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---GAGGUGCCCAAUGCCGCCGCGAAGAGUUAGGCUCUGUCAGCCG--CGGG-UCCCUCGGGGG----CCAA-----GGGCG-AGGC------------
Cavia porcellus GCGCG-GGGCUUC----CCUG---GAGGCGCCCAUGGCCGCCGCGAAGAGUUCGUCUCUGUCAGCUG--CGGG-UCGCCCGGGGG----CCGC-----GGGAG-AGUC------------
Chinchilla brevicaudata GCGCG-GGGCUUC----UCCG---GGAGCGCC-AUGGCCGCCGCGAAGAGUUCGUCUCUGUCAGCCG--CGGG-UCGCGCGGGGG----CCGC-----GGGGG-AGUC------------
Geomys breviceps GCCCG-GGGCCUC----UGCG---GAGGUGCCCAUUGCCGCCGCGAAGAGUUAGGCUCUGUCAGCCG--CGGG-AUCCGCGCGGG----CC-------GGGCCGCGGC------------
Microtus ochrogaster GCCU--GGAGUUC----UCCG---GA---CUCCGCUGCCGCCGCGAAGAGUUCGUCUCUGUCAGCCG--CGGA-GUAU-CAGGGG----CUG------GGGCCAGGCC------------
Cricetulus griseus GCCU--GGAG-UC----CUCG---GG---CUCCGCUGCCGCCGCGAAGAGCUAGACUCUGUCAGCCG--CGGG-GCGU-CAGGGG----CUG------GGGCGAGCCC------------
Mus musculus
GCCU--GGGG-UC----UUAG---GA---CUCCGCUGCCGCCGCGAAGAGCUCGCCUCUGUCAGCCG--CGGG-GCGC-CGGGGG----CUG------GGGCCAGGCC------------
Mus spretus
GCCU--GGGG-UC----UUAG---GA---CUCCGCUGCCGCCGCGAAGAGCUCGCCUCUGUCAGCCG--CGGG-GCGC-CGGGGG----CUG------GGGCCAGGCC------------
Mus musculus castaneus GCCU--GGGG-UC----UUAG---GA---CUCCGCUGCCGCCGCGAAGAGCUCGCCUCUGUCAGCCG--CGGG-GCGC-CGGGGG----CUG------GGGCCAGGCC------------
Rattus norvegicus GCCU--GGGG-UC----UUAG---AA---CUCCGCUGCCGCCGUGAAGAGCUAGUCUCUGUUAGCUA--CGGG-GCAC-CGGGCG----CUG------GGGUCAGGCC------------
Mustela putorius furo GCCCG-GGGCUUC----UCCG---GAGGCACCCAUUGCCGUCGCGAAGAGUUGGGCUCUGUCAGCCG--CGGG-ACCCUUGGGGG----CCAA-----GGGCG-AGGC------------
Procyon lotor
GCCCG-GGGCUUC----UCCG---GAGGCACCCAUUGCCGUCGCGAAGAGUUGGGCUCUGUCAGCCG--CGGG-ACCUUUGGGGG----CCAA-----GGGCG-AGGC------------
Felis catus
GCCCG-GGGCUUC----UCCG---GAGGCACCCAUUGCCGUCGCGAAGAGUUGGGCUCUGUCAGCCG--CGGG-UCCCUUGGGGG--GGCCGA-----GGGCG-AGGC------------
Bos taurus
GCCCG-GUGCUUC----UCCG---GAGGUGUCCAUUGCCGCCGUGAAGAGUUGGGCUCUGUCAGCCG--CGGG-UCGCUCGGUGG---GCCGA-----GG-CA-UGGC------------
Sus scrofa
GCCCG-GGGCUUC----UCCG---GAGGCGCCCAUUGCCGCCGCGAAGAGUUGGGCUCUGUCAGCCG--CGGG-UCCCUCGGGGG----CCAA-----GG-CG-AGGC------------
Suncus murinus GUCCG--GGCUUC----UUCG---GAAGUCCC-GUUGCCGUCGCGAAGAGUUCGCCUCUGUCAGCCG--CGGG-GCU--UGGGG-----CCAG-----GGA----CGG------------
Equus caballus GCCCG-GGGCUUC----UCCG---GAGGCGCCCAAUGCCGCCGCGAAGAGUUGGGCUCUGUCAGCCG--CGGG-UGCCUCGGGGG----CCAG-----GGACG-AGGC------------
