1
attccct aatctttcat tttctccatt acgtaacgag
541 aagctggggc tttggccgat tttcccttta aagatgattt ttatcgtcaa caagcaattt
601 cagggagtga tgagccgggg aggcggtatt agctgatgct agcgtttaag ctagtctcaa
661 ctcgtttttc ccagggactt agattcctgg gtctgccagt aaaccccggg cgccggcagc
721 gggtgcgcct gagcgtcgcg cgcgccgtcg cctccccgcc cctgcccctc ctcctccgcc
781 cggcgactta cccgccctag ttg
>sh 240 bp above exon 1
tttcc ctctaaagat gatttttatc gtcaacaagc
5461 aatttcaggg agtgatgagc cagggaggcg gtgttagttg atgctagcgt ttatgctagt
5521 ctcaactcgt ttttcccagg gacttagatt cctgggtctg ccggtaaacc ccgggcgccc
5581 gcagcgggcg cgcctgagcg tgcgcgcgcc gtcgcctccc cccccccgca gctcctcctc
5641 tgcacggcga ctcaccagcc ctagt
>ra bp above exon
ttctttccgttaggtaacctttcattttctcgactacccattatgtaacgggagcgctgggttctggatcagtcttccattaaagatgacttttatagtctgtgagcgtcgtcacagagtgctgacactggggtggggaggggagtacggggggagggggttaaacagataacaagcatttaagccagtacggagcggtgactcatcccaccgcgagaagccattggtgagcatcacgctccgcccctcgccccgcccagcccccggcctgtcgggtccctcaccacgccccgctccccc
>mo bp above exon
ccgttaggtaacctttcattttctcaactacccattatgtaacgggagcattgggtactggatcagtcttccattaaagatgatttttatagttgctgagcgtcgtcagggagtgctgacactgggggcggtttaaacagatacaagcatttaagccagtccggagcggtgactcattcccccaccccccacccccccgcgagagacgcggcgcggccattggtgagcatcacgccccgcccctcgcccagcctagctcccgcctgccccgcccctttccactcccggctcccccgcgtt
>ha above exon
tcgaaaatctccctctttagcaatttcttgctcctagagtttcagcaattgctttctcgctccattaggcaacctttcattttctcaccttccccattatgtaacgggagcaatgggttctggaccagtcttccattaaagatgatttttatagtcggtgagcgccgtcagggagtgatgacacctgggggcggtttaaaccgtacaatcccttaaaccagtctggagcggtgactcatttccccagggagaagtggcgcggccattggtgagcacgacgcaagccccgccccacccagcccggccccgccctgctacccctcctgactcactgccccgcccgctcccccgcg
>hu above exon
attcctgagcctttcattttctcgatttctccattatgtaacggggagctggagctttgggccgaatttccaattaaagatgatttttacagtcaatgagccacgtcagggagcgatggcacccgcaggcggtatcaactgatgcaagtgttcaagcgaatctcaactcgttttttccggtgactcattcccggccctgcttggcagcgctgcaccctttaacttaaacctcggccggccgcccgccgggggcacagagtgtgcgccgggccgcgcggcaattggtccccgcgccgacct
>co above exon
attccctaatctttcattttctccattacgtaacgagaagctggggctttggccgattttccctttaaagatgatttttatcgtcaacaagcaatttcagggagtgatgagccggggaggcggtattagctgatgctagcgtttaagctagtctcaactcgtttttcccagggacttagattcctgggtctgccagtaaaccccgggcgccggcagcgggtgcgcctgagcgtcgcgcgcgccgtcgcctccccgcccctgcccctcctcctccgcccggcgacttacccgccctagttg
>sh bp above exon
tttccctctaaagatgatttttatcgtcaacaagcaatttcagggagtgatgagccagggaggcggtgttagttgatgctagcgtttatgctagtctcaactcgtttttcccagggacttagattcctgggtctgccggtaaaccccgggcgcccgcagcgggcgcgcctgagcgtgcgcgcgccgtcgcctccccccccccgcagctcctcctctgcacggcgactcaccagccctagt
cow and sheep intron 1 are fully alignable w/o intervening repeats, 91% identical
cow GTAAATAGCCGCGTAGTCCTTTAAACTCCCAGCGGAGGACGCCAACCCTGGGTCTTGCGG 60
sheep GTAAATAGCCACGTAGTCCTTTAAACCCCCAGCGGAGGCCGCC---CCCGG--CTTGCGG 55
********** *************** *********** **** ** ** *******
cow CCGAGGCCC-AGGG-ACCCAGCCGAATCGGATTGG-TGGGAGGCAGACCTTGACCGTGAG 117
sheep CCGAGGCCCTAGGGCACTCAGCCGGATCGGACTGGCTGGGAGGCAGACCTTGACCGTGAG 115
********* **** ** ****** ****** *** ************************
cow TAGGGCTGGGGGCTTGCGGCGGGCGCGGGGAACGTCGGGCCTGTTGAGCGTGCTCGTTGG 177
sheep GAGGACTGGGGGCTTCCGGCGGGCGCGGGGAACGTCGGGCCTGTTTAGCGTGCTCGTTGG 175
*** ********** ***************************** **************
cow TTTTTGCCAGCCGCCGCTCGGTTTTACCCTCCTGGTTAGGAGAGCTCCATTTACTCGGAA 237
sheep TTTTTGCCAGCCACCGCTCGGTTTTGCCCTCCTGGTTAGGAGAGCTCCATTTACTCGGAA 235
************ ************ **********************************
cow TGTGGGCGGGGGCCGCGGCTGGCTGGTCCCCCTCCCGAGGTATGTGGGTGGTGTGTAGGA 297
sheep TGTGGGCGGGGGCCGCGGCTGGCTGGTCCCCCTCCTGAAGTATGTGGGTGGTGTGTAGGA 295
*********************************** ** *********************
cow ATCTAGCCCCCTCCCACGCTCGTCCACTGCGGGAGTGGGATGGGCGAATCGCACCGGTAG 357
sheep ATCTAGCCCCCTCCCACGCTCGTCCACTGCGGGAGTGGCATGGGCGGATCGCACCGGTAG 355
************************************** ******* *************
cow AGGGGCCGCAGTC-GAGGAACCGCTGGGGACCTCAGAAGAACAAGGGCGAG--CCCGGGA 414
sheep AGGGGCCGCAGTCCGAGGAACCGCTGGGGAGATCAGAAGAACAAGCGAGAGGCCCCGGGC 415
************* **************** ************* * *** ******
cow TTTGGGCCCTCCCGAAGCCCAGAGGAGTCGCGGAATTGGGGGTGGGGGTGGTGGGGAAGA 474
sheep TCTGGGCCCTCCCGAAGCCCAGCGGAGACGCGGAATTGGGGGTGGGG--GGTGGGGAAGA 473
* ******************** **** ******************* ***********
cow AACGGGCGCC-AACGGGGCCCGACCTCGGCGGTGAGGAGTGCCGGAGCATCCGTGGGCCC 533
sheep AGCGGGCGCCCAACGGGGCCAGACCTCGGCCGTGAGGAGTGCCGGAGCGACCGTGGGCCC 533
* ******** ********* ********* ***************** **********
cow CCAGCCGCTGCTGCCGAACTCCTCCCGAGAGGCGGCCCTGCCTGCCATCACGCGGCTGGG 593
sheep CCAGCCGCTGCTGCCGAACTCCTCCCGAGAGGCGGCCCTGCTTGCCATCACGCGGCTGGG 593
***************************************** ******************
cow AGGTACCTGGGTAGCCGCAGCGGGTGGGTCTCTGGCAACCCCCCGGGGATCGGCTCTGGC 653
sheep AGGTACCTGGGTAGCCGCAGCGGGTGGGTCTCTGGCAGCCCCCTGGGGATCGGCTCGGGC 653
************************************* ***** ************ ***
cow GGGCGTACGTGGCCTGGGCTTCAGCCTCGGCGCGGGGAATCATGGGCCACCTGGCGCTCT 713
sheep GGGCGTGCGTGGCCTGGGCTTCAGCCTCGGCGAGGGGAGTCATGGGCGACCCGGCCCTCT 713
****** ************************* ***** ******** *** *** ****
cow CTCCGGGCCAGAGAAATCCAGGTACCGGGAACAGTGTTTCCTGGGAGCTCTGATGTGGTG 773
