Vertebrates

10 20 30 40 50 60 70 80 90 100 110 120

....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|

CR1 P2a.1

structure ---------- ---------

Homo sapiens GGGUUGCGGAGGGUGGGCCUGGGAG--GGGUGGUGGCCA-UUUUUU--GUCUAACCCUAACUGAGAAG--GGCG-UAGGC-GCCGU--GCUUU-UGCUCCC-------------------

Tupaia glis belangeri GGG-AGUGGAGGGUGGGCCCGGGAC--GGGCGCGGACCC-GGUA----AUCUAACCCUGACUCACAAGA-GGCG-UAGGC-GCCGU--GCUUU-UGCUCCC-------------------

Oryctolagus cuniculus GGGCUGAGGAGGGUGGGCUCGGGAG--GGGCCC-GGUCA-UUUCUC--AUCUAACCCUAACUGAGCAG--GGCG-UAGGC-GCCGC--GCUUU-UGUUUCCC------------------

Cavia porcellus --------------------GGGAG--GGGUGGUGGUCU-UCCCU---GUCUAACCCUAAG-GUGAAGAGGACG-UGGGU-GCCGU--GUUUU-UCGCUCC-------------------

Chinchilla brevicaudata GGGUUGAGAAUGGUGGGCC-GGGAG--GGGAGGUGGGCA-UGUUUU--GUCUAACCCUAACUAGGAGGAGGACG-UAGGC-GCCGU--GCUUU-UGUUCCC-------------------

Geomys breviceps -----------GGCGUGCCUGGGAG--GGGGGGCUGGUC-CCACUC--UUCUAACCCUAAGGGUGUC---GGCUGUAGGC-GCCGU--GCUUUUUACUUCCC------------------

Microtus ochrogaster -------------------------------GA-CGCGC-GCCUC---UUCUAACCCUAAAAACUG-G--AGCUGUAGGU-GUUGC--UCUUU--CAGCGU-------------------

Cricetulus griseus ------------------------------------------------GUCUAACCCUGAAUUCUGAG--AGCUGUGGGU-ACUGU--GCUUU--CGUCUC-------------------

Mus musculus ------------------------------------------------ACCUAACCCUGAUUUUCAUU--AGCUGUGGGU-UCUGG--UCUUU-UGUUCUC-------------------

Mus spretus ------------------------------------------------ACCUAACCCUGAUUUUCAUU--AGCUGUGGGU-UCUGG--UCUUU-UGUUCUU-------------------

Mus musculus castaneus ------------------------------------------------ACCUAACCCUGAUUUUCAUU--AGCUGUGGGU-UCUGG--UCUUU-UGUUCUC-------------------

Rattus norvegicus ------------------------------------------------GUCUAACCCUAUUGUU-AU---AGCUGUGGGU-UCUGU--UCUUU-UGUUCUC-------------------

Mustela putorius furo GGGUUGCGGAGGGUGGGCUCGGGAG--GGGUGGCGGUCA-UUUUCU--GUCUAACCCUAACUGAAACG--GGCG-UAGGC-GCUGC--GCUUU-UGUUCCC-------------------

Procyon lotor GGGUUGCGGAGGGUGGGCCUGGGAG--GGGUGGCGGUCG-UUUUAU--GUCUAACCCUAACUGAGAAG--GGCA-UAGGC-GCUGC--GCUUU-UGUUCCC-------------------

Felis catus GGGUUGUGGAGGGUGGGCCUGGGAG--GGGAAGCGGUCA-GUUUUU--GUCUAACCCUAACUGAGAAG--GGCG-UAGGC-GCCGC--GCUUU-UGUUUCC-------------------

Bos taurus GGGUUGCGGAGGGUGGGCCCCGGGU--UGGUGGCAGCCA-UUUCUC--AUCUAACCCUAAUUGAGACA--GGCG-UAGGC-GCUGU--GCUUU-UGGUUAC-------------------

Sus scrofa GGGUUGCGGAGGGUGGGCCCAGGAG--CGGUGGCGGCCA-UUUUUUAAGUCUAACCCUAACUGAAAGA--GGCG-UAGGC-GCUGC--GCUUU-UGCUUCA-------------------

Suncus murinus -------------GGGUUGCGGGAGCUGCGAGC-GGCCG-UCUC----GUCUAACCCUAAA-GAGAAA--GGCG-UAGGU-GCUUG--GCCUU-GGCGACU-------------------

Equus caballus GGGUGGGGGAGAGUGGGUCUGGGCG--GGGCGGCGGUCA-CGUUUU--GUCUAACCCUAACUGAGCUG--GGCG-GAGGC-GCCGC--GCUUU-UGCUCCC-------------------