Dasypus novemcinctus GCCCG-GGGCUUC----UCCG---GAGGCACCCAAUGCAGCCGCGAAGAGUUAGGCUCUGUCAGCCG--CGGA-UCCCGCGGGGG----CCAA-----GGGUG-AGGC------------
Dasyurus hallucatus GUCUCGGGGCCCCUG--CGUG--CGGGGCGCCCACUGCGGCCGCCAAGAGCUCGUCUCUGUCAGCCU--CGGGUGCACGUGGGCC---CGCGGUCGAGCCCUAAGGCC------------
Elephas maximus GCCUG-GGGCUUC----UCCG---GAGGUUCCCGCUGCCGCCGCGAAGAGUUGGGCUCUGUCAGCCG--CGGG-UCCCGCGGGAA----CCAA-----GGGCG-AGGC------------
Trichechus manatus GCCUG-GGGCUUC----UCCG---GAGGUUCCCAUUGCCGCCGCGAAGAGUUAGGCUCUGUCAGCCG--CGGG-UCCUGCGGGAA----CCAA-----GGGCG-AGGC------------
Gallus gallus
GCC---GGC--------ACCC---------GCCAUUGCCGCCGCGAAGAGUUCGCCUCUGUCAGCCU--CGGCG----GCGCGCGGGA-GGUGCGG--CGCGC--GGCCCC---------
Anodorhynchus hyacinthinus GCC---GGU--------GUCC---------GCCACUGCCGCCGCGAAGAGUUCGUCUCUGUCAGCCU--CGGCG----GCGGUGGGGA-GCGAGAG--GGCUC--GUCCCC---------
Chelydra serpentina GCC---GGC--------UCGC---------GCCACUGCUGCCGCGAAGAGUUCGUCUCUGUCAGCCU--CGGGG----GCGGCCGGGG-UGGA-AG--GGCGG--GUCCC----------
Bombina japonica GUC----------UUGUUCUUAUACG--------CUGCUGUUGCGAAGAGUUCGUCUCUGUCAGCCUCCGGGG------CAACGC---CUUGAAUU--UGGAG--AG-------------
Xenopus laevis GCA--------------UCAU-------------CUGCUGUCGCGAAGAGUUCGUCUCUGUUAGCCCUUGGGG----GCCCUGGU-----GCGGAG--UGGAG--AGUCCGGGUCU----
Ceratophrys ornata ACC------------GCUGUCAC-----------UGGUAGUCGCGAAGAGUUCGUCUCUGUCAGCCUUGGGAG------CCGCGG--ACGGAGUAUGAGGUCC--AGU------------
Pyxicephalus adspersus GCC------------AAUACCCC-----------GGGCAGCCGCGAAGAGCUCGUCUCUGUCAGCCUUUGGCG------CUGCGG---CGGAGUGGGGGAGGC--CGC------------
Dermophis mexicanus GCUC--GGGCCCC--AGCUCCGGCAGGGGUUCCACUGCUGCCGCGAAGAGUUCGCCUCUGUCAGCCUU-GAGG------UGGCC----GGGAUAGAA-UAGGC--GGGCUCG--------
Herpele squalostoma GCCC--GGGCCCU--GGCUCUGCUAGGGCGUCCAAUGCUGCCGCGAAGAGUUCGUCUCUGAUUGCCUU-GAGG------UAGCC----GGGCUCGAA-UAGGU--GGGCUCG--------
Typhlonectes natans GUCC--GGGCCCU--UGCUCUGGCAUGAGGUCCAUUGCUGCCGCGAAGAGUUCGUCUCUGUCAGCCUU-GAGG------UGGCC----AGCAUGGAA-UUGGC--GGGCUUG--------
Oryzias latipes GCUCG-------------------------------GCUGCUGCGAAGAGUUCGUCUCUGUU-------GUUUCG-------------GGGA----------------------------
Gasterosteus aculeatus GCUUGU------------------------------GCUGCCGCGAAGAGUUCGUCUCUGUU-------GCUCCGGUGUUCUCAUGGCGGGA----------------------------
Takifugu rubripes GUCCG-------------------------------GCUGCCGCAAAGAGUUGGUCUCUGCU-------GCUCCGGUGUCUUG---GCGGGA----------------------------