sheep CTCC-----AGAGAAATCCAGGTACCGGGAGCAGTGTTTCCTGGGAGCTCTGATGTGGTC 768
**** ********************* ****************************
cow GACCCAAAAGCAAAGCGAAATTTTCCCTGTCTCGACTGATCCTCCAGAAGGAGGGAACTC 833
sheep GACCCAAAAGCAAAGCGATATTTTCGCTGTCTCGACT---------GAAGGAGGGAACTC 819
****************** ****** *********** **************
cow GGCCGTCAGGAGACTGAGGGGAGGGGATTCAGGCGCCTCTCAGAGAACCACCCTCATCTG 893
sheep GGCCCTCAGGAGACTGAGGGGAGGGGAT-CAGGCGCCTCTTGGAGAACCACCCTCATCTG 878
**** *********************** *********** ******************
cow CCAGTAAGGGTGGCACCTTCACGCTTGATTTTTTTTTTTTTTTCCC--CTCACACGTTTG 951
sheep CCAGTAAGGGTGGCACCTTCACGTTTTTTTTTTTGTTGTTGTTGTTTTCTCACACGTTTG 938
*********************** ** ****** ** ** ** ************
cow ATTATTAAACAACGAG---AAGTCCGTTTTTTGCTGTCCTTTTTCGTTTTTGTTTTTTTT 1008
sheep ATTATTAAACAACGAGGAGAAGTCCGTTTTTTGCTGTTCTTTTTCGTT----TTTTCCCC 994
**************** ****************** ********** ****
cow TTTTCCTTTTCTTTTGGTACCATATGTAGCAAATAGATTTTTTAAAATCATAAGCCCACC 1068
sheep CCTCTCTTTTCTTTTGGTACCATATGTAGCAAATAGATTTTTTAAAATCATAAGACCACC 1054
* ************************************************* *****
cow ACCCTCACCATCTT-TTTTTCAGTTTCCTCGTCTCCAGATTCTTAACAACAAAGCAGTTT 1127
sheep ATCCTCACCATCTTGTTTTTCAGTTTCCTCGTCTCCAGATTCTTAACAA---AGCAGTTT 1111
* ************ ********************************** ********
cow CACCTCCCTGATCATGGTTATCCTTATCTCATGGCCGGGTTATTTTCTTGTACTTAAGAG 1187
sheep CACTTCCCTGATGATGGTTATCCTCATCTCATGGCCAGGTTATTTTCTTGTACTTAAGAG 1171
*** ******** *********** *********** ***********************
cow CAATCACGTTTTATTAAGCAGTTCCCCGAATGCTGAACCTTTGAAGTGTTACCTTTCCTT 1247
sheep CAATCACTGTTTATTAAGCAGTTTCCCGAATGCTGAACCTTTGAAGTGTTACCTTTCCTT 1231
******* ************** ************************************
cow ACAAAAGATACCACATAGAATAGGATTAAAAATTTTCACAAGTTGTCAGAGAAAAATAGG 1307
sheep GCAAAAGATTCCGTATAGAATAGGATTAAAAATTTTCACAAGTTGTCAGAGAAAAATAAG 1291
******** ** ******************************************** *
cow AACAGAAAATTGTATAAAAATGTCAGACCTCTGGAAAATGAACAGCTCTCTCAGATTTGA 1367
sheep AACAGAAAATTGAATAAAA-TGTCAGACCTCTGGAAAATGAACAGCTTTCTCAAATTTGA 1350
************ ****** *************************** ***** ******
cow AAATTAACCTATGAAAAGGAACAGTTTTCCTACGGAAACATTGAGGTGCTCT-------- 1419
sheep AAATTAAC-TATAAAAAGGAACAGTTTTCCTACGGAGACACTGAGGCGCTCTCAGTGAAA 1409
******** *** *********************** *** ***** *****
cow ---AACAATGAAAAAGAATCAGAAAAGGAAA-AAAACAGAGTTAGGATGTGATTTGTATA 1475
sheep AAGAACGATGAAAAAGAACCAGAAAAGGAAAGAAAACGGAGTTA----------TGTATA 1459
*** *********** ************ ***** ****** ******
cow TGATTTGTATCTGATGCAAATTTTTCATACTTGTGAAAGAAAAATATCAAGATTATAAAA 1535
sheep TGATTTGTATCTGATGCAAATTTTTCATACTTGTGAAAGAAAAATATCAAGATTATAAAA 1519
************************************************************
cow AGATAAATGGTGAAATGAACAATCATTTATGAAATAAAATACAAATCAAAGCAAGTCTGG 1595
sheep AGATAAATGGTGAAATGAAGAATCATTTATGGAATAAAATACAAATCAAAGCAAGTCTGG 1579
******************* *********** ****************************
cow ATT-------TACAACTACTAGTAAAAACAACAGTAACAGCAACCACTTCTGGAAAGTTA 1648
sheep ATTATCGTTTTACAACTACTAGTAAAAACA---GTAACAGCAACCACTCCTGGAAGGTTA 1636
*** ******************** *************** ****** ****
cow CCTAGAAATTTGCATATTCAGT-ATGTGAGGTGGCAAGGCTTTGGAGTTAGAAATATGG- 1706
sheep CCTAGAAATTTGCATATTCGTTTATGTGAGGTGGCAAGGCTTTGGAGTTAGAAATATGGC 1696
******************* * ************************************
cow TCTGCAACTAATTTTACAATTTGGGACCTAATTTCCTCATCCCCCTTTTGGACATTCATA 1766
sheep TCTGCAGCTAATTTTACAATTTGGGACCTAATTTCGTCATCGTCCTTTTGTCCATTTATA 1756
****** **************************** ***** ******* **** ***
cow AAATAGAGGAAATTATACCTACTTCAG-AGTTTGCCAAGATTAACTGTGTAAAACTGACC 1825
sheep AAATAGAGGAAATTATACCTACTTCAGGAGTTTGCCAAGATTAACTGTGTAAAACTGACC 1816
*************************** ********************************
cow TTTAGTGTGTATACTTTTATTCTTTTCCTAGTCACACTGCACTGGGGGACGTT-GTGAAT 1884
sheep TTTAGCATGTATACATTTATTCTTTCCCTAGTCACACTGCACTGGGGGACATTTGTGAAT 1876
***** ******* ********** ************************ ** ******
cow CTGTATGAAATTTGTGAAAAACAGTCAGGTGATCCTTTAAGCCATGACCCTAAAACCC-A 1943
sheep CT--ATGAAATTTGTGAAAAATGG-------ATCCTTTAAGCCATGACCCTGAAACCCCA 1927
** ***************** * ******************** ****** *
cow CTCCTGGGAACTTACCTGTAATGGAGGAAACCAGGAAAGAAGAAGAAAAGCTGCATTCAC 2003
sheep CTCCTGGGAACTTACCTGCAATGGAAGAAATTCGGAAAGAAGAA---AAGCTGCATTCAC 1984
****************** ****** **** *********** *************
cow CCACAGAACTCAGAATGATCTAAAATTAGATCCAGTCCGGAGTCAACCTAAATGTATTAA 2063
sheep CCACAGGGCTCAGAATGATCTAAAATTAGATCCAGTCCAGAGACAACCTAAAGGTATTAA 2044
****** ****************************** *** ********* *******
cow TAAAATAGCAGGGCAGCAGCTAAGAAAATCATAGCACTTTAACTGAAAGGAACATTGTGT 2123
sheep GAAAATAGCAGGGCAGCAGCTAAGAAAATCATAGCACTTTAACTGAAAGGAACATTGTGT 2104
***********************************************************
cow AACC-ATCACGAGTCATAATTTTAGAGCCTCTCTGTGATATACAGGAAAAAACTGACAGG 2182
sheep AACCCATCACGTGGCATAATTTTAGAGCCTCTCTGTGATATATAGGAAAAAAGTGACAGG 2164
**** ****** * **************************** ********* *******
cow TCAAAGTAAGATTACTCAGACATGGATGCGTTTGTGGAAAATCTGAATGAAAAATGAATC 2242
sheep TCAAAGTAAGATTACTCAGACATGGATGCATATGTGGAAAATCTGAATAAAAAATGGACC 2224
