LOCUS       NM_131122               1500 bp    mRNA    linear   VRT 03-APR-2024
DEFINITION  Danio rerio homeobox C4a (hoxc4a), mRNA.
ACCESSION   NM_131122
VERSION     NM_131122.2
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 1500)
  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   2  (bases 1 to 1500)
  AUTHORS   Zhang,C. and Featherstone,M.
  TITLE     A zebrafish hox gene acts before gastrulation to specify the
            hemangioblast
  JOURNAL   Genesis 58 (6), e23363 (2020)
   PUBMED   32302038
REFERENCE   3  (bases 1 to 1500)
  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   4  (bases 1 to 1500)
  AUTHORS   Barsh,G.R., Isabella,A.J. and Moens,C.B.
  TITLE     Vagus Motor Neuron Topographic Map Determined by Parallel
            Mechanisms of hox5 Expression and Time of Axon Initiation
  JOURNAL   Curr Biol 27 (24), 3812-3825 (2017)
   PUBMED   29225029
REFERENCE   5  (bases 1 to 1500)
  AUTHORS   Yu,C., Yao,X., Zhao,L., Wang,P., Zhang,Q., Zhao,C., Yao,S. and
            Wei,Y.
  TITLE     Wolf-Hirschhorn Syndrome Candidate 1 (whsc1) Functions as a Tumor
            Suppressor by Governing Cell Differentiation
  JOURNAL   Neoplasia 19 (8), 606-616 (2017)
   PUBMED   28654864
REFERENCE   6  (bases 1 to 1500)
  AUTHORS   Moghadam,H.K., Ferguson,M.M. and Danzmann,R.G.
  TITLE     Evolution of Hox clusters in Salmonidae: a comparative analysis
            between Atlantic salmon (Salmo salar) and rainbow trout
            (Oncorhynchus mykiss)
  JOURNAL   J Mol Evol 61 (5), 636-649 (2005)
   PUBMED   16205980
REFERENCE   7  (bases 1 to 1500)
  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 1500)
  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 1500)
  AUTHORS   Amores,A., Suzuki,T., Yan,Y.L., Pomeroy,J., Singer,A., Amemiya,C.
            and Postlethwait,J.H.
  TITLE     Developmental roles of pufferfish Hox clusters and genome evolution
            in ray-fin fish
  JOURNAL   Genome Res 14 (1), 1-10 (2004)
   PUBMED   14707165
REFERENCE   10 (bases 1 to 1500)
  AUTHORS   Scemama,J.L., Hunter,M., McCallum,J., Prince,V. and Stellwag,E.
  TITLE     Evolutionary divergence of vertebrate Hoxb2 expression patterns and
            transcriptional regulatory loci
  JOURNAL   J Exp Zool 294 (3), 285-299 (2002)
   PUBMED   12362434
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC092923.1.
            
            On May 1, 2005 this sequence version replaced NM_131122.1.
            
            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 :: BC092923.1, BC164612.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505370, SAMEA3505371
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1500
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Singapore"
                     /db_xref="taxon:7955"
                     /chromosome="23"
                     /map="23"
     gene            1..1500
                     /gene="hoxc4a"
                     /gene_synonym="hoxc4; z-96; zgc:110513"
                     /note="homeobox C4a"
                     /db_xref="GeneID:30345"
                     /db_xref="ZFIN:ZDB-GENE-990415-112"
     exon            1..441
                     /gene="hoxc4a"
                     /gene_synonym="hoxc4; z-96; zgc:110513"
                     /inference="alignment:Splign:2.1.0"
     CDS             9..815
                     /gene="hoxc4a"
                     /gene_synonym="hoxc4; z-96; zgc:110513"
                     /note="hox-C4; homeobox gene C-4; homeo box C4a"
                     /codon_start=1
                     /product="homeobox protein Hox-C4a"
                     /protein_id="NP_571197.1"
                     /db_xref="GeneID:30345"
                     /db_xref="ZFIN:ZDB-GENE-990415-112"
                     /translation="

MIMSSYLMDSNYIDPKFPPCEEYSQNSYIPEHSPEYYSRARDSGYQHHHQELYPPRASYQERQYNCASIPEPDTQRGHGLPHAGHLLGKGQSASCEPPPLPLSPATPSAASSACNQATPEHPNSSASAKQPVVYPWMKKIHVSTVNSSYNGAEPKRSRTAYTRQQVLELEKEFHYNRYLTRRRRIEIAHSLVLSERQIKIWFQNRRMKWKKDHRLPNTKVRSSSSTGISSGSNTSSAAGVVAAASTTNTMSASEDLSGTERGEDITRL"

     misc_feature    216..395
                     /gene="hoxc4a"
                     /gene_synonym="hoxc4; z-96; zgc:110513"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9PWM3.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    405..422
                     /gene="hoxc4a"
                     /gene_synonym="hoxc4; z-96; zgc:110513"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9PWM3.1);
                     Region: Antp-type hexapeptide"
     misc_feature    471..641
                     /gene="hoxc4a"
                     /gene_synonym="hoxc4; z-96; zgc:110513"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    642..812
                     /gene="hoxc4a"
                     /gene_synonym="hoxc4; z-96; zgc:110513"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9PWM3.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            442..1470
                     /gene="hoxc4a"
                     /gene_synonym="hoxc4; z-96; zgc:110513"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

agaaattaatgatcatgagctcgtatttgatggactctaactacatcgatccgaaatttcctccttgcgaggaatattcgcaaaatagctacattcccgaacatagcccagaatattacagccgtgcaagggacagtggctaccagcatcaccaccaggagttataccctccgcgggcaagctaccaggagcgtcagtataactgtgcaagcatccctgagcctgatactcaaagaggacatggactgcctcacgcggggcacctgcttggaaaagggcaatcagcctcatgtgagcccccaccgttacccctgtctcctgccaccccttcggctgcatcttccgcctgcaatcaagccaccccggagcatcccaacagctcagcctctgccaaacaacccgtagtgtacccatggatgaagaaaattcacgtcagcaccgtcaactctagttacaatggagcggaacccaagcggtctagaactgcttacactcgccagcaagtcttagaattggagaaggaattccactataatcgctacttaacacggcgaagacgtatcgagattgctcattccttggtcctctcggagaggcaaatcaaaatttggtttcagaaccgaaggatgaagtggaaaaaagaccataggctgccaaacaccaaagtcagatcctcgtcctccacgggcatttcctccgggtccaacacaagctcagcggctggcgttgtggcggcagcttccaccactaacaccatgtcagcctccgaggacctctccggaaccgagcgtggcgaggatattacaaggttataagagaactatttcgaggagagaaagcaagatcaaatgactgattatttataaaatataatatattttgttttcgtaggtatcttgtgcgtaaagggggttcctttaagtccacagttatataaaatgcatgttatatagcatggattattgcgaatacctatggattattttttacgcgacacagggtttaatttatctaaaactgaatcaatatgatgtttgtttttgttatatgttttttcaagagaaatgttttgggcgaagcaggttatggacattttattcaaatgttattcgtgggcctttttgcccagctgccaaggtgaagtgcacaacgaatctatttatttctcacttgagagagctggtacgtttttcttttttgcactgtaaatgaaaaatgctatcgtgagtatcgatagaaaaaagatcttaaaggtttttttttttgttgttgttggttttatttaaaagtaaatcatgctgtgggttatctgtcgtatggaaaggttaagatttttaaattatcatttagtttttgttgtgatggcgttgtgtttaggctattaacagcagattgttgtgagatgcaataaaaccagtttagtgtatttgtgctaattatattggtcaataaaacgtaagtgtctattaggaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

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