Tetraodon nigroviridis GUCUG-------------------------------GCUGCCGCGAAGAGUUGGUCUCUGCC-------GCUCCGGUGUCUUCAUGUCGGGA----------------------------
Danio rerio
GUUUG-------------------------------ACUGCCGCCAAGAGUUCGGCUCUGCU-------GCACAUUCGGCAGGUCUGU-GGA----------------------------
Rhizoprionodon porosus GCCC--GGGCUUU---CCCUACUUU-GGGGCCCAAUGCUGUCGCGAAGAGUUCGGCUCUGUCAGCCC--GGCU------GGGUC------CGGGUGG-GGGCC--GGCACAGAGGGACAC
Mustelus canis GCCCG-GGGCUUUCCCCCCCACCAUGGGGGCCCAAUGCUGCCGCGAAGAGUUCGGCUCUGUCAGCCC--GGCU------GGGCC------AGGGUGG-GGGCC--GGCACAGAGGGACAC
Dasyatis sabina GCGC--CGGUUUC-CACGCCAGUGU-GGGGCUUGAUGCUGUCGCGAAGAGUUCGUCUCUGUUAGCCU--GGCA------GGGUG----UGCUACGCA-GGGUC--GGGGU----------
Rhinoptera bonasus GCGC--CGGCUUC-CACGCCAGUGU-GGGGCUUGAUGCUGUCGCGAAGAGUUCGUCUCUGUCAGCCU--GGCA------GGGGG----UGCUACGCA-GGGUC--GGGGU----------
structure
((
|------------------------------| ))))))))) (((( ))))
))))|----------------------------------------------
L6 P6 P6.1 P6.1
P5
Hypervariable paired region
610
620
630
640
650
660
670
680
690
700
710
720
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
CR6
CR7
structure
-------------
---------------
Homo sapiens
----------------UCAGGCCUUUCAGG---CCGCAGG-AAGAGGAA-CG-----GAGC-GA-GUCCC-------CGCGCGCGGCGCGAUUCCC-UGAG-CUGUGGGACGUGCAC--C
Tupaia glis belangeri ----------------UUAGGCC-UCGUGG---CCGCAGG-GACAGCAA-CG-----GAGC-GG-GUCCC------CGCGAGCCUGUGCGCGUCCC-UGAG-CCGUGGGACUUGCAC--C
Oryctolagus cuniculus ----------------GCAGGCC-GUCUGG---CCGCAGG-GAGAGGAA-CG-----GAGC-GG-GUCCC-------CCAGCGUGGUGCGCUUCCC-UGAG-CUGUGGGACUUGCAC--C
Cavia porcellus ----------------CCAGGCC---UUGG---CCGCAGG-GAGAGAAA-CG-----GAGC-AG-GUCCU---------CGCGCGGUGCACUCCCC-UGAG-CUGUGGGAAGUGCAC--C
Chinchilla brevicaudata ----------------CUAGGCC-GAGUGG---CCGCAGG-AAGAGAAA-CG-----GAGC-CU-GUCCC-------UGUGCACGGGGCGCUUCUC-UGAG-CUGUGGGAAGUGCCC--C
Geomys breviceps --------------------CGGACGCCGAU--CCGCAGG-GACAGCAA-CG-----GAAC-CG-GCCCC-------UUCGCCCUGUGCGCUUCCC-GGAG-CUGUGGGAUGAGCAC--C
Microtus ochrogaster --------------------CGGAC-AGCG---UCGCAAG-UACAGUAA-CG-----GAGC-UG-GUCCU---------UGUUCGGUGG-CUUCCC-UGAG-CUGUAGGAAGUACAC--C
Cricetulus griseus --------------------CGGC--AGCG---CCGCAAG-CAGAGAAA-CG-----GAGC-UG-GUCCC--------GUGAACGGUGA-CUUCCC-UGAG-UUGUGGGAAAUGCAC--C
Mus musculus
---------------------GGGCGAGCG---CCGCGAG-GACAGGAA-UG-----GAAC-UG-GUCCC-------CGUGUUCGGUGU-CUUACC-UGAG-CUGUGGGAAGUGCAC--C