***************************** * **************** ******* * *
cow CACAGTTTGCTGTGTATGGGAGGAGAGTTCAGTGTCACGTTTGCTGCTTTTTTTAAGTTA 2302
sheep CACAGTTTTCTGTGTATGGGAGGAGAGTTCAGTGTCATGTTTGCTGCTTTTTTTTAGTCA 2284
******** **************************** **************** *** *
cow GCATCATCTCTTTTTTAAAAATACTATCATATTTTTTCCCT-GAGTAGATTCATTAGTGG 2361
sheep GCGTCATCTCTTT--TAAAAATACTATCATATTTTTTTCCTTGAGTAGATTCATTAGTGG 2342
** ********** ********************** *** ******************
cow TTTAATAATTTATATACTGTTATTCTGTTAAATAATCCGTTCTTAGATTTATCAATTATA 2421
sheep TTTAATAATTTATATACTGTTATTCTATTAAATAATCCGTTCTTAGATTTATCAATTATA 2402
************************** *********************************
cow GTTTTTTCTTTTTTTTTTAAG 2442
sheep GTTTGT--TTTTTTTTTTAAG 2421
**** * *************
rat and mouse are 81% identical over intron 1
ra GTAAGCGGGCTGCTGAAGCCAGGCGTCAGCGAGCATTCAGCCTTCCTCCCGTCGACAAGC 60
mou GTAAGCGGGCTGCTGAAGCCAGGCCTTGGCGAGCACTCAGCCTTCC----GTCGTCAAGC 56
************************ * ******* ********** **** *****
ra TCGGCTTACTGTGCCTCTCCGGGACTTGAGGCCGCGGGG-------------CTGGGACT 107
mou TCGGCTCACTGCGCCTCTCGGGGCCTTGAGGCCACGGGGACTAGGACTGGGACTGGGACT 116
****** **** ******* *** ********* ***** ********
ra GGGGTTGAGCTTGGCTAGGAGGTGGCTGTGCACCCGCTGTGCGCGACTCCTGGAGGGACC 167
mou GGGGCTGAGTCTGGCTGGGAGGTGACTGTACACCCCCTGTGCGCGACTCCTGGAGGAACC 176
**** **** ***** ******* **** ***** ******************** ***
ra GAATCCCAGGGCAGCGAGGCCGGGAGCC--------------GAGCCTGATTCACAGCTC 213
mou GAATCCCAGGGCAGCCAGGCCGGGAGCCAGCCTTTCCTTCCCGAGCCAGATTCACAGCTC 236
*************** ************ ***** ************
ra AACATCGCTGTGGGGGATGGGGGGTTGGGGGGGTGGCATCTTTTAACTGCCCTGTGCTGT 273
mou AGCATCGCT---GGGGATGG----------GGGTGGCATCTTTTGACTGTCCTTGGCTGT 283
* ******* ******** ************** **** *** *****
ra TTTCTTCTCTCGTTGTAATAGCTACAGCGAACATAATTTCACCCCGTGATTCCACCACGG 333
mou TTTCTTCTCTCTTTGTAGTAGCTACAGCGAACATAATTTTACCTCGTTATTCCACCACAG 343
*********** ***** ********************* *** *** ********** *
ra TCTCATCCGTCCTCAGCACCACACTCATTGCTCCCCTTGCTCAGTTTCATACTCAGCGCA 393
mou TC------------------------ATTACTCCC-TTGCACAGTTTCATTCTCAACGTC 378
** *** ***** **** ********* **** **
ra GCCGTTCGCCTTCACTGCCCTGCCTAGGCGTTTTCATGGTTGTCTTATATTCTTTTACTT 453
mou GCCGTGCGCCTTCACTGCCCTGTCTAGGCGTTTTCATGATTGTCT-ATTTTCTTGTACTT 437
***** **************** *************** ****** ** ***** *****
ra TGAATATCGTGGTTTAATAGCAGTTGCCGGTGTGCTAAATTCCTCATTTCCTTAAGAGAA 513
mou TGAATACCGTGGTTTAATAGCAGTTGCGGGTGCGCAGAATTCTCCATTTCCTTAAGAGAA 497
****** ******************** **** ** ***** ****************
ra ACTCCTGGGAGGATGGAATTAAAGACGTTGCAAATTTAATTATACCACAAACAGGAATCA 573
mou ACTCCTGGGAGAATGGGACTAAAGACGT-GCAAATTTAATTATATCGCAAACAGGAATCA 556
*********** **** * ********* *************** * *************
ra AAATTTTGCATTAAAATGCCAGACATCTTGAAAAATTTAACTATTCAATAAAAAAAAAAA 633
mou AAATTTTGCATTAAAATGCCAAACATCTTGAAAAATT-AACTATTCAATGAAGAAAA--- 612
********************* *************** *********** ** ****
ra AGGAACTACTTTACCTACACACACATCCGAGTGCTTCAAAGAGTCCAAGGAAATAGAAAG 693
mou -GGAACTACTTTACCTACACACACATCCGAGAGCTTCGAGGAGGCGAAGGAAATAGAAAG 671
****************************** ***** * *** * **************
ra CTAAGGGATGATTTGGGTTGTATTTGAATCTGACACGAGCTTTCCATATTATTTATAGCA 753
mou CTAAGGGATGATTTGGGTTGTATTTGAATCTGACACAAGCTTTCCATATTATTTATAGCA 731
************************************ ***********************
ra GGGACTGAAGGATGAGTCATTTTCTGAATAAGATGCAAATTAAAGCAAGTTTGTT----G 809
mou GGGACTAAACGATGAGTCATTTTCTGAATAAGATGCAAATTAAAGCAAGTTTGTTTGTTG 791
****** ** ********************************************* *
ra TCTTTACATCGATTAAACAGACAGAGATGATGACAGCAGCAACCCTAACCTAGAGGTTGT 869
mou TCTTTACATCTATTAAATAGACAGAGACAATGGCAACAGCAACCCTAACCTAGAGGTTGC 851
********** ****** ********* *** ** ***********************
ra CTGAAACCACCGTGTTCAAGTTTGGGGAGCAGGTGGCCCTCCTTAAGAGCTCGATTGATT 929
mou CTGAAA-----GTGT-CAGGTTTGGG-AACAAGTGGCCCTGCTTAAGGGCTAGAAAGATT 904
****** **** ** ******* * ** ******** ****** *** ** ****
ra GCTTTACAACCAACGTT-ATGACTTGGCATTGCCTGGGGTTCCTTTTATTTATTCCTTTC 988
mou GCTTTACAACCAACAATCATGACTTGACATTGCCTGGGGTTCCTTTTGTCTATTCCTTT- 963
************** * ******** ******************** * *********
ra TTTAAAAGACTACTATCTATTTTATGAGCATGAGTGTTTCGC-TCCACAGAAGCATGTAT 1047
mou TTTAAAAGACTAGTGTTTATTTTATGTGCATGAGTGTTTTGCATCCACATTCGCCTGTAT 1023
************ * * ********* ************ ** ****** ** *****
ra ACAAGCCTGGTTCTGCGGAGGTCAGAAGAGACAGGGTGTTGGAAGCCCTGGAACTAGAGC 1107
mou ACACACCTGGTTCTGTGGAGGTCAGGAGA----GGGTGCTGGATGCCCTGGCACTAGAGC 1079
*** ********** ********* *** ***** **** ******* ********
ra TAGGGATGATTCTGTGAGCCCCTGCCACAGGGGAGCTCAGATCCCCAATCCAGGCTGTCT 1167
mou CGTGAATGGTTATGTGAGCCCCTGCCACAGGGGAGCTCAGAACCA-AATCCAGGTCCTCT 1138
* *** ** ***************************** ** ******** ***
ra GGAAGAGCAGCCAGAGCTCTTAA--CTACCGAACACCCCCCCCCCCATCCCCTCTCATTC 1225
mou GGAAGAGCAACCAGAGCTCTTAAAACTTCTAAGTATCCCTC----CATCCCCTTTCCATC 1194
********* ************* ** * * * *** * ******** ** **
ra ACATTTAGAAAGGAGAAAACTGCTACCCATGTCTGGCATTTATTTCAGAGATTAACTGT- 1284
mou ATATTTGGAAAGGAGAAAACTGCTACCCATGCCTGGCATTTATTTCAGAGATTAACTGTC 1254
* **** ************************ ***************************
ra ---GCAAAACTCGATGT-GAAAGTATACTATTCTGTTTCCCAGTCACACTTAGTTGACAG 1340
mou TGTGTAAAACTTGACATTGAAAGTGCACTATTCTGTTTCCCATTCATACTTAGTTGAGAC 1314