Dasypus novemcinctus GGGUUGCGGAGGGAGGGCCCGGGAG--GGGUGAGCGUCC-AUUAUC--GUCUAACCCUAACUGAGAUG--GGCG-UAGGC-GCCGC--GCUUU-UGCUUCC-------------------

Dasyurus hallucatus ---GUGCGGACGGGCUGCGUGGGCGGGUCGGUCCGUCCU-GGCAC---AUCUAACCCUAAAUGCGCGC--UGGU-UGAAG-UGGCU--UCUCC-UGGGCGAU------------------

Elephas maximus GGGUUGAGGAGGGUACGCCCGGGA---GGGCGGUGGUCU-GUUCUG--UUCUAACCCUAACUGAUAAG--GGCG-UAGGC-GCCGU--GCUUU-UGUUCCC-------------------

Trichechus manatus GGGUUGAGGAUGGCGCCCCCGGGUC--GGGCAGUGGUCU-UUUUUG--UUCUAACCCUAACUGGCAAG--GGCG-UAGGU-GCUGU--GCUUU-UGUUCCC-------------------

Gallus gallus ----------------GCGU-GGCGGGUGG--AAGGCUC-CGCUGU--GCCUAACCCUAAUCGGGGGAAUUGAUGGUGCUGUCGCCGCGCUCC-CUCCGCC-------------------

Anodorhynchus hyacinthinus ----------------GCGU-GGCGGAUGG-GGAGGCUC-CAGUCU--CACUAACCCUAAU---------------GGCUGCCGCCGUGCUCC-CCGCACC-------------------

Chelydra serpentina ----------------GCUGCGGCGGCAGGUGGGGGCUC--AGUCU--UUCUAACCCUAAGCG--AAAUGUGACC-------------CCUCC-CCGCUGCAGC----------------

Bombina japonica -----------GUUUAAUUAGAGGGAUUGGAAG-GUUCC-GCUUA---UGCUAACCCUAAUAUUGGGGGUCUGUUGAAAA--------CCUCU-UUAAGAUA------------------

Xenopus laevis GAAUCAGCGUUUAAAGCUCAAUGUGGAC-GGAGGUCUCU-GUUU----CGCUAACCCUAAUACACUGGCUUCAGGGCGAUG-------GCUCU-UCGCGGCGG-----------------

Ceratophrys ornata -----------------ACAGUGGGAAUAGGAG-GGAGU-CUAUAU--UUCUAACCCUAAUAUACCCGGU--UCAGG-----------GCUCU-UAUGUGG-------------------

Pyxicephalus adspersus -----------------CCAGCGGUAAUAGGAG-AGU-U-CUAUCC--UUCUAACCCUAAUGCACAGACCCCUCGCU-----------GCUCU-UCA-----------------------

Dermophis mexicanus ---------------CUCUCUCCGGAGAGGGGCGGUUUC-UCUGUC--UUCUAACCCUAAUGCGGUGCUUCGGCAGAA----------GCUCUCCACUGCGUA-----------------

Herpele squalostoma ---------------UUCUCUCUGGAGCGGGGCGAUUUC-UCUUCC--UUCUAACCCUAAUGCGGUGCUUAGGCGACA----------GUUCU---CCGGGUG-----------------

Typhlonectes natans ---------------GUCAUUCCGGAGAGGGGCGUUUUC-UUCUUU--CUCUAACCCUAAUGUAUUGCUUGGGCAGCA----------GCUCU---CUCGGUA-----------------

Oryzias latipes -------------------------------GCGGGGUG--UUCU---ACCUAACCCUAAUUAGAGGCU-------------------GCCUCGUGUACUUAA-----------------

Gasterosteus aculeatus -------------------------------ACGGAGUG--UCUC---UUCUAACCCUAAAUACGGAGG-------------------CCCUCCUGUACUCAA-----------------

Takifugu rubripes -------------------------------ACGGAGUG--UCUC---UUCUAACCCUAAAUUAUCUCG-------------------GCUCCCUGUACUCGG-----------------

Tetraodon nigroviridis -------------------------------GCGGAGUG--UCUC---UUCUAACCCUAAGUUAAACUA-------------------GCUCCCUGUACUCGG-----------------

Danio rerio -------------------------------GCAGAGUA--CUUU---CUCUAACCCUAACGCUUCUUU-------------------GCUUCCUGUACGGCU-----------------

Rhizoprionodon porosus ---------------CUCACAUUGCUGCGGGGUGGAGGC-GUUUUU--AACUAACCCUAAUGCAGAGUAAGUGGCUGG----------GCCUUCCUCACACUGCCUCCCGCUG-------

