LOCUS       NM_001328159            1425 bp    mRNA    linear   VRT 30-SEP-2023
DEFINITION  Danio rerio homeobox C6b (hoxc6b), transcript variant 2, mRNA.
ACCESSION   NM_001328159
VERSION     NM_001328159.1
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 1425)
  AUTHORS   Mukaigasa K, Sakuma C and Yaginuma H.
  TITLE     The developmental hourglass model is applicable to the spinal cord
            based on single-cell transcriptomes and non-conserved
            cis-regulatory elements
  JOURNAL   Dev Growth Differ 63 (7), 372-391 (2021)
   PUBMED   34473348
REFERENCE   2  (bases 1 to 1425)
  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 1425)
  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   4  (bases 1 to 1425)
  AUTHORS   Barsh GR, Isabella AJ and Moens CB.
  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 1425)
  AUTHORS   Nakayama Y, Inomata C, Yuikawa T, Tsuda S and Yamasu K.
  TITLE     Comprehensive analysis of target genes in zebrafish embryos reveals
            gbx2 involvement in neurogenesis
  JOURNAL   Dev Biol 430 (1), 237-248 (2017)
   PUBMED   28756106
REFERENCE   6  (bases 1 to 1425)
  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 1425)
  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   8  (bases 1 to 1425)
  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 1425)
  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 1425)
  AUTHORS   Yekta S, Shih IH and Bartel DP.
  TITLE     MicroRNA-directed cleavage of HOXB8 mRNA
  JOURNAL   Science 304 (5670), 594-596 (2004)
   PUBMED   15105502
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            CABZ01085067.1.
            
            Transcript Variant: This variant (2) differs in the 5' UTR and
            coding sequence compared to variant 1. The resulting isoform (2)
            has a shorter and distinct N-terminus compared to isoform 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 :: CT634685.2 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505370, SAMEA4476752
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-169               CABZ01085067.1     26922-27090         c
            170-184             CABZ01085067.1     25242-25256         c
            185-522             CABZ01085067.1     22500-22837         c
            523-1425            CABZ01085067.1     21167-22069         c
FEATURES             Location/Qualifiers
     source          1..1425
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="11"
                     /map="11"
     gene            1..1425
                     /gene="hoxc6b"
                     /gene_synonym="hoxy6"
                     /note="homeobox C6b"
                     /db_xref="GeneID:58045"
                     /db_xref="ZFIN:ZDB-GENE-000822-1"
     exon            1..169
                     /gene="hoxc6b"
                     /gene_synonym="hoxy6"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    168..170
                     /gene="hoxc6b"
                     /gene_synonym="hoxy6"
                     /note="upstream in-frame stop codon"
     exon            170..184
                     /gene="hoxc6b"
                     /gene_synonym="hoxy6"
                     /inference="alignment:Splign:2.1.0"
     CDS             180..824
                     /gene="hoxc6b"
                     /gene_synonym="hoxy6"
                     /note="isoform 2 is encoded by transcript variant 2;
                     homeobox protein Hox-C6b; homeobox gene Y-6; homeo box
                     C6b"
                     /codon_start=1
                     /product="homeobox protein Hox-C6b isoform 2"
                     /protein_id="NP_001315088.1"
                     /db_xref="GeneID:58045"
                     /db_xref="ZFIN:ZDB-GENE-000822-1"
                     /translation="

MFGQEVLPSVAISSTNYDPVRHFSPYGAAVAQNRIYSNPFYSHQENVMFGSSRPYDYGSNMFYQDKDVLPSCRQGFGQTQGSLTQDYASDQGKTMEPKGSVQIYPWMQRMNSHSGVGYGSDRRRGRQIYSRYQTLELEKEFHYNRYLTRRRRIEIANTLCLSERQIKIWFQNRRMKWKKESNLTSILNDNGSVGAGQDTDKEETGETAEKDEHD"

     misc_feature    order(546..560,564..566,615..617,633..635,672..674,
                     678..683,690..695,699..707,711..716)
                     /gene="hoxc6b"
                     /gene_synonym="hoxy6"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(552..554,561..563,681..683,690..695,702..704)
                     /gene="hoxc6b"
                     /gene_synonym="hoxy6"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    555..713
                     /gene="hoxc6b"
                     /gene_synonym="hoxy6"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     exon            185..522
                     /gene="hoxc6b"
                     /gene_synonym="hoxy6"
                     /inference="alignment:Splign:2.1.0"
     exon            523..1425
                     /gene="hoxc6b"
                     /gene_synonym="hoxy6"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gtatgtacactaagacgagaacgttgtctttgctgtgaaggaaaaagaaatggatgttcgctttggattaccgcagctaattctgaagctcttgcaattacctcccaccctttcctcaggagctgaagatctctcaaaacgcgtcacaagagaaatgtgttaagatatgatttggaactatgttcggtcaagaagttctacccagcgttgccatcagctcgacaaactatgacccggtgcgacatttttcgccatatggcgccgccgttgcccaaaaccggatatactccaatccgttctattcacaccaagaaaacgttatgtttgggtcaagccgaccgtacgattacggatcaaatatgttctaccaggacaaagatgtgcttccaagttgcaggcaaggctttgggcaaacacagggttcattgacgcaggattacgcttcagaccaaggcaagactatggaaccgaaaggaagtgttcaaatatatccatggatgcagcggatgaactcgcatagtggagttggctatgggtctgacagacggcgaggtcgccaaatctattcgcgataccaaactttagaacttgagaaagaatttcattacaatcgctatttgacaagacgcagacgaattgagattgccaacacattgtgtctgtcggaacgccagattaaaatttggtttcagaaccgccggatgaaatggaagaaggagagcaatctcacgtccatcctcaatgacaatggctcggtaggagctggccaagacacggacaaagaagaaacaggggaaaccgccgaaaaagatgagcatgactgattgacttactaactaattaaaagacattccgtttgaaaacgttcttacataactaagctacctatggaatttacacaatttgcacaattaaaaccaaaaactgttacaattcctttagatgcaaagcgtgtgttgcttcgccacttatttcactatgattctgaaaagctgtttatccagagcaatttaattcataaatcagtgctctgactgaaaatgttttacctatcttgtgtgatttaatcttgtcattaaacatcttatttgttctgatgtactctgaagtgcaaataagggactgttgatgtagaccaaatatgaaaattccaaatattaaactacaatcatttcttctggtcctaggaagtgcattgtacatgtttgtaaatatgagattcaaatacttttgatgagcatttgtttagattgacgtactgttttgtgttttttctttactttgtgatgcgttctgggagaaccacatacgttgtaaaaagtatccttcattactctttttttccaaatgttgaattttagcaaaaaagcaagataataaaatgttcgaacatttacgcaataaagttgtaatcaatataacaat

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