Mus spretus
---------------------GGGCGAGCG---CCGCGAG-GACAGGAA-UG-----GAAC-UG-GUCCC-------CGUGUUUGGUGU-CUUACC-UGAG-CUGUGGGAAGUGCAC--C
Mus musculus castaneus ---------------------GGGCGAGCG---CCGCGAG-GACAGGAA-UG-----GAAC-UG-GUCCC-------CGUGUUCGGUGU-CUUACC-UGAG-CUGUGGGAAGUGCAC--C
Rattus norvegicus ---------------------GGGAGAGCG---CCGCAAG-GACAGUAA-CG-----GAAC-UG-GUCCC-------UGAGUUCGGUGG-CUUUCC-UGAG-AUGUGGGAAGUGCAC--C
Mustela putorius furo -------------------------UCUGG---CCGCAGG-GAGAGAAA-CG-----GAGC-GG-GUCCC-------CUCGCGCGGUGCGCUUCCC-UGAG-CUGUGGGACUUGCAC--C
Procyon lotor
-------------------------UCUGG---CCGCAGG-GAGAGAAAACG-----GAGC-GG-GUCCC-------CUUGCGCGGUGCGCUUCCC-UGAG-CUGUGGGACUUGCAC--C
Felis catus
-------------------------UCUGA---CCGCAGG-GAGAGAAA-CGG----GAGC-AG-GUCCC-------CGCGCGCGGUGCGCUUCCC-UGAG-CUGUGGGACUUGCAC--C
Bos taurus
-------------------------UGUAA---CCGCAGG-GAAAGGAA-CG-----GAGUGGG-GUCCC-------CGCGCGCGGUGCGCUUCCC-UGAG-CUGUGGGACUUGCAC--C
Sus scrofa
-------------------------UCUGA---CCGCAGG-GAAAGGAA-CG-----GAGU-UG-GUCCC-------CGCGCGCUGUGCGCUUCCC-UAAG-CUGUGGGCUGUGCAC--C
Suncus murinus ----------------------GACCCUGU---CCGCAGG-GAGAGAAACUG-----GAGC-CG-GGCCC---------UCCACGGUGC-C-UCCC-CGAG-CUGUGGGAUCUGCAC--C
Equus caballus -------------------------UCUGG---CCGCAGG-GAGAGGAA-CG-----GAGC-GG-GUCCC-------CGCGCGCGGUGCGCUUCCC-UGAG-CUGUGGGACGUGCAC--C
Dasypus novemcinctus ----------------UUAGGCC--GCGGG---CCGCAGG-AAGAAAAA-CC-----GAGC-GA-GUUCU-------CACGCGCGGUGCGCUUCCC-UGAG-CUGUGGGUCGUGCGC--C
Dasyurus hallucatus -----GGGCGUGGGG-CUG-----------GGGUCGCAGG-GAGAGUAACCGU----GAGCCGGCGCCC--------AGCCUUCAGGGCGC-UCCCUCGAG-CUAUGGGAGCUGCCC--C
Elephas maximus ----------------UGGGGCC-UCCUGA---ACGCAGG-GAGAGAAA-CG-----GAGC--G-GUUCC-------CCGCGUGCGUGCGCUUCCC-UGAG-UUGUGGGAUGUGCGC--U
Trichechus manatus ----------------UUAGGCC-UCCUGA---ACGCAGG-GAGAGAAA-UG-----GAGC--G-AUUCC-------CCGAGUACGUGUGCUUCCC-UGAG-UUGUGGGAUGUGCGU--C
Gallus gallus
----------------GCG--------------CCCCCAG-CAGAGCAAACGG----GAGC-GG-CGCC---CCCGGGGUAACCCCCGCGCUCCCC-UGCG-CCGUGGGGCGCGCGG--A
Anodorhynchus hyacinthinus ----------------GCGCCGGGG--------ACCCCAG-CAGAGCAAAACG----GAGC-GG-CGUC---CUCGGCACAGCCGCCGCGCUUCCC-UCAA-CCGUGGGAUGCGCGG--A
Chelydra serpentina ----------------GAGCCCGUC--------GGCC-GG-GAGAGCAAACGU----GAGCGGC-AGCCCC-------UGCGCCACCGCCCUCCCC-UAAG-CUGUGGGGCCCGCGG--U