Mustelus canis ---------------CUCACAUUGCUGCGGGGUGGAGGC-GAUUUU--AACUAACCCUAAUGCAGAGUAAGUGGCUGG----------GCCUUCCUCACACUGCCUCCCGCUG-------

Dasyatis sabina ----------------GUGUCCAGCUGCGGGG--GAGACAGUGUCGCUCUCUAACCCUAAUGUGGGGGCAA-CGCGGG----------CCCUU-UGUUUAAAG--UCCCGCUGU------

Rhinoptera bonasus ----------------GCGUCCAGCUGCGGGG---AGAAAGUGUCGUUCUCUAACCCUAAUGCGAGGGCAA-UGCGGG----------CCCUU-UGUUUAAAG--UCCCGUUGUCGCGCG

structure (((((((((((((((((((((( CUAACCCU (((((|--------------------------

P1 Template P2a J2a|2b

130 140 150 160 170 180 190 200 210 220 230 240

....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|

CR2 P2a.1

structure -------------- ---------- ----- ----------

Homo sapiens ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUCG--GCCUG-CCGCC-UUCCACCGUUCAUUCU-----------------------------

Tupaia glis belangeri ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGUUCG--GA-AAAGCCCUGUGGCCUA-UCGCC-AUCCACCAUCCUUUCU-----------------------------

Oryctolagus cuniculus ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGCGUG-GGA-AAAGCCUUG--GCCUA-CCGCC-GUCCACCGUUCAUUUC-----------------------------

Cavia porcellus ---------CGCACGCUGUUUUUCU--CGCUGACUUU-CAGCGUGCA--GA-AAAGCCUUG--GCCUA-CCGUC-GGUUAUUGUCUAAUUA-----------------------------

Chinchilla brevicaudata ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGUGCG--GA-AAAGCCUUG--GCCUG-CCGUC-GACCACUGUCUAAUUA-----------------------------

Geomys breviceps ---------CGCGCGCUGUUUUUCU--GGCUGGCUUU-CAGCGAGCG-GAA-AAAGCUUUG--GUCUA-CAGGCCACUCACUUUGUAUCCC-----------------------------

Microtus ochrogaster ---------CGCCCGCUGUUUUUCU--CGCUGGCUUU-CAGCGGGCC--AG-AAAGUUCAG--ACCUCUCAGCA-GAUCGUCGCGUCGUUC-----------------------------

Cricetulus griseus ---------CGCCCGCUGUUUUUCU--CGCUGACUUC-CAGCGGGCG--GG-AAAGUCCAG--ACCUG-CAGCG-GGCCAUCGCGCGUUUU-----------------------------

Mus musculus ---------CGCCCGCUGUUUUUCU--CGCUGACUUC-CAGCGGGCC-AGG-AAAGUCCAG--ACCUG-CAGCG-GGCCACCGCGCGUUCC-----------------------------

Mus spretus ---------CGCCCGCUGUUUUUCU--CGCUGACUUC-CAGCGGACC-AGU-AAAGUCCAG--ACCUG-CAGCG-GGCCACCGCGCGUUCC-----------------------------

Mus musculus castaneus ---------CGCCCGCUGUUUUUCU--CGCUGACUUC-CAGCGGGCC-AGG-AAAGUCCAG--ACCUG-CAGCG-GGCCACCGCGCGUUCC-----------------------------

Rattus norvegicus ---------CGCCCGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCC-UGG-AAAGUUCAG--ACCUG-CAGCG-GGUCACCGCGCAUUCU-----------------------------

Mustela putorius furo ---------CGCACGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUUG--GCCUA-CUGCC-ACACACCAUCCAGUUU-----------------------------

Procyon lotor ---------CGCACGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUCG--GCCUA-CUGCC-AUCCACCAUCCAGUUU-----------------------------

Felis catus ---------CGCACGCUGUUUUUUU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUCG--GCCUA-CCGCC-GUCCACCGUACAGUUU-----------------------------

Bos taurus ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUCG--GCCUA-CCGCC-AUCCACCAUCCAGUCU-----------------------------

Sus scrofa ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUCG--GCCUA-CCGCC-AUCCACCAUCCAGUCU-----------------------------

Suncus murinus ---------CGCCCGCUGUUUUU-U--GGCUGGCUUU-CAGCGGGUG--AA-GAGGCCCAAG-ACCUA-CCGCC-ACCCACCGUCUAGUGUCUUAAGGGCACAAAGUCCUGCCCGCCACC

Equus caballus ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUCG--GUCUA-CCGCC-ACUUACCAUCCAGUCU-----------------------------

