LOCUS       NM_131531                909 bp    mRNA    linear   VRT 29-MAY-2023
DEFINITION  Danio rerio homeobox C1a (hoxc1a), mRNA.
ACCESSION   NM_131531
VERSION     NM_131531.1
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 909)
  AUTHORS   Franke M, De la Calle-Mustienes E, Neto A, Almuedo-Castillo M,
            Irastorza-Azcarate I, Acemel RD, Tena JJ, Santos-Pereira JM and
            Gomez-Skarmeta JL.
  TITLE     CTCF knockout in zebrafish induces alterations in regulatory
            landscapes and developmental gene expression
  JOURNAL   Nat Commun 12 (1), 5415 (2021)
   PUBMED   34518536
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 909)
  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 909)
  AUTHORS   Mitchell JM, Sucharov J, Pulvino AT, Brooks EP, Gillen AE and
            Nichols JT.
  TITLE     The alx3 gene shapes the zebrafish neurocranium by regulating
            frontonasal neural crest cell differentiation timing
  JOURNAL   Development 148 (7) (2021)
   PUBMED   33741714
REFERENCE   4  (bases 1 to 909)
  AUTHORS   Farnsworth DR, Saunders LM and Miller AC.
  TITLE     A single-cell transcriptome atlas for zebrafish development
  JOURNAL   Dev Biol 459 (2), 100-108 (2020)
   PUBMED   31782996
REFERENCE   5  (bases 1 to 909)
  AUTHORS   Malmstrom M, Britz R, Matschiner M, Torresen OK, Hadiaty RK, Yaakob
            N, Tan HH, Jakobsen KS, 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   6  (bases 1 to 909)
  AUTHORS   Mungpakdee S, Seo HC and Chourrout D.
  TITLE     Spatio-temporal expression patterns of anterior Hox genes in
            Atlantic salmon (Salmo salar)
  JOURNAL   Gene Expr Patterns 8 (7-8), 508-514 (2008)
   PUBMED   18620079
REFERENCE   7  (bases 1 to 909)
  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   8  (bases 1 to 909)
  AUTHORS   Corredor-Adamez M, Welten MC, Spaink HP, Jeffery JE, Schoon RT, de
            Bakker MA, Bagowski CP, Meijer AH, Verbeek FJ and Richardson MK.
  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   9  (bases 1 to 909)
  AUTHORS   Thummel R, Li L, Tanase C, Sarras MP Jr and Godwin AR.
  TITLE     Differences in expression pattern and function between zebrafish
            hoxc13 orthologs: recruitment of Hoxc13b into an early embryonic
            role
  JOURNAL   Dev Biol 274 (2), 318-333 (2004)
   PUBMED   15385162
REFERENCE   10 (bases 1 to 909)
  AUTHORS   Prohaska SJ and Stadler PF.
  TITLE     The duplication of the Hox gene clusters in teleost fishes
  JOURNAL   Theory Biosci 123 (1), 89-110 (2004)
   PUBMED   18202881
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AJ306432.1.
            
            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 :: AJ306432.1, BC162691.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505372, SAMEA3505373
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..909
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="23"
                     /map="23"
     gene            1..909
                     /gene="hoxc1a"
                     /gene_synonym="z-42"
                     /note="homeobox C1a"
                     /db_xref="GeneID:58046"
                     /db_xref="ZFIN:ZDB-GENE-000822-2"
     CDS             1..909
                     /gene="hoxc1a"
                     /gene_synonym="z-42"
                     /function="transcription factor"
                     /note="homeo box C1a"
                     /codon_start=1
                     /product="homeobox protein Hox-C1a"
                     /protein_id="NP_571606.1"
                     /db_xref="GeneID:58046"
                     /db_xref="ZFIN:ZDB-GENE-000822-2"
                     /translation="

MNSYHGFRDTTSLFIKGYHATGVMRLHQDHGSTADFPSREDVNNEADFLQYHFTNLCATATGACSKPCEDPGRANSTRPPFPQNQDFYRPVHPNRPQVPSFQSCREQGLSRKGFSPSSDTFRTFSSAHCELGPVNNTQTEVRTYDGPVRHSAVEDDNTGHGALNTLNETLHSGKTFEWMRVRRNQSRAAKIQLGKCSDRELKTNHGRDSDEDTSSGGSRTNFTTKQLTELEKEFHFNKYLTRARRIEIANPLQLSETQVKIWFQNRRMKQKKMLREGLAQGLMLISGCDEDSKKSDTCSSPD"

     misc_feature    592..672
                     /gene="hoxc1a"
                     /gene_synonym="z-42"
                     /note="propagated from UniProtKB/Swiss-Prot (Q98SH9.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    652..816
                     /gene="hoxc1a"
                     /gene_synonym="z-42"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:395001"
     misc_feature    order(655..660,664..666,715..717,733..735,772..774,
                     778..783,790..795,799..807,811..816)
                     /gene="hoxc1a"
                     /gene_synonym="z-42"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(661..663,781..783,790..795,802..804)
                     /gene="hoxc1a"
                     /gene_synonym="z-42"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            1..565
                     /gene="hoxc1a"
                     /gene_synonym="z-42"
                     /inference="alignment:Splign:2.1.0"
     exon            566..909
                     /gene="hoxc1a"
                     /gene_synonym="z-42"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

atgaattcttatcatgggttcagggacacaacgtcacttttcatcaagggctatcatgctactggagtaatgcgtctgcatcaggaccacggatcaactgctgacttcccaagcagggaggatgtcaacaacgaggcggattttcttcaatatcatttcacgaatctctgtgccacggccacaggcgcgtgctcaaagccctgtgaagaccctggccgtgctaactctaccagaccccccttcccccaaaatcaagatttctatagaccagtgcaccccaatcgaccccaagtcccctccttccaaagctgtcgtgagcagggtctctccagaaagggcttctcgccttcatcagacactttcagaactttctccagcgcgcactgtgaactcggccctgtcaacaacacacagaccgaagtgcgcacatacgacggcccagtgcgtcactccgcagtggaggatgataatactggacacggggctctaaacacgttaaacgagactttacacagtggaaagacattcgaatggatgagagtgaggagaaatcagtcccgtgcagctaagatacaactgggaaaatgctcggaccgggagctgaagacgaaccacggacgagattctgacgaggacacttcgagtggaggctcgcgaactaattttacaacgaaacaactcacagaacttgaaaaggagtttcatttcaacaaatatctgactcgagccagacggatagagatcgcaaaccctctccagctgagcgaaacacaagtgaagatctggtttcagaacagacgcatgaaacagaagaaaatgctgcgggaaggcctagctcaaggattaatgctgatttctggatgtgatgaggactcgaaaaaaagtgacacttgttcatctcctgattaa

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