#NEXUS
[!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file.


Generated on September 19, 2025; 0:33 GMT

TreeBASE (cc) 1994-2008

Study reference:
Parrie L.E., Renfrew E.M., Mueller R.L., & Garrity D.M. 2012. Zebrafish tbx5 paralogs
are not functionally redundant in cardiac or pectoral fin development. Developmental
Biology, .

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S12622]

BEGIN TAXA;
        TITLE  TaxaForAnalysisStep8996;
        DIMENSIONS NTAX=19;
        TAXLABELS
            Ambystoma_mexicanum_tbx5
            Anolis_carolinensis_tbx5
            Danio_rerio_tbx5a
            Danio_rerio_tbx5b
            Gallus_gallus_tbx5
            Gasterosteus_aculeatus_tbx5a
            Gasterosteus_aculeatus_tbx5b
            Homo_sapiens_tbx5
            Monodelphis_domestica_tbx5
            Notophthalmus_viridescens_tbx5
            Oryzias_latipes_tbx5a
            Oryzias_latipes_tbx5b
            Silurana_tropicalis_tbx5
            Taeniopygia_guttata_tbx5
            Takifugu_rubripes_tbx5a
            Takifugu_rubripes_tbx5b
            Tetraodon_nigroviridis_tbx5a
            Tetraodon_nigroviridis_tbx5b
            Xenopus_laevis_tbx5
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M12386]

	TITLE Parrie_et_al_tbx5_alignment;
	LINK TAXA = TaxaForAnalysisStep8996;
	DIMENSIONS NCHAR=311;
	FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -;