Dasypus novemcinctus ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUCG--GCCUA-CUGCC-GUCUACUGUCGUAUCU-----------------------------

Dasyurus hallucatus ---------CGCUCGCUGUUUUUGU--GGCUGGCUUU-CAGCGGGCU-GGA-GGAGCCGGG--AGCGG--AGGCGGAGGACCGAG-----------------------------------

Elephas maximus ---------CGCGCGUUGUUUUUCU--CGCUGACUUU-CAGCGGGCG-GGA-AAAGCCUCG--GUCUA-CCGCC-GUCUACCG-AUAGCCU-----------------------------

Trichechus manatus ---------CGCGCGUUGUUUUUCU--CGCUGACUUU-CAGCGGGCG-GGA-AAAGCCCUG--GCCUA-CCGCC-GUCUACCG-AUAGUUU-----------------------------

Gallus gallus ---------CGCCCGCUGUUUUACU--CGCUGACUUU-CAGCGGGCG-AGA-GGAGCCGCCCCGGGGGGGAGGCGGGCGGCGGGAGGGGGCCGGGGCGCCGCGGCGGUGGGGGUCGGGGG

Anodorhynchus hyacinthinus ---------CGUCCGCUGUUUUAUU--CGCUGACUUU-CAGCGGACG-GGG-GGAGCCGCCUGGGGGGGA--------------------------------------------------

Chelydra serpentina ---------CGUCCGCUGUUUUACU--CGCUGACUUU-CAGCGGACG-GGG-GGAGCGGGU-----------------------------------------------------------

Bombina japonica ---------UGCGUGUUGUUUUAUU--GGCUGACUUU-CAGCGCGCA-UUG-AGAGGAGUU-----------------------------------------------------------

Xenopus laevis ---------UGCCUGUUGUUUUACU--UGCUGACUUU-CAGCGGGCA-CGG-AGAGCAAGC-----------------------------------------------------------

Ceratophrys ornata ---------CGCUCGUUGUUUUGCC--GGUUGCCUUU-CAGCGGGCG--AA-AGAGCUCAG-----------------------------------------------------------

Pyxicephalus adspersus ---------UGCUCGUUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--AA-AGAGCAAUG-----------------------------------------------------------

Dermophis mexicanus ---------CGCUCACUGUUUUUCU--AGCUAACUUU-CAGUGAGCA-GGG-AGAGCGAAGUC---------------------------------------------------------

Herpele squalostoma ---------CGCUCGCUGUUUUUCU--GGCUAACUUU-CAGCGAGCG-GAG-AGAGCGAAGCC---------------------------------------------------------

Typhlonectes natans ---------UGCUCGCUGUUUUGCU--GGCUAACUUU-CAGCGAGCA--G--AGGGCGAAGUC---------------------------------------------------------

Oryzias latipes ---------CGUAUGCUGUUUUGUUGUUUCUGGCUUU-CAGCAGAC-UACAUGAGGCGUUG-GGCG------UGAAGCUUGAAAAUAUCCGUA---------------------------

Gasterosteus aculeatus ---------CGUUUGCUGUUUU-UU---UCUGGCUUUUCAGUAAAC-UACGGGAGGGGCUGACGCGACGCUGGGAACGUUUCCGAACGACAAC---------------------------

Takifugu rubripes ---------CGUUUGCUGUUUU--UG--UCUGGCUUU-CAGGAAAC-UACAGGGAGUCUUG-GACG------UCUCGGUUCACGGAU---------------------------------

Tetraodon nigroviridis ---------CGUUUGCUGUUUU-UUG--UCUGGCUUU-CAGGAAAC-UACAGGGAGUCUUG-AGAG------UCUCGGUUCACGGAC---------------------------------

Danio rerio ---------UGUAUGCUGUUUUGUC---UUAAGCUUU-CAGCAUAU-UACAUGAAGCUUUC-CGC-----------GGUUUCGAUACUU-------------------------------

Rhizoprionodon porosus ---CGUGAAACCUCGCUGUUUUCUU--GGCUAACUUU-CAGCGAGGUGAGGCAAGGCGGCAAA----------------------------------------------------AAAAA

Mustelus canis ---CGCGAAACCUCGCUGUUUUCUU--GGCUAACUUU-CAGCGAGGUGAGGAGAGGCGGCAAA-------------------------------------------------AAAAAAAG

Dasyatis sabina ---CGGGAGCCCUCGCUGUUUUCUU--GGCUAACUUU-CAGCGAUGG-CGA-AAGGGCCCAGC-----------------------------------------------------AAAG