Bombina japonica ----------------CCUGGGAAUGUAACAAGGGGUAGG-GAAAAUAACGA-----GAGCUGA-GUUG-------GCUUCUCCUGUGCUG-UUCC-UGAG-CUGUGGAACUUGCAA--U
Xenopus laevis ----------------GGG--------------GGGUCGG-GAGAACAAAAG-----GGGGCGC-GCUGGUGCUCAGGCUCAGUCAUGCUU-UCCC-UUAG-UUGUGGGAUAUGCGU--G
Ceratophrys ornata ----------------AAUGAG------------AGCAGGGAAGAGUAAAGC-----GAGCCGC-GCUA------CUUGUCCUAUCUGCCG-CUCC-UAAG-CUGUGGGGCGUGUAG-GG
Pyxicephalus adspersus ----------------UGAU--------------GGCAGCUGAGAAUAAAGC-----GAGCCCA-GCUG----CCCCGCUCUGUUCCACUG-CCCC-UGAG-CUGUGGGGUUGGUGA-AU
Dermophis mexicanus ----------------CGGCAGC----------GCGCGGGAAAGAGCAAAU-G--GUGAACUGG-GUGC-------CUGUUGGGGUCGC-G-UCCC-UGAA-GAGUGGGAAGUGCGA--U
Herpele squalostoma ----------------CGGCGAU----------GCGCAGGAAAGAGCAAAACA--GUGAACUGG-GCGU-------GUGCUGGGGUCGC-G-UCCC-UGAA-GUGUGGGAUGUGCGA--U
Typhlonectes natans ----------------UGGCGGC----------GCGCGGGAAAAAGCAAAU-G--GUGAACUAG-GUGC-------GUGUUGUGGUCGU-G-UUCC-UGAAGC-GUGGAAUGUGCGA--U
Oryzias latipes ------------------------UUGUCAACAGCUGAGC--AGAUAAAAA-----UGAGCA--AGGCGAU-----------CCUGCCG---AACC-UCA---UGUGGUC---CGGUUCG
Gasterosteus aculeatus ------------------------CUUGUGAUAACUGAGC--AGAGUAAAAC----UGAGCA--GGGCGAC-----------UCUCCCA---GAUCGUUC--CAGUGAUC---CGGUCAG
Takifugu rubripes ------------------------UCACCAAGGACUGAAC--AGAGAAACAG----UGAGCG--UGGUGAC-----------UCUACCG---GUUC-UUC--CAAUGUCC---CGGUUAG
Tetraodon nigroviridis ------------------------UCACCGAGGACCGAAC--AGAGCAAAAC----UGAGCC--UGGUGAC-----------UCUACCG---GUUC-UCC--CAGUGUUC---UGGUAGG
Danio rerio
------------------------CUGCACAACACUGAGC--AGAUUAACU-----UGAGCA--UGGCGAA---------GGUUUGC-G---GACC-UCAAACACUGAUC---CUGCAAA
Rhizoprionodon porosus ACCGGGCCGGGGCGCCGAGGAUAGCUACCGC--CCGCAGG-GAUAGUAAAUAUCCGUGACCAGU-GGC--------CUCGGUGGCUGCGUC-UCCC-GGAG-CAAUGGGACC-CGCAAGG
Mustelus canis ACCGGGCCGGGGCGCCGGGGAUAGCUACCGC--CCGCAGG-GAUAGCAAAUAUCCGUGACCAGU-GGU--------CUCGGUGGCUGCGUC-UCCC-GGAG-CAAUGGGACC-CGCAAGG
Dasyatis sabina ----------------GCGGAG------------GGCAGG-GAGAUUAAAUAG-CUUGACCAGA-CGC-----UAUGGCCUGUACUGCAUU-UCCC-AGAG-CUGUGGGACC-UGCAAAU
Rhinoptera bonasus ----------------ACGGGG------------GACAGG-GAGAUUAAAUAG-CUUGACCAGA-CGC-----UAUAACCUGUACUGCAUC-UCCC-AGAG-CUGUGGGACC-UGCAAAU
structure
--------------------------------|
)))))) ANANNAA
(((( (((
(((( ((((
)))) ))))
P4 BoxH
P7a P7b
P8a P8b
P8b P8a
730
740
....|....|....|....|...
