2025-02-20 23:20:39, GGRNA.v2 : RefSeq release 228 (Jan, 2025)
LOCUS NM_001134685 1943 bp mRNA linear VRT 07-DEC-2024 DEFINITION Danio rerio homeobox C3a (hoxc3a), mRNA. ACCESSION NM_001134685 NM_131182 XM_001923793 XM_001923794 VERSION NM_001134685.2 KEYWORDS RefSeq. SOURCE Danio rerio (zebrafish) ORGANISM Danio rerio Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio. REFERENCE 1 (bases 1 to 1943) AUTHORS Sundaramoorthi,H., Fallatah,W., Mary,J. and Jagadeeswaran,P. TITLE Discovery of seven hox genes in zebrafish thrombopoiesis JOURNAL Blood Cells Mol Dis 104, 102796 (2024) PUBMED 37717409 REFERENCE 2 (bases 1 to 1943) AUTHORS Yamada,K., Maeno,A., Araki,S., Kikuchi,M., Suzuki,M., Ishizaka,M., Satoh,K., Akama,K., Kawabe,Y., Suzuki,K., Kobayashi,D., Hamano,N. and Kawamura,A. TITLE An atlas of seven zebrafish hox cluster mutants provides insights into sub/neofunctionalization of vertebrate Hox clusters JOURNAL Development 148 (11) (2021) PUBMED 34096572 REFERENCE 3 (bases 1 to 1943) AUTHORS Pillay,S., Takahashi,H., Carninci,P. and Kanhere,A. TITLE Antisense RNAs during early vertebrate development are divided in groups with distinct features JOURNAL Genome Res 31 (6), 995-1010 (2021) PUBMED 33795334 REFERENCE 4 (bases 1 to 1943) AUTHORS Malmstrom,M., Britz,R., Matschiner,M., Torresen,O.K., Hadiaty,R.K., Yaakob,N., Tan,H.H., Jakobsen,K.S., Salzburger,W. and Ruber,L. TITLE The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes JOURNAL Genome Biol Evol 10 (4), 1088-1103 (2018) PUBMED 29684203 REFERENCE 5 (bases 1 to 1943) AUTHORS Lin,Q., Fan,S., Zhang,Y., Xu,M., Zhang,H., Yang,Y., Lee,A.P., Woltering,J.M., Ravi,V., Gunter,H.M., Luo,W., Gao,Z., Lim,Z.W., Qin,G., Schneider,R.F., Wang,X., Xiong,P., Li,G., Wang,K., Min,J., Zhang,C., Qiu,Y., Bai,J., He,W., Bian,C., Zhang,X., Shan,D., Qu,H., Sun,Y., Gao,Q., Huang,L., Shi,Q., Meyer,A. and Venkatesh,B. TITLE The seahorse genome and the evolution of its specialized morphology JOURNAL Nature 540 (7633), 395-399 (2016) PUBMED 27974754 REFERENCE 6 (bases 1 to 1943) AUTHORS Kurosawa,G., Takamatsu,N., Takahashi,M., Sumitomo,M., Sanaka,E., Yamada,K., Nishii,K., Matsuda,M., Asakawa,S., Ishiguro,H., Miura,K., Kurosawa,Y., Shimizu,N., Kohara,Y. and Hori,H. TITLE Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes JOURNAL Gene 370, 75-82 (2006) PUBMED 16472944 REMARK Erratum:[Gene. 2006 Jul;376(2):298-9] REFERENCE 7 (bases 1 to 1943) AUTHORS Corredor-Adamez,M., Welten,M.C., Spaink,H.P., Jeffery,J.E., Schoon,R.T., de Bakker,M.A., Bagowski,C.P., Meijer,A.H., Verbeek,F.J. and Richardson,M.K. TITLE Genomic annotation and transcriptome analysis of the zebrafish (Danio rerio) hox complex with description of a novel member, hox b 13a JOURNAL Evol Dev 7 (5), 362-375 (2005) PUBMED 16174031 REFERENCE 8 (bases 1 to 1943) AUTHORS Santini,S. and Bernardi,G. TITLE Organization and base composition of tilapia Hox genes: implications for the evolution of Hox clusters in fish JOURNAL Gene 346, 51-61 (2005) PUBMED 15716008 REFERENCE 9 (bases 1 to 1943) AUTHORS Prohaska,S.J. and Stadler,P.F. TITLE The duplication of the Hox gene clusters in teleost fishes JOURNAL Theory Biosci 123 (1), 89-110 (2004) PUBMED 18202881 REFERENCE 10 (bases 1 to 1943) AUTHORS Fritz,A., Rozowski,M., Walker,C. and Westerfield,M. TITLE Identification of selected gamma-ray induced deficiencies in zebrafish using multiplex polymerase chain reaction JOURNAL Genetics 144 (4), 1735-1745 (1996) PUBMED 8978059 COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence was derived from BX005254.9. On or before May 14, 2009 this sequence version replaced NM_131182.4, NM_001134685.1. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC154496.