Rhinoptera bonasus AAGCGGGAGCCCUCGCUGUUUUCUU--GGCUAACUUU-CAGCGAUGG-UGA-AAGGGCCUAGC-----------------------------------------------------AAAG

structure --------|((((((((( ((((((((( ))))))))) ))))) |----------------------------------------------------------||-

P2b P3 P2b P2a J2a|3

250 260 270 280 290 300 310 320 330 340 350 360

....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|

CR3

structure --------------

Homo sapiens ---------------------AGAGCAAA----CA-----AAAAAUGUC--AGC-UGC---UGG-CC-CGUUCGCCCCUCCC-----GGGGA------------CCUGCGGCGGGUC---

Tupaia glis belangeri ---------------------GGAACAAACAGACAAAAAAAAAAAUGUC--AGC-UGC---UGG-UC-CGUUCGCUCCUCCC-----GGG-C------------CCUGCGGUGGCCGCCA

Oryctolagus cuniculus ---------------------GCAGUAAA----CA-----AAAAAUGUC--AGC-CGC---UGG-CC-GGUUCGCCCUUCCC-----GGGGA------------CCUGCGGUGGCUC---

Cavia porcellus ---------------------GAAGCAAA----CA-----AAAAAUGUC--AGC--G----UGG-CC-GGGCCGCCCCUCCC-----GGAUA------------CCUGCGGCGGCUC---

Chinchilla brevicaudata ---------------------AAAGCAAA----CA-----AAAAAUGUC--AGC--G----UGG-CC-GGUCCGCCCCUCCC-----GGGUA------------CCUGCGGCAGCUC---

Geomys breviceps ---------------------GAAACCAAAUU-GAAAAAAAAAAAUGCC--AGC-UCC---GGCCGGU---CCACCCCUCCC-----GGGGU------------CCUGCGGCCCGGCC--

Microtus ochrogaster ---------------------UCAACCA-----CA-----AAAAAUGCC--AGCGCAAA--GCGCGUC---A---GCCU--------AGAAC------------CUUGCGGCCCCG----

Cricetulus griseus ---------------------CCA-CCA-----CAA----AAAAAUGUC--AGCGCUGG--GCUC-AU---GU--GCCU--------GGAGC------------CUUGCGGCC-------

Mus musculus ---------------------CGAGCCU-----CAAAA--ACAAACGUC--AGCGCAGGA-GCUCCAG---GUUCGCCG--------GGAGC------------UCCGCGGCGCCG----

Mus spretus ---------------------CGAGCCU-----CAAAA--ACAAACGUC--AGCGCAGGA-GCUUCAG---GUUCGCCG--------GGAGC------------UCCGCGGCGUCG----

Mus musculus castaneus ---------------------CGAGCCU-----CAAAA--ACAAACGUC--AGCGCAGGA-GCUCCAG---GUUCGCCG--------GGAGC------------UCCGCGGCGCCG----

Rattus norvegicus ---------------------GGAACCU-----CA-----AAAAAUGUC--AGCGUAGGA-GCUC-UG---GU--GCC---------AGAGC------------UCCGCGGCGCUG----

Mustela putorius furo ---------------------GGAGCAAA----CA-----AAAAAUGUC--AGC-GGC---UGG-CC-UGCUCGCCCCUCCC-----GGGAG------------CCUGCGGCGACUC---

Procyon lotor ---------------------GGAGCAAA----CA-----AAAAAUGUC--AGC-CGC---CGG-CC-UGCUCGCCCCUCCC-----GGGAU------------CCUGCGGUGGCUC---

Felis catus ---------------------GGAGCAAA----CA-----AAAAAUGUC--AGC-UGC---UGA-CU-UGCUCGCCCCUCCC-----AGGAC------------CCUGCGGUGGCUC---

Bos taurus ---------------------GCAACAAA----CA-----AAAAAUGUC--AGC-CGC---UGG-CU-CGCUCACCUCUCCC-----GGGAA------------CCUGCGGUGGUCC---

Sus scrofa ---------------------GAAACAAA----CA-----AAAAAUGUC--AGC-CUC---UGG-CU-CGCUCACUGCUCCC-----GGGAA------------CCUGCGGUGGUUC---

Suncus murinus CUUCGA---------------GGAGCGAAA---CCC----AAAAAAGUC--AGC-CCC---UGGCCGCCUCUCGC-CCUCUC-----GC-AA------------CCCGCCU---------

Equus caballus ---------------------GGAGUAAA----CA-----AAAAAUGUC--AGC-CGC---UGG-CU-CGCUCGCCCCUCCC-----GGGAC------------CCUGCGACGGCUC---

