LOCUS       NM_131546               1582 bp    mRNA    linear   VRT 15-MAY-2023
DEFINITION  Danio rerio homeobox C13b (hoxc13b), mRNA.
ACCESSION   NM_131546
VERSION     NM_131546.2
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 1582)
  AUTHORS   Banu S, Gaur N, Nair S, Ravikrishnan T, Khan S, Mani S, Bharathi S,
            Mandal K, Kuram NA, Vuppaladadium S, Ravi R, Murthy CLN, Quoseena
            M, Babu NS and Idris MM.
  TITLE     Understanding the complexity of epimorphic regeneration in
            zebrafish caudal fin tissue: A transcriptomic and proteomic
            approach
  JOURNAL   Genomics 114 (2), 110300 (2022)
   PUBMED   35134499
REFERENCE   2  (bases 1 to 1582)
  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 1582)
  AUTHORS   Ye Z and Kimelman D.
  TITLE     Hox13 genes are required for mesoderm formation and axis elongation
            during early zebrafish development
  JOURNAL   Development 147 (22) (2020)
   PUBMED   33154036
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1582)
  AUTHORS   Soh GH, Pomreinke AP and Muller P.
  TITLE     Integration of Nodal and BMP Signaling by Mutual Signaling Effector
            Antagonism
  JOURNAL   Cell Rep 31 (1), 107487 (2020)
   PUBMED   32268105
REFERENCE   5  (bases 1 to 1582)
  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 1582)
  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 1582)
  AUTHORS   Phillips RB, Amores A, Morasch MR, Wilson C and Postlethwait JH.
  TITLE     Assignment of zebrafish genetic linkage groups to chromosomes
  JOURNAL   Cytogenet Genome Res 114 (2), 155-162 (2006)
   PUBMED   16825768
REFERENCE   8  (bases 1 to 1582)
  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 1582)
  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   10 (bases 1 to 1582)
  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
  REMARK    GeneRIF: maternally expressed and is detectable in every cell of
            early cleavage embryos through gastrulae
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC139597.1.
            
            On Apr 22, 2007 this sequence version replaced NM_131546.1.
            
            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 :: BC139597.1, AY452738.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505373, SAMEA3505374
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1582
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="11"
                     /map="11"
     gene            1..1582
                     /gene="hoxc13b"
                     /gene_synonym="hoxf13"
                     /note="homeobox C13b"
                     /db_xref="GeneID:58063"
                     /db_xref="ZFIN:ZDB-GENE-000822-5"
     exon            1..690
                     /gene="hoxc13b"
                     /gene_synonym="hoxf13"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    78..80
                     /gene="hoxc13b"
                     /gene_synonym="hoxf13"
                     /note="upstream in-frame stop codon"
     CDS             132..953
                     /gene="hoxc13b"
                     /gene_synonym="hoxf13"
                     /note="homeobox gene F-13; homeo box C13b"
                     /codon_start=1
                     /product="homeobox protein Hox-C13b"
                     /protein_id="NP_571621.2"
                     /db_xref="GeneID:58063"
                     /db_xref="ZFIN:ZDB-GENE-000822-5"
                     /translation="

MEGLSGNCPASHCRDFISHPALGRHSGSLASHQGTVYPDITTQDAGRQFPAPQASSGTSLGYGYAFGSPYYGCRLSYSHNVNLQQKSYHPAEKYMETSGALPAEELSSRSKEFAIYPSFASSYQTVPGYLDVPVVPGISAHPESRHEALFPMDSYQHWALSNGWDEQLYCSKEQTHFNHLWKSQFSDVVPHQAEMNGYRRGRKKRVPYTKIQLKELEKEYAASKFITKDRRRRISATTSLSERQVTIWFQNRRVKEKKFVCKSSKLSTNMHSV"

     misc_feature    132..458
                     /gene="hoxc13b"
                     /gene_synonym="hoxf13"
                     /note="Hox protein A13 N terminal; Region: HoxA13_N;
                     pfam12284"
                     /db_xref="CDD:432453"
     misc_feature    order(735..749,753..755,804..806,822..824,861..863,
                     867..872,879..884,888..896,900..905)
                     /gene="hoxc13b"
                     /gene_synonym="hoxf13"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    741..902
                     /gene="hoxc13b"
                     /gene_synonym="hoxf13"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(741..743,750..752,870..872,879..884,891..893)
                     /gene="hoxc13b"
                     /gene_synonym="hoxf13"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            691..1552
                     /gene="hoxc13b"
                     /gene_synonym="hoxf13"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gtagtcgagttttaaaaagcatcgacaacccatgaccatgatttcgccgatcctgcatggacgctgggcggacacactgatttacgtgtaatgagaaaaaaacctcgaatgaaagttattctcataaaaccatggagggactgagcgggaattgccctgcctctcattgcagggattttatctcgcaccctgcgctgggacgccactctgggagcctcgcgagtcaccagggcacagtgtacccggatatcacgacacaagatgccggccggcaattccctgcgccccaggcctcgtcggggacttcactgggctatggatacgcattcgggagtccatattatgggtgtcgtctttcctactctcacaacgtaaacttgcaacagaagtcataccatcctgccgaaaaatacatggaaacaagcggtgcgctgccagctgaagagctttccagccggtcaaaagaatttgctatttacccaagcttcgccagctcttatcaaactgtccctggctatttggacgtcccagttgtgccaggaatcagtgcgcacccagaatccaggcatgaagcgttgtttcctatggacagttatcagcactgggcactgtcgaacggctgggatgagcaattgtattgttctaaggaacaaacacattttaaccacctatggaaatcccaattttcggatgtggtgccacaccaagccgagatgaacggctaccgtcgcggtcgtaagaagagggtaccttacactaaaatccaattaaaggaactggaaaaggagtatgcagccagcaagttcatcaccaaagacagaagaaggcgcatctccgccacaacgagtctctccgagcgccaggtgaccatctggttccagaaccgacgtgttaaggaaaagaagttcgtttgtaaatcctcaaagttaagcactaacatgcattcagtttgattattttcggtgttctttggctcgacaaattcatcaaggaatttctttttatttaagtgggcttaataaggcctaaatatgacggcggatccgacacagacctatgcatcgatgaggtcctgcatttacagatgtagtagacctaagctgcagtaagaaatgagtttccagaagacattcacacatgaatcgctttataacatttctgttttttaactccatgttgttacaactttcaacctttctgttggtactgttgttgttgtttaatgaaaaagaaatggaaattgtttgttaagactacgatggaggcatagttttaactccattttaacttttaaaaaagttttcaattcaaatatagtaatatgtatgtcaaaatgttcggttatcaaaacgtaatgtcatccatgaattggttaatattcatctgtcaatgtacttttccctcgtggtgtgttttctcaattttatagcaatggtgtcgtgtttaaaaacgatttaaagtgtttaggagctgaaataaagcttagcgttaggtttgaacacaagaaaatcacacacttatttcccccaatattaaactgtttgtgttatgtcaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

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