* ****** ** * ****** **************** *** ********** *
ra T---GTAAGTCAGTAAGGGCTTTGGTTGGTTGGTTTGGTTGGTTGGTTCCTGGGTTAGTC 1397
mou TACTGTAAGTCAGTTAGGGCTTT------TT-------TTGTTTGGTTCCTTGGTTAGTT 1361
* ********** ******** ** *** ********* *******
ra TGGA-TGTGCTTGTTGAGAGCTCAATAACAGGCTTTCAATATGGATATGTAGCTGGGAAT 1456
mou TGGAGTGTGTTTGT---GAGCTCATTAACAGGCTTTCAGTAT------GTAGCTGA-AAT 1411
**** **** **** ******* ************* *** ******* ***
ra TCGCTATGTAGACCAGGCAGGCCTCAAATTTGTGGCAATCCTCCCTGTGATTCCCCAGAA 1516
mou TTGCTGTGTAGACCAGACAGGCCTCAAATTTGTGGCAATCCTCCCTGCATCTTCCCAGAA 1471
* *** ********** ****************************** * *******
ra TGCCCTGGTACAGGCATAAGCCACTGTGCCCAGCCGTAAAACAATCTGGTGAGGTATTAT 1576
mou TGCCCTGGTACAGGCATAAACCACCGTGCCCAGCAGTAAAACAATCTGGTGAGGTATTAT 1531
******************* **** ********* *************************
ra TAGTTGCATGCTGTGACCCAGAAACCCCACTTCTGGCAATTCACCTGCCGTGGTGGAACC 1636
mou TAGTCGTGTGCTGTGACCCAGAAACCCCACTCCTGGCAATTTACTGG----GAAGGAACA 1587
**** * *********************** ********* ** * * *****
ra AACAAAGGGCTAGGGGAGCCATATGGCCAACAGTTACAGAAAATTAGATCCAAGGGAAAA 1696
mou AACAAAGGGCTAGGGGAGCCATATGGCCTGCAGTTAGAGAAAATTAGATCCAACTGAAAA 1647
**************************** ****** **************** *****
ra G-CAACCTAAATGTTTAACAGGCGAGCAGCTAAGAAACTGACAGGCTCGTGAGGGA-GCT 1754
mou ATCAACCTAAAGGTGTAAAAGCCAAGCAGTTAAGAAACTGACAGGCTCATGATGGAAGCC 1707
********* ** *** ** * ***** ****************** *** *** **
ra GTAGCAATCCCGAAGAACACTCTTCATTTTAGACTCCATGTATCCCTGGGAAAAAC--AG 1812
mou GAGGCCATCGTGAA---CACTCTTCATTTTAGGCCCCACGTATCACTGGGGACAACTGAG 1764
* ** *** *** *************** * *** ***** ***** * *** **
ra AGTCAAAGTACAGGTTAGGAGACCGGGACTCCTCTGGACCCATGCTGTC-CTCTGAAAAG 1871
mou AGTCAAAGTACAGGTAAGGAGACCAAGGCTTTTCAGGACTCAGGCTGTCTCAGTGAAAAG 1824
*************** ******** * ** ** **** ** ****** * *******
ra CCCAGAAGAGCTATAAT-GAAAGAGCTCAGAAGATGT--CTGATCTTGGCTTTCTTTATG 1928
mou CCCAGAAGAGCAGTAATTGAAAGAGCTCAGACGATGTGTCTGATCTCC----TCTGTTTG 1880
*********** **** ************* ***** ******* *** * **
ra TTTGTTGCTGTATTGTTTCCACTAACAAACAACTAAAAAAAAAAAAAAAGTTCACAGGCT 1988
mou TTTGTTGCTGTATTATTTCCACTAACTTATTTGGGAGGAAAAAAAACA-GTTCACAGGCT 1939
************** *********** * * ******** * ***********
ra TCTTTCCTTAAAATACTGGGGATTG---------AACCCAGGGATAGTTTTTTAGTGTCT 2039
mou TCTTTTCTTGAAATACTGGGGATTGCTGGGATCGAACCCAGGGATAGGTTTTTAGTTTCT 1999
***** *** *************** ************* ******** ***
ra AAATTAACAT-GACCATGCCCTGTTTGCCTTTTTGGAGTATGTTTGAATCTGCCCTTATT 2098
mou AAAATAACATAGATCATGCCCTGTTTGC-TTTTTGGAATATGTTTGCG-CTGCCCTTATT 2057
*** ****** ** ************** ******** ******** ***********
ra TCCATTCTCAAATACTGCTCCATTTTATATGACTATTTAGTTTTGGCTTGATAATTTGCA 2158
mou TTCATGTTCAAATACTGCTCCATTTTGCGTGACTCTTTAGTATTGGTTTGATGATTTGCA 2117
* *** ******************* ***** ****** **** ***** *******
ra TATGAGATTAGATCATCTTTCAGTTCTCAGACTTATTTATCAATTCTAGTTTT-TCTTTT 2217
mou TATTAGATTAGATTGTATTTCAGTTCTCAGACTTATTTATCAATTCTAGTTTTCTCTTTT 2177
*** ********* * ************************************ ******
ra TGTTGTTTTAAAG 2230
mou TGTTGTTTTAAAG 2190
*************
mouse and rat align fairly well upstream of motif 1 but not forever
ra TACATCAGT--GATGCTGCCTTTCACCACT------GAA----AGGC--ATTTACGGT-- 44
mo ----TGAGTTTGAGGTCAGCTTAAATTACTTAGTAGGAACACCAGGCCAAATTGGGCTAT 56
* *** ** * *** * *** *** **** * ** * *
ra -GGTTTATGT---ATGATATCAAATAAAGAGTATTTAACACTTCTTTATAGTTGAAAAAG 100
mo GGGATTGTCTCCAAAGATAAAGAAAAAAGGGAAGGAGAGA------AAA----GAAAAAG 106
** ** * * * **** ** **** * * * * * *******
ra AAAGGAAAGAAGGG----------AATCAACCGAGAATGA-TAAACCAACATTCAATGGC 149
mo AAAGGAAAGAAGGGGAAAAGAAGGAATCAGCAGAGAATAAATAAGTCAACATGCAATGGC 166
************** ***** * ****** * *** ****** *******
ra CAATATACTTTCTAAGCCTCTAATTCTTTTATAGTTTATGGGGAAATGTCAAAAATCTTC 209
mo CAATATACTTTCTAGGCCTCTAATTCTTTTATAGTTTGTGGGAAAATGTCGAAAATCTTC 226
************** ********************** **** ******* *********
ra CTCTTTACCAATTTCTTGTTACCAAAGTTCCACGATGGCTTTTTCTTTCCGTTAGGTAAC 269
mo GT---TACCAATTTCTTGTTACCAAAGTTCAACGATGGCTTCCTCGCTCCGTTAGGTAAC 283
* ************************* ********** ** *************
ra CTTTCATTTTCTCGACTACCCATTATGTAACGGGAGCGCTGGGTTCTGGATCAGTCTTCC 329
mo CTTTCATTTTCTCAACTACCCATTATGTAACGGGAGCATTGGGTACTGGATCAGTCTTCC 343
************* *********************** ***** ***************
ra ATTAAAGATGACTTTTATAGTCTGTGAGCGTCGTCACAGAGTGCTGACACTGGGGTGGGG 389
mo ATTAAAGATGATTTTTATAGTTGCTGAGCGTCGTCAGGGAGTGCTGACACTG-----GGG 398
*********** ********* ************ ************** ***
ra AGGGGAGTACGGGGGGAGGGGGTTAAACAGATAACAAGCATTTAAGCCAGTACGGAGCGG 449
mo -----------------GCGGTTTAAACAGATA-CAAGCATTTAAGCCAGTCCGGAGCGG 440
* ** *********** ***************** ********
ra TGACTCAT---------------CCCACCGCGAGAA----------GCCATTGGTGAGCA 484
mo TGACTCATTCCCCCACCCCCCACCCCCCCGCGAGAGACGCGGCGCGGCCATTGGTGAGCA 500
******** *** ******** **************
ra TCACGCTCCGCCCCTCGCCCCGCCCAGCCCCCGGCCTGTCGGGTCCCTCACCACGCCCCG 544
mo TCACGCCCCGCCCCTCGCCCAGCCTAGCTCCCG-CCTGCCCCGCCCCTTTCCACTCCCGG 559
****** ************* *** *** **** **** * * **** **** *** *
ra CTCCCCC----- 551
mo CTCCCCCGCGTT 571
*******
14408-14504 human unrelated
7607-7703 sheep same as book
7773-7865 mouse