Dasypus novemcinctus ---------------------GGAGCAAA----CA-----AAAAAUGUC--AGC-CGC---UGG-UC-CGCUCGCCCCAUCC-----GGGAA------------CCUGCGGUGGCUC---

Dasyurus hallucatus --------------------------------CC------AAAAACGUC--AGC-CG----AGGCCGG---GCGGCCC------------CG------------CUCGUGGC-CCGUCCG

Elephas maximus ---------------------GGAGCAAA----CAA----AAAAAUGUC--AGC-CGC---CGG-CC--GCUCGCCCCUCCC-----GGGAA------------CCUGCAGUGGCUC---

Trichechus manatus ---------------------GGAGCAAA----CAA----AAAAAUGUC--AGC-CGC---UGG-CC--GCUCACCCCUCCC-----GGGAA------------CCUGUGGUGGCUC---

Gallus gallus GGGGAGAGAAAGGGCCGAAAGGGGCUCCGCGGCCAA----AAAAACGUC--AGC-GAG---GGGUCCG---CUCGCCCCGAU-----CCGCC------------CUGGGGU---------

Anodorhynchus hyacinthinus --------------------AGGGGUUUGCAAUCA-----AAAAACGUC--AGC-GAC---GGGUCUC---CCCAGCCCAGC-----CCGCC------------CUGGGGUCUCCGUCCC

Chelydra serpentina ----------------------GGAGACGCCAACCA----AAAAACGUC--AGC-GAG---GGGCCCU---CCCCUCCCACG-----CCGAC------------CUGGGCCUGUGG----

Bombina japonica ----------------------GCUGCCCAGGACUA----AAAAAUGUC--AGC-UG----GGAGUCCU--UCCUC-UCCCU-----UAUU-------------UCUGCCUCACAACCU-

Xenopus laevis ----------------------GUAGACGACGACUA----AAAAACGUC--AGC-UG----GGAGA-CU--CCUCCGUUCGCACAGCCCGA-------------CCUGCUCCAUUGCCCA

Ceratophrys ornata ----------------------AGAAGCGAGGACCA----AAAAACGGC--AGC-CG----CGGGCCC---UCCUGUUCCCA-----CCAU-------------CCCAGCUUUUCCACAC

Pyxicephalus adspersus ----------------------GAAGCUCAGGACUA----AAAAACGUC--AGC-CG----UAGGCUU---UCCUAUAGCCG-----CAGG-------------CCUGCCUGU-CAGUG-

Dermophis mexicanus --------------CAGUUUC-ACGACAACGGAGA-----AAAAAUGUU--AGC-UG----GGGAACG---UCCCUUUCCCG-----AGAG-------------CCCGCGCCGUCCUUUU

Herpele squalostoma ------------GUGGUUUACGACGAUAGAGGAGA-----AAAAAUGUU--AGC-UG----GGGAACG---UCCCUUUCCCG-----AGAG-------------CCCGCGCCAUCCU---

Typhlonectes natans --------------GAAUUUCG--GACAAGGGAGA-----AAAAAUGUU--AGC-CG----GGGAACG---CCCCUUUCCCG-----AAUG-------------CCCGUGCCGUCCUUCC

Oryzias latipes ---------------------------------CA-----AAAAAAGCC-AGAAAAGA-CUCCCCG----------------------------------UCGCGCUCAG----------

Gasterosteus aculeatus ---------------------------------CAA----AAAAAAGCCAAGA--UGACCACUCCG----------------------------------UCGUGUUCAG----------

Takifugu rubripes ---------------------------------C------AAAAAAGCCAAGA--AAAUCACUCCG----------------------------------UCGCGUUCAG----------

Tetraodon nigroviridis ---------------------------------C------AAAAAAGCCACGA--UGAUCGCUCCG----------------------------------UCGUGUUCGG----------

Danio rerio ---------------------------------U------AAAAAAGCUAUAG----AGUACUCUG------------------------------------GCGCUCGG----------

Rhizoprionodon porosus GUUGGGAG------------CAGCAACGGCAAGCAAA---AAAAAAGUUCCAGC-CGAG--GCCUCC--UCA-CCACGCGGCCUGGGUCUGAGGGUAACAUGGCCCUGCGGGAGAGAGCC

Mustelus canis GUUGGGAG------------CAGCAGCGGCAAACAAAA--AAAAAAGUUCCAGC-CGAG--GCCUCC--UCACCCCCGCGGCCUGGGUCUGAGGGUAACACGGCCCUGCGGGAGAGAGGC