MATRIX
[                                          10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310 ]
[                                           .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         . ]
Ambystoma_mexicanum_tbx5           --------------------------------------------------QGMEGIKVFLHERELWLKFH-EVGT-EMVITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFSETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKV-------------------------------------
Anolis_carolinensis_tbx5           MADAEEGFGLPTTPVEADTKELGGEGKAEGPATGTPSKPPASPQAAFT-QQGIEGINIFLDPCALHLCLACATGTNDPSFSSLGRRMFPSYKVKVTGLNPKTKYILLMDIVPSDDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSSRKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFAETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHPYKKPYMETSPQEDDSFYRSQRQACMYAS
Danio_rerio_tbx5a                  MADSEDTFRLQNSPSDSEPKDLQNEGKSDKQNAAVSKSP--SSQTTYI-QQGMEGIKVYLHERELWTKFH-EVGT-EMIITKAGRRMFPSFKVKVTGLNPKTKYILLMDVVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRIHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQSTKEYPVVPRSTVRQRVYHCIKRKHPYKKPYVESSSSEDDHYYRPQRQACMYAS
Danio_rerio_tbx5b                  MANPMFESLRACSGGNSPAMDFERDKDSGHHGRNKTGSPP--LQTQLS-QQSMEGIKVYLHEKDLWAKFH-DVTT-EMIITKAGRRMFPSYKVKVTGLNPKAKYILLMDIISADEHRYKFADNKWSI--SGKAEPAIPGRLYVHPDSPASGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADERNSFGSSNTSFCTHSFAETTFIAVTSYQNHTITQLKIENNPFAKGFRGNDDIELHRMSRTPS-KEYPLVPRSTARQRAFTCSDTS-------LTETPSIHDPTYPLQHQPCMYGG
Gallus_gallus_tbx5                 MADTEEGFGLPSTPVDSEAKELQAEAKQDPQLGTTSKAPT-SPQAAFT-QQGMEGIKVFLHERELWLKFH-EVGT-EMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHPYKKPYMETSPAEEDPFYRSQRQACMYAS
Gasterosteus_aculeatus_tbx5a       MADQEETFALENSPGGSESRELQSDNKSEKQNGTSSKSP--SSQTTYI-QQGMEGIKVYLHERELWIKFD-EVGT-EMIITKAGRRMFPSFKVKVTGLNPKTKYILLMDVVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRIHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQSTKEYPVVPRSTVRQRVYHCIKRKQSYKKAYLESSSSEEDHYYRPQRQACMYAS
Gasterosteus_aculeatus_tbx5b       MANGGDQFGLAERP-DSHCMDSPKEAKQKHS-SYTLDSPA-SPQKASS-QPGMEGIKVFLHDRELWTKFD-GVGT-EMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPGDDHRYKFADNKWSI--TGKAEPAMPGRLYVHPDSPATGAHWSRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFSETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDNELHRMAKLQG-RMTSCCCGSAQRLRVFLCLHPSHPFKKCFTGRSSSEGESYY--QRQACMFAG
Homo_sapiens_tbx5                  MADADEALAGAHLWSLTQKTCLRFEPRAR---SGPPASPPGRPRSRLH-PAGMEGIKVFLHERELWLKFH-EVT--EMIITKAGRRMFPSYKVKVTGINPKTKYILLMDIVPADDHRYKFADNKWCV--TGKAEPAMAGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHPYKKPYMETSPSEEDSFYRSQRQACMYAS
Monodelphis_domestica_tbx5         MADADEAFGLPHTPLEAESKELPPEAKQENPLGSSSKAPA-SPQAAFT-QQGMEGIKVFLHERELWLKFH-EVGT-EMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKW?AWGAGRTEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHPYKKPYMETSPTEEDPFYRSQRQACMYAS
Notophthalmus_viridescens_tbx5     MADSDEGFGMPDTPVDPESKELQSDSKQDSQLGAGSKPPS-SPQAAFT-QQGMEGIKVFLHERELWLKFH-DVGT-EMIITKAGRRMFPSYKVKVSGLNPKTKYILLMDIVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFSETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHTYKKSYMETSPTEEDPFYRSQRQACMYAS
Oryzias_latipes_tbx5a              MADQEETFVLQNSPGSSDTREIQSDNKPEKQNGTSSKSP--SSQTTYIQQVGKR?IKVYLHERELWMKFH-EVGT-EMIITKAGRRMFPSFKVKVTGLNPKTKYILLMDVVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRIHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQSTKEYPVVPRSTVRQRVYHCIKRKHSYKKAFLESSSSEDDHYYRPQRQACMYAS
Oryzias_latipes_tbx5b              MANGGEQFGLAEHP-DPGCVDSPEEPKLENP-RLNLSSAN-SPQTASS-QQGMGSIKVVLHDRELWTKFD-EVGT-EMIITKAGRRMFPSYKVKVIGLNPKTKYILLMDIVPGDDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWSRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDNELHRMAKLQG-KDYPVVPRSTVRQRSYNCSKRKHAYKKTFNSGSPSGTESYCHPQRQACMFAS
Silurana_tropicalis_tbx5           MADTEEAYGMPDTPVEPEPKELQCEPKQDNQMGASSKTPT-SPQAAFT-QQVREVIHIYVHEEMYAFKFY-KRMT-ELLIKRAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFSETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHSYKKPYMDTSPSEEDPYYRSQRQACMYAS
Taeniopygia_guttata_tbx5           MADGEEGFGLPGTPADSEAKELQAEGKQDTQLGATSKSPT-SPQAAFT-QQGMEGIKVFLHERELWLKFH-EVGT-EMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYRPKMHLSP--------------CLHSL----------WKYLPITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHPYKKPYMETSPADEDPFYRSQRQACMYAS
Takifugu_rubripes_tbx5a            MADQEETFGLQNSPSGSDSRDLPNDNNKSEKQNGTSSKSP-SSQTTYI-QQGMEGIKVYLHERELWTKFY-EVGT-EMIITKAGRRMFPSFKVKVTGLNPKTKYILLMDVVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRIHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQSTKEYPVVPRSTVRQRVYHCIKRKHSYKKAYMDSSSSEEDHYYRPQRQACMYAS
Takifugu_rubripes_tbx5b            MANGGDQFGLSDPP-NSDCMDSPKETKQEKQ-SYALNSPA-SPHTTSTQQQGMEGIKVFLHDRDLWTKFD-EVGT-EMIITKAGRRMFPGYKVKVTGLNPKTKYILLMDIVPGDDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWSRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIGVTSYQNHKITQLKIENNPFAKGFRGSDDNELHRMAKLQS-KDFPVVPRTAGRQRAYHCPERKHPYKKLFPGSSPSESDSYYHPGRQACMFAG
Tetraodon_nigroviridis_tbx5a       MADQEETFGLQNSPSGSDSRDLQNDNNKSEKQNGTSSKSP-SSQTTYI-QQGMEGIKVYLHERELWTKFY-EVGT-EMIITKAGRRMFPSFKVKVTGLNPKTKYILLMDVVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRIHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQSTKEYPVVPRSTVRQRVYHCIKRKHSYKKAYMDSSSSEEDHYYRPQRQACMYAS
Tetraodon_nigroviridis_tbx5b       MANGGDQFGLSEPP-NSDCMDSPKEAKEEKQ-SYALDSPA-SPQTIFS-QQGMEGIKVFLHDRDLWTRFD-EVGT-EMIITKAGRRMFPGYKVKVVGLNPKTKYILLMDIVPGDDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWSRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETTFIAVTSYQNHKITQLKIENNPFAKGFRGSDDNELHRMAKLQS-KDFPVVPRSAVRQSAYRCPERKHPYKKLFPASSPSECDSYYHPQRQACMFAG
Xenopus_laevis_tbx5                MADTEEAYGMPDTPVEAEPKELQCEPKQDNQLGASSKTPT-SPPAAFT-QQGMEGIKVFLHERELWLKFH-EVGT-EMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFSETDFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHSYKKPYMDTSPSEEDPFYRSQRQACMYAS
;
END;