D26150 Bovine 803-855 3298-3395
Query: 9 gatcctttaagccatgaccctgaaaccccactcctgggaacttacctgcaatggaagaaa 68
||||||||||||||||||||| |||||| ||||||||||||||||||| |||||| ||||
Sbjct: 2770 gatcctttaagccatgaccctaaaaccc-actcctgggaacttacctgtaatggaggaaa 2828
Query: 69 ttcgga---aagaagaaaagctgcattcaccc 97
||| |||||||||||||||||||||||
Sbjct: 2829 ccaggaaagaagaagaaaagctgcattcaccc 2860
2461 actagtaaaa acaacagtaa cagcaaccac ttctggaaag ttacctagaa atttgcatat
2521 tcagtatgtg aggtggcaag gctttggagt tagaaatatg gtctgcaact aattttacaa
2581 tttgggacct aatttcctca tccccctttt ggacattcat aaaatagagg aaattatacc
2641 tacttcagag tttgccaaga ttaactgtgt aaaactgacc tttagtgtgt atacttttat
2701 tcttttccta gtcacactgc actgggggac gttgtgaatc tgtatgaaat ttgtgaaaaa
2761 cagtcaggtg atcctttaag ccatgaccct aaaacccact cctgggaact tacctgtaat
2821 ggaggaaacc aggaaagaag aagaaaagct gcattcaccc acagaactca gaatgatcta
2881 aaattagatc cagtccggag tcaacctaaa tgtattaata aaatagcagg gcagcagcta
2941 agaaaatcat agcactttaa ctgaaaggaa cattgtgtaa ccatcacgag tcataatttt
3001 agagcctctc tgtgatatac aggaaaaaac tgacaggtca aagtaagatt actcagacat
3061 ggatgcgttt gtggaaaatc tgaatgaaaa atgaatccac agtttgctgt gtatgggagg
3121 agagttcagt gtcacgtttg ctgctttttt taagttagca tcatctcttt tttaaaaata
3181 ctatcatatt ttttccctga gtagattcat tagtggttta ataatttata tactgttatt
3241 ctgttaaata atccgttctt agatttatca attatagttt tttctttttt ttttaaggac
3301 ttctgaatat atttgaaaac tgaacagttt caaccaagcc gaagcatctg tcttcccaga
3361 gacacaaatc caacttgagc tgaatcacag cagatgtagg tacc
U29185 Homo sapiens 12634-12767 15390-15488 14413..14498 L1MC1 14583..14653 MIR 14752..14947 L1ME3
Query: 23 tgaccctgaaaccccactcctgggaacttacctgcaatggaagaaa 68
|||||| ||||||||||||||| |||||||||||||||||||||||
Sbjct: 14755 tgacccagaaaccccactcctgagaacttacctgcaatggaagaaa 14800
repeat_region 14413..14498 L1MC1 = 86 bp
repeat_region 14583..14653 MIR = 71 bp
repeat_region 14752..14947 L1ME3 = 196 bp
14401 atttacacaa taaaatgcaa attagagcat gtttgggtta tcattttaca tctattaaaa
14461 taaccaaaat aattaatagt aacagcaacc cttgctggaa ggttgcccaa aacttggcat
14521 tttcaagtgt ctggggaggt ggcagggctt tggggtcaca aagatggttc tgcagtcaat
14581 tttgtgacct tggacaggct acctaatttc ctgatcctcc ttttgtccat tcatagaatg
14641 gaggaaatga tagctacttt ctgcgtctgt atgtatgagt tattgggggc atttcgaacc
14701 agtgacaaac attttgttaa gcaatctggt gatgcattaa gaagctggaa gctgtgaccc
14761 agaaacccca ctcctgagaa cttacctgca atggaagaaa caaacaaaca aaaacaggca
14821 tgtattccta gcagaatgat ctaaaattag aacacctgga aaagagccta aatgtataac
14881 accagggcag tagctaagaa aattatgaca cattaactga aatgaacatt atgtaaccac
14941 taaaaatcat gattttggag cctgtgatat gtggggaaaa actgacaagt aaaaaagtgg
15001 gttattaact gcacctgctt actctaacgt gaacgcatat gtgaaaaatc tgaaaggaaa
15061 agcacagaaa atggacgttt tcattgaaat tgtcggtgat cttaattttc ctttggtgaa
15121 tatattgctc tcactaaggg cgtttaaaaa atagttcaca ggttttaatt ttttagatga
15181 aatggaccca cagttttctg taagagaaag gagagattgt tatatttgct acttagaata
15241 aaagattttt agccaacgtt gtttcctttt tcaaatattt ttccattttt ttagttgatt
15301 aatgatttag taatttgtgt attgggtttt tttaagaatc agttcttaga ttcatttatc
15361 aattctagtt ttttgttgtt gtttttaagg actcctgaat atttttcaaa actgaacaat
15421 ttcagccatg tctgagcttt ccgtcttcct ggaggcacaa atctagttta gctgaaccac
15481 aacagattgt acatatcctg cagaacctct gtggtcttag gaaggttgaa agtcaccaaa
U29186 Mus musculus short inc U52821 8612-8658 10849-10946 10044..10163 B1-F PB1D7
Query: 23 tgaccctgaaaccccactcctgg 45
|||||| ||||||||||||||||
Sbjct: 10203 tgacccagaaaccccactcctgg 10225
9841 cccctttcca tcatatttgg aaaggagaaa actgctaccc atgcctggca tttatttcag
9901 agattaactg tctgtgtaaa acttgacatt gaaagtgcac tattctgttt cccattcata
9961 cttagttgag actactgtaa gtcagttagg gctttttttg tttggttcct tggttagttt
10021 ggagtgtgtt tgtgagctca ttaacaggct ttcagtatgt agctgaaatt tgctgtgtag
10081 accagacagg cctcaaattt gtggcaatcc tccctgcatc ttcccagaat gccctggtac
10141 aggcataaac caccgtgccc agcagtaaaa caatctggtg aggtattatt agtcgtgtgc
10201 tgtgacccag aaaccccact cctggcaatt tactgggaag gaacaaacaa agggctaggg
10261 gagccatatg gcctgcagtt agagaaaatt agatccaact gaaaaatcaa cctaaaggtg
10321 taaaagccaa gcagttaaga aactgacagg ctcatgatgg aagccgaggc catcgtgaac
10381 actcttcatt ttaggcccca cgtatcactg gggacaactg agagtcaaag tacaggtaag
10441 gagaccaagg cttttcagga ctcaggctgt ctcagtgaaa agcccagaag agcagtaatt
10501 gaaagagctc agacgatgtg tctgatctcc tctgtttgtt tgttgctgta ttatttccac
10561 taacttattt gggaggaaaa aaaacagttc acaggcttct tttcttgaaa tactggggat
10621 tgctgggatc gaacccaggg ataggttttt agtttctaaa ataacataga tcatgccctg
10681 tttgcttttt ggaatatgtt tgcgctgccc ttattttcat gttcaaatac tgctccattt
10741 tgcgtgactc tttagtattg gtttgatgat ttgcatatta gattagattg tatttcagtt
10801 ctcagactta tttatcaatt ctagttttct ctttttgttg ttttaaagga ctcctgagta
10861 tatttcagaa ctgaaccatt tcaaccgagc tgaagcattc tgccttccta gtggtaccag
10921 tccaatttag gagagccaag cagactgtga gtgccctgtg aatcatgatg gtcttgggga
D50092 Rat 2832-2878 5109-5206
Query: 1 caatctggtgaggtattattagtcgtgtgctgtgacccagaaaccccactcctggcaatt 60
||||||||||||||||||||||| | ||||||||||||||||||||||| |||||||||
Sbjct: 4436 caatctggtgaggtattattagttgcatgctgtgacccagaaaccccacttctggcaatt 4495
4081 ccccccccca tcccctctca ttcacattta gaaaggagaa aactgctacc catgtctggc