Dasyatis sabina GUUGGGAAGCGUGAUUUAUUGUUGGUGGGCAGAGAG----AAAAAAGUUUAAGC-CGCG--GCCUCC--UC--CCCGGCGGCCCAGGACCC-------------CCUGUU-GCAACGUGC

Rhinoptera bonasus GUUGGGAAGCGUGAUUUAUUGUUGGUGGGCAGAGAG----AAAAAAGUUUCAGC-CGCG--GCCUCC--UC--CCCGGCGGCCCAGGACCC-------------CCUGUU-GCAACGUGC

structure ---------------------------------------| ))) ))) ))) ))))))))))))))))))))))))))))) ((((((|---------

P3 P1 P4

370 380 390 400 410 420 430 440 450 460 470 480

....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|

CR4

structure -----------

Homo sapiens ---------------------------------------------------GCCUGCCC-----------AG-------CCCCCGAAC--CCCG--CCUGG-------AGGCCGCGGUCG

Tupaia glis belangeri GCCC-----------------------------------------------GCCCUCUC-----------AU-------CCCCCGCGU--CCCG--CCUAG-------AGGCCGCGGUCG

Oryctolagus cuniculus ---------------------------------------------------GCCCGCCC-----------GG-------CCCCCGUGC--CCCG--CCUG--------AGGCCGCGGUCG

Cavia porcellus ---------------------------------------------------GUCCA-CC-----------GG-------CCCCCGAGC--CCCG--CCU---------AGGCCGCGGCCG

Chinchilla brevicaudata ---------------------------------------------------GCCCGGCU-----------GG-------CCCCCGAGC--CCCG--CCCA--------GGGCCACGGCUG

Geomys breviceps ---------------------------------------------------GCCCGCCC---------GAAC-------CCCCCGCGA--CCCG--CCUG--------AGGCCACGGCCG

Microtus ochrogaster ---------------------------------------------------GGCCGCCC-----------AG--------CCCCG-CA--CCCG--CCUUG-------AGGCCGCGGUUG

Cricetulus griseus ---------------------------------------------------GGCCGCCC-----------AG--------CCCCG-CA--CCCG--CCUG--------AGGCCGCGGUCG

Mus musculus ---------------------------------------------------GGCCGCCC-----------AG--------UCCCG-UA--CCCG--CCUAC-------AGGCCGCGGCCG

Mus spretus ---------------------------------------------------GGCCGCCC-----------AG--------UCCCG-UA--CCCG--CCUAC-------AGGCCGCGGCCG

Mus musculus castaneus ---------------------------------------------------GGCCGCCC-----------AG--------UCCCG-UA--CCCG--CCUAC-------AGGCCGCGGCCG

Rattus norvegicus ---------------------------------------------------GGCCGCCC-----------AG--------CCCGG-UA----CC--CGCCUGG-----AGGCCGCGGACG

Mustela putorius furo ---------------------------------------------------GCCCGCUU-----------AG-------CCCCCG-CA--UCCC--GCCUGG------AGGCCGCGGUCG

Procyon lotor ---------------------------------------------------GCCCGCUU-----------AG-------CCCCCGCGU--CCCG--CCUGG-------AGGCCGCGGUCG

Felis catus ---------------------------------------------------GCCUCCUU-----------AG-------CCCCCGCGU--CCCG--CCUAG-------AGGCCGCGGUCG

Bos taurus ---------------------------------------------------GCCCGCCC-----------AG-------CCCCAGUGC--CCCG--CCUG--------AGGCCGCAGUCG

Sus scrofa ---------------------------------------------------GCCCGCCC-----------AG-------CCCCCGCGC--CCCG--CCUG--------AGGCCGCGGUCG

Suncus murinus ---------------------------------------------------CCG-UCCC-----------AG--------CCUCCAUC--CCCG--CCCC--------AGGCCGCGGUCG

Equus caballus ---------------------------------------------------GCCCGCCC-----------AG-------CCCCCGCGC--CCCG--CCUGG-------AGGCCGCGGUCG

Dasypus novemcinctus ---------------------------------------------------GUCCGCCC-----------UG-------CCCCCGCGC--UCCG--CCUAG-------AGGCCGCGGUCC

Dasyurus hallucatus CACUGUCCGGGCCAGGCCCCGGCCCGAACCCCCUGGAGACAACUCCCGCAGGGUCUGCGCUGCGCCGCGGAG--------CCCCG-GCUGCCCACGUAG---------AGGCGGCGG-CC

Elephas maximus ---------------------------------------------------GCCCGCCC-----------AG--------CCCCGCUC--CCCG--CCUGG-------AGGCCGCGGUCG