CR8
structure
---------
Homo sapiens
C-AGGACUCG-GCUCACACAUGC
Tupaia glis belangeri G-GGGACUUU-GCUCGGACAAUC
Oryctolagus cuniculus C-GGGACUCG-GCUCAAACACGC
Cavia porcellus --GGGAC-GG-GCUCCUACAAGC
Chinchilla brevicaudata --GAGACUCG-GCUCCUACAAGC
Geomys breviceps C-GGGGU-CG-GCUCCUACAGUU
Microtus ochrogaster C-AGAGCUCG-GCUCCUACAACC
Cricetulus griseus A-GGAACUCG-GUUCCCACAACC
Mus musculus
C-GGAACUCG-GUUCUCACAACC
Mus spretus
C-GGAACUCG-GUUCUCACAACC
Mus musculus castaneus C-GGAACUCG-GUUCUCACAACC
Rattus norvegicus U-GGAACUCA-GUUCCUACAACC
Mustela putorius furo C-GGGACUAG-GCUCACACACAC
Procyon lotor
C-GGGACUAG-GCUCACACACAU
Felis catus
C-GGGACUGG-GCUCAGACACAU
Bos taurus
C-GGGACUCG-GCUCAGACAUCU
Sus scrofa
U-GGGACUCG-GCUCAGACACUU
Suncus murinus C-GGGACUCG-AACCCUACACUU
Equus caballus C-GGGACUCG-GCUCAAACACGU
Dasypus novemcinctus U-GGGACUCG-GCUCAGACACGU
Dasyurus hallucatus C--GGGCACG-GCUCGGACACCC
Elephas maximus C-GGGGCUCA-GCUCCGACAGGU
Trichechus manatus C-GGGACUCA-GCUCCGACAGGU
Gallus gallus
C--GGCGUC--GCUCCCACACGC
Anodorhynchus hyacinthinus C--GGCGCC--GCUUCGACACCC
Chelydra serpentina CGGGGCUGC--GCUCAGACACGC
Bombina japonica CG-CAGUC-G-GCUCUGACACUU
Xenopus laevis UU-CAGCCAG-UCCCCGACAUGU
Ceratophrys ornata UA-CACAA-G-GCUCCGACAUUC
Pyxicephalus adspersus UG-CAGCAUG-GCUCCGACAACU
Dermophis mexicanus CU-GUGUUCCUGUUCAGACACAC
Herpele squalostoma CU-GUCCGCUUGUUCAGACAUUG
Typhlonectes natans CU-GUGCGCUAGUUCAUACACAC
Oryzias latipes GUA-UCCUAC-GCUCAGACAAAU
Gasterosteus aculeatus AAA-GCCCCC-GCUCAAACACCC
Takifugu rubripes GAU-ACCCAA-GCUCAAACACUC
Tetraodon nigroviridis AAU-GUCCAA-GCUCAAACACCC
Danio rerio
UAC-GCCACC-GCUCAGACAUGC
Rhizoprionodon porosus CU--GCCCU--GGUCAUACACGC
Mustelus canis CU--GCCCU--GGUCAUACACAU
Dasyatis sabina CU--GCGCU--GGUCAUACAUUU
Rhinoptera bonasus CU--GCGCU--GGUCAUACAUUU
structure
))) ))))
ACA
P7b P7a BoxACA