4141 atttatttca gagattaact gtgcaaaact cgatgtgaaa gtatactatt ctgtttccca
4201 gtcacactta gttgacagtg taagtcagta agggctttgg ttggttggtt tggttggttg
4261 gttcctgggt tagtctggat gtgcttgttg agagctcaat aacaggcttt caatatggat
4321 atgtagctgg gaattcgcta tgtagaccag gcaggcctca aatttgtggc aatcctccct
4381 gtgattcccc agaatgccct ggtacaggca taagccactg tgcccagccg taaaacaatc
4441 tggtgaggta ttattagttg catgctgtga cccagaaacc ccacttctgg caattcacct
4501 gccgtggtgg aaccaacaaa gggctagggg agccatatgg ccaacagtta cagaaaatta
4561 gatccaaggg aaaagcaacc taaatgttta acaggcgagc agctaagaaa ctgacaggct
4621 cgtgagggag ctgtagcaat cccgaagaac actcttcatt ttagactcca tgtatccctg
4681 ggaaaaacag agtcaaagta caggttagga gaccgggact cctctggacc catgctgtcc
4741 tctgaaaagc ccagaagagc tataatgaaa gagctcagaa gatgtctgat cttggctttc
4801 tttatgtttg ttgctgtatt gtttccacta acaaacaact aaaaaaaaaa aaaaagttca
4861 caggcttctt tccttaaaat actggggatt gaacccaggg atagtttttt agtgtctaaa
4921 ttaacatgac catgccctgt ttgccttttt ggagtatgtt tgaatctgcc cttatttcca
4981 ttctcaaata ctgctccatt ttatatgact atttagtttt ggcttgataa tttgcatatg
5041 agattagatc atctttcagt tctcagactt atttatcaat tctagttttt ctttttgttg
5101 ttttaaagga ctcctgaata tatttcaaaa ctgaaccatt tcaacccaac tgaagtattc
5161 tgccttctta gcggtaccag tccggtttag gagagccaag ccgactgtaa gtgccctgtg
sheep 5666-5717 8139-8236
7261 atttatggaa taaaatacaa atcaaagcaa gtctggatta tcgttttaca actactagta
7321 aaaacagtaa cagcaaccac tcctggaagg ttacctagaa atttgcatat tcgtttatgt
7381 gaggtggcaa ggctttggag ttagaaatat ggctctgcag ctaattttac aatttgggac
7441 ctaatttcgt catcgtcctt ttgtccattt ataaaataga ggaaattata cctacttcag
7501 gagtttgcca agattaactg tgtaaaactg acctttagca tgtatacatt tattctttcc
7561 ctagtcacac tgcactgggg gacatttgtg aatctatgaa atttgtgaaa aatggatcct
7621 ttaagccatg accctgaaac cccactcctg ggaacttacc tgcaatggaa gaaattcgga
7681 aagaagaaaa gctgcattca cccacagggc tcagaatgat ctaaaattag atccagtcca
7741 gagacaacct aaaggtatta agaaaatagc agggcagcag ctaagaaaat catagcactt
7801 taactgaaag gaacattgtg taacccatca cgtggcataa ttttagagcc tctctgtgat
7861 atataggaaa aaagtgacag gtcaaagtaa gattactcag acatggatgc atatgtggaa
7921 aatctgaata aaaaatggac ccacagtttt ctgtgtatgg gaggagagtt cagtgtcatg
7981 tttgctgctt ttttttagtc agcgtcatct cttttaaaaa tactatcata tttttttcct
8041 tgagtagatt cattagtggt ttaataattt atatactgtt attctattaa ataatccgtt
8101 cttagattta tcaattatag tttgtttttt tttttaagga cttctgaata tatttgaaaa
8161 ctgaacagtt tcaaccaagc tgaagcatct gtcttcccag agacacagat ccaacttgag
8221 ctgaatcaca gcagatgtag gtacctgcgg aatctctctg gtcttgtgat ggttgaaagt
U78769 golden hamster
intron 1 <1..177
exon 2 178..276
intron 2 277..>492
1 gaacgtgcca tgtttgcttt tgggaatcta tctgagctgt tcttatttcc gttttcaaat
61 actgccccat ttttatgtgc ctgtatttat tagtggtttg gtaatttgta tattagatgg
121 tatttcagta cttagattta ttcatcaatt ctaatttttc tttttcatgt tttgaaggac
181 tcctgaatat attccaaaac tgaacaattt caactgagct gaagtactct gtttttctag
241 aggtaccagt tcagtttagg agagtcacag cagatcgtaa gtgccctgtc aatcttggta
301 gagggcttga aaatctccaa ctgtctgggg agatggggac cagaaaagac taagctccac
361 acttgctcca gaggctccta gtaacgtggg acataagcct tgctgtgcac taatgtcctg
421 taaagtcagc tttgtccagg ggacaaaggc cagagctttc tctaggactg tgccggttta
481 gggaactgca ag
>ra 2832 2878 5109 5206
>mo 8612 8658 10849 10946 28680 30687
>ha 333 342 349 351 354 410
>hu 12634 12767 15390 15488 25464 27817)
>sh 5666 5717 8139 8236 22268 26295
>co 803 855 3298 3395
exon 1 intron 1 exon 2
>rat 47 2230 98 83% identical to mouse over intron 1
>mouse 47 2190 98 539 bp in 3 retrotransposons in intron 1
>hamster 57 - 98
>human 134 2622 99 only last 180 bp related to cow in intron 1, 353 bp in 3 retrotransposons
>sheep 52 2421 98 91% identical to cow over intron 1
>cow 53 2442 98
Though the prion gene is chock-full of retrotransposons, there are no recognizable ones here except for 3 each in human and mouse intron 1:
>mouse intervening repeats in region of exon 1-2
repeat_region 7980..8069 PB1D7
exon 1 8612..8658
repeat_region 9619..9844 B3 = 226 bp
repeat_region 10044..10163 B1-F = 120 bp
repeat_region 10070..10163 PB1D7 = 193 bp
exon 2 10849..10946
>human intervening repeats in region of exon 1-2
repeat_region 11478..11800 AluJo
exon 1 12634..12767
repeat_region 14413..14498 L1MC1 = 86 bp
repeat_region 14583..14653 MIR = 71 bp
repeat_region 14752..14947 L1ME3 = 196 bp
exon 2 15390..15488
>sheep intervening repeats in region of exon 1-2
repeat_region 3756..4215 MLT1F
exon 1 5666..5717
exon 2 8139..8236
>She gaaatttgtgaaaaa---------------tggatcctttaagccatgaccctgaaaccccactcctgggaacttacctg-caat--ggaagaaattcggaaagaagaa--
>Bov gaaatttgtgaaaaa--------cagtcaggtgatcctttaagccatgaccctaaaaccc-actcctgggaacttacctg-taat--ggaggaaaccaggaaagaagaaga
>Hom acattttgttaagcaatctggtgatgcattaagaagctggaagctgtgacccagaaaccccactcctgagaacttacctg-caat--ggaagaaacaaacaaacaaaaac-
>Mus cccagcagtaaaacaatctggtgaggtatta-ttagtcgtgtgctgtgacccagaaaccccactcctggcaatttac-tgggaa---ggaacaaacaaagggctagggg--
>Rat cccagccgtaaaacaatctggtgaggtatta-ttagttgcatgctgtgacccagaaaccccacttctggcaattcacctgccgtggtggaaccaacaaagggctagggg--
>She -aagctgcattcacccacagggctcagaatgatctaaaattagatccagt-ccagagacaacctaaaggtattaagaaaatagcagggcagcagctaagaaaatcatagcactttaa
