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