Trichechus manatus ---------------------------------------------------GCCCGCCC-----------AG--------CCCCGCGC--CCCG--CCUGG-------AGGCCGCGGUCG

Gallus gallus -----------------------------------------------------------------------------------------CCCCG--CUCGCG------UGGCCGCGGUCG

Anodorhynchus hyacinthinus CCCACGCAGCC-------------------------------------GGGGGCCUGCC---------GCGGAGG---CUCCCUC----CGCCG--CACUUCACGG--AGGCCGCGGUCG

Chelydra serpentina ------------------------------------------------UGGGGCCCGCC--------AGCGAAGU--CCCCGCCG----CCCCG--CCCCGGUG----AGGCCGCGGUCA

Bombina japonica GGA-------------------------------------------------CUCUUUA---------UUUA-------GCGGUG-----CCCC-AUUUGUCG-----AGGCCGCAGUCA

Xenopus laevis AGA--------------------------------------------GCCCCGGGUUUUCU----CUGUGGAAUGU---AUCAGGCGCU-CCCCGGUCUGUCUGUCUGGGGCCGCGGUCG

Ceratophrys ornata UGC------------------------------------------------GCCUGGGU----UCUCACUCAA-GUGUUCGGCAG-----CUUC-CACUUACG-----AGGCCGCGGUCU

Pyxicephalus adspersus UGC------------------------------------------------GCGGCCUC-------UGCUCGCAAUGU-CCGCAG-----CGCC-UUCCUAUG-----AGGCCGCAGUCU

Dermophis mexicanus UCUUCCU----------------------------------------CGGGCCCGUUGG-------C-AUAGCCCCU---GGCCU-----CCUC-GCUCUAU------AGGCCGCGGUCA

Herpele squalostoma -CUUCCU----------------------------------------CGGGCCCAUUGG-------CGAUAGCCCCC---GGCCU----CCCUC-GCUCACC------AGGCCGCGGUCA

Typhlonectes natans UCUCCUC----------------------------------------UGGGCCCGUUGG-------CGAUAGCCCCC---GGCCU----CCCUC-GCUCCUU------AGGCCGCGGUCA

Oryzias latipes ---------------------------------------------------------------------U-UCCCUGCU---------GGAAAC----------------GCCGCGGUCA

Gasterosteus aculeatus ---------------------------------------------------------------------UGUCCCGCCU-GAAACACCGCGAAU-----------UUCCUGCCGUGGUCG

Takifugu rubripes ----------------------------------------------------------------------GUCCCCCCCAGGAACACCGAGAGC-------------CCUGUUGUGGUCA

Tetraodon nigroviridis -----------------------------------------------------------------------UCCCCCCUCAAAGCACCGCGAGC-------------CCGGUUGCGGUCA

Danio rerio ---------------------------------------------------------------------UCUCACAGGU---UUGGCUGUUUGU-----------------ACGCGGACA

Rhizoprionodon porosus AACACGG---------GGGGGCCCCGGUCCGGCUAACAGGGCAGGAG----GUCGGCCC------CAAUUGCCU--CA--GGCCC-----AGCC--ACUCC-------GGGCCGCGAUCA

Mustelus canis AACACG----------GGGGCCCCCGGUCCGGCGAACAGGGCAGGAG----GUCGGUCC------CAAUCGCCUCACA--GGCCC-----AGCC--ACUCC-------GGGCCGCGGUCA

Dasyatis sabina GGAAUGGCG----------------------------------------GCCUCGGCCC------CCCU--GCU-GCA--CGCCC-----AGCC--GUUU--------AGGCCGCGGUCA

Rhinoptera bonasus GAAAUGGCG----------------------------------------GCCUCGGCCC----CCACCUUUGCUCGCA--UGCCC-----AGCC--GAGU--------AGGCCGCGGUCA

structure -----------------------------------------------------------------------------------------|(((( ((((( ((

Hypervariable paired region P5 P6

490 500 510 520 530 540 550 560 570 580 590 600

....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|

CR5

structure - -----------------------------------

Homo sapiens GCCCG-GGGCUUC----UCCG---GAGGCACCCACUGCCACCGCGAAGAGUUGGGCUCUGUCAGCCG--CGGG-UCUCUCGGGGG----C-GA-----GGGCG-AGGU------------

Tupaia glis belangeri GCCCG-GGGCUUC----UCCG---GAGGUGCCCAUUGCCGCCGCGAAGAGUUAGGCUCUGUCAGCCG--CGGG-CUCUCGGGGGG----CCCA-----GGGCG-AGGU------------

Oryctolagus cuniculus GCCCG-GGGCUUC----UCCG---GAGGUGCCCAAUGCCGCCGCGAAGA