>Bov aaagctgcattcacccacagaactcagaatgatctaaaattagatccagt-ccggagtcaacctaaatgtattaataaaatagcagggcagcagctaagaaaatcatagcactttaa
>Hom aggcatgtattcc----tag----cagaatgatctaaaattagaacacctggaaaag--agcctaaatgtat------aacaccagggcagtagctaagaaaattatgacacattaa
>Mus agccatatggcctg----------cagttagag--aaaattagatccaactgaaaaatcaacctaaaggtgt------aaaagccaagcagt---taagaaact---gaca--ggct
>Rat agccatatggccaa----------cagttacag--aaaattagatccaagggaaaag-caacctaaatgttt------aacaggcgagcagc---taagaaact---gaca--ggct
>She ctgaaaggaacattgtgtaacccatcacgtggcataattttagagcctctctgtgatatataggaaaaaagtgacaggtcaaa--gtaag---attact----cagacatggatgcatatgtggaaaatctgaa
>Hum ctgaaatgaacattatgtaaccactaaaaat-catgattttggagcct----gtgatatgtggggaaaaactgacaagtaaaaaagtgggttattaactgcacctgcttactctaacgtgaacgcatatgtgaa
>Bov ctgaaaggaacattgtgtaacc-atcacgagtcataattttagagcctctctgtgatatacaggaaaaaactgacaggtcaaa--gtaag---attact----cagacatggatgcgtttgtggaaaatctgaa
>She taaaaaatggacccacagttttctgtgtatgggaggagagttcagtgtcatgtttgctgcttttttttagtcagcgtcatctctttt--aaaaatactatcatatttttttccttgagtagattcattag
>Bov tgaaaaatgaatccacagtttgctgtgtatgggaggagagttcagtgtcacgtttgctgctttttttaagttagcatcatctcttttttaaaaatactatcatatttttt-ccctgagtagattcattag
>Hum aaatctgaaaggaaaagcacagaaaatggacgttttcattgaaattgtcggtgatcttaattttcctttggtgaatatattgctctcactaagggcgtttaaaaaatagttcacaggttttaatttttt
>Hum agatgaaatggacccacagttttctgtaagagaaaggagagattgttatatttgctacttagaataaaagatttttagccaacgttgtttcctttttcaaatatttttccatttttttagttgattaat
>Mus catgatggaagccgaggccatcgt--gaacactcttcattttaggccccacgtatcactggggacaactgagagtcaaagtacaggtaaggagaccaaggcttttcaggactcaggctgt-ctcagtgaa
>Rat cgtgagggagctgtagcaatcccgaagaacactcttcattttagactccatgtatccctgggaaaaac--agagtcaaagtacaggttaggagaccgggactcctctggacccatgctgtcctc--tgaa
>Mus aagcccagaagagcagtaattgaaagagctcagacgatgtgtctgatct----cctctgtttgtttgttgctgtattatttccactaacttatttgggagg--aaaaaaaacagttcacaggcttcttt
>Rat aagcccagaagagctataat-gaaagagctcagaagatgt--ctgatcttggctttctttatgtttgttgctgtattgtttccactaac-aaacaactaaaaaaaaaaaaaaagttcacaggcttcttt
>Mus tcttgaaatactggggattgctgggatcgaacccagggataggtttttagtttctaaaataacatagatcatgccctgtttgc-tttttggaatatgtttgcg-ctgcccttattttcatgttcaaat
>Rat ccttaaaatactggggatt--------tgaacccagggata-gtttttagtgtctaaattaacat-gaccatgccctgtttgcctttttggagtatgtttgaatctgcccttatttccattctcaaat
>Ham ..................................................................gaacgtgccatgtttgc-ttttgggaatctatctgag-ctgttcttatttccgttttcaaat
>Hum .......................................gatttagtaatttgtgtattgggtttttttaagaatcagttcttagattcatttatcaattctagttttttgttgttgtttttaag
>She ....................................tggtttaataatttatatactgttattctattaaataatccgttcttagatttatcaattatagtttgt---tttttttttt---aag
>Bov ............................tggtttaataatttatatactgttattctgttaaataatccgttcttagatttatcaatt-atagtttt----ttcttttttttttaagg
>Mus actgctccattttgcgtgactctttagtattggtttgatgatttgcatattag----attagattgtatttcagttctcagacttatttatcaattctagttttctctttttgttgttttaaagg
>Rat actgctccattttatatgactatttagttttggcttgataatttgcatatgag----attagatcatctttcagttctcagacttatttatcaattctagttttt-ctttttgttgttttaaagg
>Ham actgccccatttt-tatg--tgcct-gtatttattag-tggtttggtaatttgtat-attagatggtatttcagtacttagatttattcatcaattctaattttt-ctttttcatgttttgaagg
-
exon 1b's
>Ham 411-810
gtaagcggct
421 tctgaagcct ggccccggga agggtgctgg agccaggcct cggtaagcct tcggcttccc
481 agagccaagc ccggcttact ccggctctcg gggcgctgag gccgcggggc tgaggttgag
541 tctggctggg aggtgaccgc gcacccgcag ccgcgcgtct ccttgaggga ccgaacccca
601 ggagaggcca ggagccatcc cttcctcccg agcccggctc acccccagag tcgctcgggg
661 atgggggatg ggggatgggg tggcatcttt tgactgtcgt ttgctgtttt cttctctctt
721 tgtaatagct acagcgaaca taattttacc cagggttcca ccgtggtctc gtccgtcctc
781 ggcatctctc agtccagtac atacccaagg
>Mus
t aagcgggctg ctgaagccag gccttggcga gcactcagcc
8701 ttccgtcgtc aagctcggct cactgcgcct ctcggggcct tgaggccacg gggactagga
8761 ctgggactgg gactggggct gagtctggct gggaggtgac tgtacacccc ctgtgcgcga
8821 ctcctggagg aaccgaatcc cagggcagcc aggccgggag ccagcctttc cttcccgagc
8881 cagattcaca gctcagcatc gctggggatg ggggtggcat cttttgactg tccttggctg
8941 ttttcttctc tctttgtagt agctacagcg aacataattt tacctcgtta ttccaccaca
9001 gtcattactc ccttgcacag tttcattctc aacgtcgccg tgcgccttca ctgccctgtc
9061 taggcgtttt catgattgt
>Rat
gt
2881 aagcgggctg ctgaagccag gcgtcagcga gcattcagcc ttcctcccgt cgacaagctc
2941 ggcttactgt gcctctccgg gacttgaggc cgcggggctg ggactggggt tgagcttggc
3001 taggaggtgg ctgtgcaccc gctgtgcgcg actcctggag ggaccgaatc ccagggcagc
3061 gaggccggga gccgagcctg attcacagct caacatcgct gtgggggatg gggggttggg
3121 ggggtggcat cttttaactg ccctgtgctg ttttcttctc tcgttgtaat agctacagcg
3181 aacataattt caccccgtga ttccaccacg gtctcatccg tcctcagcac cacactcatt
3241 gctccccttg ctcagtttca tactcagcgc agccgttcgc cttcactgcc ctgcctag
>cow 1b 856-
gtaaa tagccgcgta gtcctttaaa ctcccagcgg aggacgccaa
901 ccctgggtct tgcggccgag gcccagggac ccagccgaat cggattggtg ggaggcagac
961 cttgaccgtg agtagggctg ggggcttgcg gcgggcgcgg ggaacgtcgg gcctgttgag
1021 cgtgctcgtt ggtttttgcc agccgccgct cggttttacc ctcctggtta ggagagctcc
1081 atttactcgg aatgtgggcg ggggccgcgg ctggctggtc cccctcccga ggtatgtggg
1141 tggtgtgtag gaatc
>She 5718-
gta aatagccacg tagtccttta aacccccagc ggaggccgcc
