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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
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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]