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA3505371, SAMEA3505372 [ECO:0000348] ##Evidence-Data-END## PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-111 BX005254.9 126785-126895 c 112-163 BX005254.9 86918-86969 c 164-333 BX005254.9 68999-69168 c 334-601 BX005254.9 68541-68808 c 602-1943 BX005254.9 65150-66491 c FEATURES Location/Qualifiers source 1..1943 /organism="Danio rerio" /mol_type="mRNA" /strain="Tuebingen" /db_xref="taxon:7955" /chromosome="23" /map="23" gene 1..1943 /gene="hoxc3a" /gene_synonym="HOX-114; zgc:110503" /note="homeobox C3a" /db_xref="GeneID:30421" /db_xref="ZFIN:ZDB-GENE-980526-532" exon 1..111 /gene="hoxc3a" /gene_synonym="HOX-114; zgc:110503" /inference="alignment:Splign:2.1.0" exon 112..163 /gene="hoxc3a" /gene_synonym="HOX-114; zgc:110503" /inference="alignment:Splign:2.1.0" misc_feature 133..135 /gene="hoxc3a" /gene_synonym="HOX-114; zgc:110503" /note="upstream in-frame stop codon" exon 164..333 /gene="hoxc3a" /gene_synonym="HOX-114; zgc:110503" /inference="alignment:Splign:2.1.0" CDS 178..969 /gene="hoxc3a" /gene_synonym="HOX-114; zgc:110503" /note="homeobox protein Zf-114; hox[zf-114]; homeobox gene C-3a; homeo box C3a" /codon_start=1 /product="homeobox protein Hox-C3a" /protein_id="NP_001128157.2" /db_xref="GeneID:30421" /db_xref="ZFIN:ZDB-GENE-980526-532" /translation="
MAKQSKNADENGITVWLLTCSLQLKHRVRKAIGGGHHVTTLFTLVGKQLKTRENSSTWKRHAEESSSENDKGNVWNFQNLSNVQHPYSFSDDGNHSLDPANALEREKACELSTSCLSTMKYPWMRETHAPTHFSSINAMESGDSKYSNGEAVVRNSSSKRARVAFTSSQLLELEKEFHFSAYLCRNRRLEMAELLKLTDRQIKIWFQNRRMKYKKDHKEKSTAKSSYTYLGTENQPLIISRSTTDSPVPLKFQNNYETPSMNW"
misc_feature 544..915 /gene="hoxc3a" /gene_synonym="HOX-114; zgc:110503" /note="Homeodomain-containing transcription factor [Transcription]; Region: COG5576" /db_xref="CDD:227863" misc_feature 652..822 /gene="hoxc3a" /gene_synonym="HOX-114; zgc:110503" /note="Region: Homeodomain; pfam00046" /db_xref="CDD:459649" exon 334..601 /gene="hoxc3a" /gene_synonym="HOX-114; zgc:110503" /inference="alignment:Splign:2.1.0" exon 602..1943 /gene="hoxc3a" /gene_synonym="HOX-114; zgc:110503" /inference="alignment:Splign:2.1.0" ORIGIN
cgctacgatatgatggactgaacacggaagaattaaagagctacagccgcggcgaatgaatgagagaatcctatgagcgacgttaatcagaccatgtgcagaacgctcaagctcatgaggaaattgtgaacgtgagtgaaaggacaacctcatcgttgcactggaaaatcactcgaaatggcaaaacagtcgaagaatgcggatgaaaacggaatcaccgtttggctgcttacatgcagtttacaactcaaacaccgagtgcgcaaggctattggaggaggccaccacgtgactacattgtttactcttgttggcaaacaattaaagacgcgagagaacagttctacgtggaaacgacatgctgaagaaagttcatcagaaaatgataaaggcaacgtgtggaactttcaaaacctctcgaatgtccaacatccctattcattctctgatgatggcaaccactctttggaccctgcgaatgcattggaaagagaaaaggcatgtgagctgtcaacttcctgcttatcaaccatgaagtacccttggatgagagagacacatgcacccacgcacttcagctccattaacgccatggaatcaggtgattctaaatacagcaatggtgaagcagttgtacggaatagcagcagtaaacgggctcgtgtggcgttcacctcctctcagctgctggagttagagaaggagtttcacttcagcgcttacctgtgccgcaaccggagacttgaaatggctgagctgctgaagctcaccgaccggcagattaaaatctggttccaaaaccgtcgcatgaagtataagaaggaccacaaggaaaagtcaacggcaaagtcctcttacacctacctgggaacagaaaaccagccattaataattagcagaagcacaacagattctccagtgccattgaaattccagaataactatgaaacaccatcaatgaactggtgaaattacagaaaaactgaaaactggtgacttttgcttttagaacttatataatgatagtaatctgcatcaaccataaagactgaaaatgaatgaatgaatgaatgaatgaatgtgtgaatgaatgaaatttctacaaaacatgtacatgatctgtcactgttcagctatttctccatttgtaactctctctgacatgatttatatttaaaaacattgatgattaattgcctctggatgatgatttatgtgcaaagttaacttggaagagttcaataggcaagctcgctctgaaccagattacatgatatcagctagtacatttcagagttagtctctattgtgcataaactgctgtagtaatatctttgcaaagcaccaagatttattgcaaccctacttgtgcaagtttatctcttgggcacagaaaatacaattttaaaagggcattcaagactttgaatggtcattaacatcctctcaactttttaagtgcacaacatattttttattactctcaaaatgatatgctacttttcccaaggcatgagctaaaatgtacaacttgcagcgttgttcattatgatggtcacaattgttccatgttaaagcctattgacctgctctactattaacaatgaatttgaatgactttttttctgctttacactgaaagtaggtgcgtttaagtctgaatttacagcatatctactgacaaaatgaatgaaagagcaaagcaggattttcacaatgctatatcaatgcatttatagtgtaattactttacccattcatgtacacaaaagtgtcaacatggcagctgcaatgtaaaatatgtgcatatttgtaatttataccatttcaattataacctgtccatatttgacaaaaaaacatgcattttgaaaataataagtggttgttttttaaactgatttattccctctggatagtcaataaataatcattgtaattca
//
by
@meso_cacase at
DBCLS
This page is licensed under a
Creative Commons Attribution 4.0 International License (CC BY 4.0).
If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596.
[Full Text]