5761 cccggcttgc ggccgaggcc ctagggcact cagccggatc ggactggctg ggaggcagac
5821 cttgaccgtg aggaggactg ggggcttccg gcgggcgcgg ggaacgtcgg gcctgtttag
5881 cgtgctcgtt ggtttttgcc agccaccgct cggttttgcc ctcctggtta ggagagctcc
5941 atttactcgg aatgtgggcg ggggccgcgg ctggctggtc cccctcctga agtatgtggg
6001 tggtgtgtag gaatcta
>hum
gta aacgcccggg
12781 gtgggaggaa cgcgggcggg ggcaggggag ccgcgggggc cgagtgagga ccccgggcct
12841 cgggtcccag gcgcaagggt gcccggccgg gcggggtcgg gaccccagtg aggaggggcc
12901 gggggctgcc ccgcgggcgc gtgacggtct cgggcctgcc cggctgcgct ggtctccgct
12961 cgggtgaggc ggcttggctt cgcttttcag gttaggaaag ctccctttac tgcgcgttgg
13021 ggggctgggg gagctggcgg agccacgtta gggaggtcgg tggcgccggg gtgtctcagc
13081 gccccctgca ccccgcgcgg gtccggccca gcgggcgatc gctggcgccc agggaactcc
13141 gggagggccg ccagcgggct ccgcaggcgc ggggcgggga ggggcgc
cow: 1 gtaaatagccgcgtagtcctttaaactcccagcggaggacgccaaccctgggtcttgcgg 60
|||||||||| ||||||||||||||| ||||||||||| |||| || || |||||||
she: 5718 gtaaatagccacgtagtcctttaaacccccagcggaggccgcc---cccgg--cttgcgg 5772
Query: 61 ccgaggccc-aggg-acccagccgaatcggattgg-tgggaggcagaccttgaccgtgag 117
||||||||| |||| || |||||| |||||| ||| ||||||||||||||||||||||||
Sbjct: 5773 ccgaggccctagggcactcagccggatcggactggctgggaggcagaccttgaccgtgag 5832
Query: 118 tagggctgggggcttgcggcgggcgcggggaacgtcgggcctgttgagcgtgctcgttgg 177
||| |||||||||| ||||||||||||||||||||||||||||| ||||||||||||||
Sbjct: 5833 gaggactgggggcttccggcgggcgcggggaacgtcgggcctgtttagcgtgctcgttgg 5892
Query: 178 tttttgccagccgccgctcggttttaccctcctggttaggagagctccatttactcggaa 237
|||||||||||| |||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct: 5893 tttttgccagccaccgctcggttttgccctcctggttaggagagctccatttactcggaa 5952
Query: 238 tgtgggcgggggccgcggctggctggtccccctcccgaggtatgtgggtggtgtgtagga 297
||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||
Sbjct: 5953 tgtgggcgggggccgcggctggctggtccccctcctgaagtatgtgggtggtgtgtagga 6012
Query: 298 atc 300
|||
Sbjct: 6013 atc 6015
>cow 1b 856-
gtaaatagccgcgtagtcctt taaactcccagcggaggacgccaaccctgggtctgcggccgaggcccagggacccagccgaatcgga ttggtgggaggcagaccttgacc
gtgagtagggctgggggctt gcggcgggcgcgggg.flanker
Multalin version 5.3.3
150
Ham GTAAGCGGCT TCTGAAGCCT ...GGCCCCG GGAAGGGTGC TGG..AGCCA
Mus .......... .......... ........TA AGCGGGCTGC TGA..AGCCA
Rat .......... .......... .......GTA AGCGGGCTGC TGA..AGCCA
hum GTAAACGCCC GGGGTGGGAG ...GAACGCG GGCGGGG.GC AGGGGAGCCG
cow GTAAATAGCC GCGTAGTCCT TTAAACTCCC AGCGGAG.GA CGCCAACCCT
She GTAAATAGCC ACGTAGTCCT TTAAACCCCC AGCGGAG.GC CGCC..CCCG
Consensus gtaaa..gcc .cg.ag.cct ....acccc. aGcgGgg.Gc .G...agCC.
gtaaatagccacgtagtcct
gtaaatagccgcgtagtcctt taaactcccagcggaggacgccaaccc
tgggtctgcggccgaggcccagggacccagccgaatcgga ttggtgggaggcagaccttgacc with flanker gtgagtagggctgggggctt gcggcgggcgcgggg.
Comparison of bovine exon 1b - intron 1 junction to other species
112
51 100
Ham CGGTAAGCCT TCGGCTTCCC ....AGAGCC AAGCCCGGCT TACTCCGGCT
Mus TGGCGAGCAC TCAGCCTTCC ....GTCGTC AAGCTCGGCT CACTGCGCCT
Rat CAGCGAGCAT TCAGCCTTCC TCCCGTCGAC AAGCTCGGCT TACTGTGCCT
cow GGGTCTTGCG GCCGAGGCCC ....AGGG.. A..CCCAGCC GAATCGGATT
She G...CTTGCG GCCGAGGCCC ....TAGGGC A..CTCAGCC GGATCGGACT
Consensus ggg.cttgcg gCcGaggcCC ......gG.c A..CtCaGCc gaaTcgGacT
101 150
Ham CTCGGGGCGC TGAGGCCGCG GGG....... .......... ..CTGAGGTT
Mus CTCGGGGCCT TGAGGCCACG GGGACTAGGA CTGGGACTGG GACTGGGGCT
Rat CTCCGGGACT TGAGGCCGCG GGG....... ......CTGG GACTGGGGTT
cow GG.TGGGAGG C.AGACCTTG A......... .......... ..CCG....T gga ttggtggg
She GGCTGGGAGG C.AGACCTTG A......... .......... ..CCG....T
Con ggctGGGagg c.AGaCCttG a......... .......... ..CcG....T
151 200
Ham GAGTCTGGCT GGGAGGTGAC CGCGCACCCG CAGCCGCGCG TCTCCTTGAG
Mus GAGTCTGGCT GGGAGGTGAC TGTACACCCC CTGT.GCGCG ACTCCTGGAG
Rat GAGCTTGGCT AGGAGGTGGC TGTGCACCCG CTGT.GCGCG ACTCCTGGAG
cow GAGTAGGGCT GGGGGCTTGC GGCGGGCGCG GGGA.ACGTC GGGCCTGTTG
She GAGGAGGACT GGGGGCTTCC GGCGGGCGCG GGGA.ACGTC GGGCCTGTTT
Con GAGtagGgCT gGGgGcTt.C gGcgggCgCg ggGa.aCGtc gggCCTgttg
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>Consensus
gtaaatagcc gcgtagtcct ttaaactccc aGcgGagGa cGCCacCct
gggtcttgcg gCcGaggcCC aggGc ACtCaGCc gaaTcgGacT
ggctGGGagg cAGaCCttG aCcGT
GAGtagGgCT gGGgGcTtgC gGcgggCgCg ggGaaCGtc gggCCTgttg
agcgtGctcg ttgGtttttg ccaGccgccg ctCggtttTa ccctcCtggt
taggagagCt ccatttactc gGaATgtggG cggggGccgc GGcTGGC
TggTccCcct CctgaggTaT gTgggTggtg tgTaGgAaTC
Comparison to human
1 50
cow GTAAATAGCC GCGTAGTCCT TTAAACTCCC AGCGGAGGAC GCCAACCCTG
She GTAAATAGCC ACGTAGTCCT TTAAACCCCC AGCGGAGGCC GCC..CCCGG
hum GTAAACGCCC GGGGTGGGAG GAACGCGGGC GGGGGCAGGG GAGCCGCGGG
Consensus GTAAAtagCC gcGtaGtcct ttAaaC.ccC aGcGGagG.c Gcc..cCcgG
51 100
cow GGTCTTGCGG ...CCGAGGC CCAGGG..AC CCAGCCGAAT CGGA..TTGG
She ...CTTGCGG ...CCGAGGC CCTAGGGCAC TCAGCCGGAT CGGA..CTGG
hum GGCCGAGTGA GGACCCCGGG CCTCGGG.TC CCAGGCGCAA GGGTGCCCGG
Consensus gg.CttGcGg ...CCgaGGc CCt.GGg.aC cCAGcCG.At cGGa..ctGG
101 150
cow .TGGGAGGCA GACCTTGACC ...GTGAGTA GGG.CTGGGG GCT.TGCGGC
She CTGGGAGGCA GACCTTGACC ...GTGAGGA GGA.CTGGGG GCT.TCCGGC
hum CCGGGCGG.. GGTCGGGACC CCAGTGAGGA GGGGCCGGGG GCTGCCCCGC
Consensus ctGGGaGGca GacCttGACC ...GTGAGgA GGg.CtGGGG GCT.tcCgGC
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