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