LOCUS       NM_001005771            2320 bp    mRNA    linear   VRT 03-APR-2024
DEFINITION  Danio rerio homeobox C8a (hoxc8a), mRNA.
ACCESSION   NM_001005771
VERSION     NM_001005771.1
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 2320)
  AUTHORS   Xue,S., Ly,T.T.N., Vijayakar,R.S., Chen,J., Ng,J., Mathuru,A.S.,
            Magdinier,F. and Reversade,B.
  TITLE     HOX epimutations driven by maternal SMCHD1/LRIF1 haploinsufficiency
            trigger homeotic transformations in genetically wildtype offspring
  JOURNAL   Nat Commun 13 (1), 3583 (2022)
   PUBMED   35739109
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2320)
  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 2320)
  AUTHORS   Lu,J.K., Tsai,T.C., Lee,H., Hsia,K., Lin,C.H. and Lu,J.H.
  TITLE     Pectoral Fin Anomalies in tbx5a Knockdown Zebrafish Embryos Related
            to the Cascade Effect of N-Cadherin and Extracellular Matrix
            Formation
  JOURNAL   J Dev Biol 7 (3), 15 (2019)
   PUBMED   31336923
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2320)
  AUTHORS   Wang,J., Fei,F., Berberoglu,M.A., Sun,S., Wang,L., Dong,Z. and
            Wang,X.
  TITLE     Csy4-based vector system enables conditional chimeric gene editing
            in zebrafish without interrupting embryogenesis
  JOURNAL   J Mol Cell Biol 10 (6), 586-588 (2018)
   PUBMED   30063795
REFERENCE   5  (bases 1 to 2320)
  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   6  (bases 1 to 2320)
  AUTHORS   Thisse,B., Wright,C.V. and Thisse,C.
  TITLE     Activin- and Nodal-related factors control antero-posterior
            patterning of the zebrafish embryo
  JOURNAL   Nature 403 (6768), 425-428 (2000)
   PUBMED   10667793
REFERENCE   7  (bases 1 to 2320)
  AUTHORS   Amores,A., Force,A., Yan,Y.L., Joly,L., Amemiya,C., Fritz,A.,
            Ho,R.K., Langeland,J., Prince,V., Wang,Y.L., Westerfield,M.,
            Ekker,M. and Postlethwait,J.H.
  TITLE     Zebrafish hox clusters and vertebrate genome evolution
  JOURNAL   Science 282 (5394), 1711-1714 (1998)
   PUBMED   9831563
REFERENCE   8  (bases 1 to 2320)
  AUTHORS   Prince,V.E., Price,A.L. and Ho,R.K.
  TITLE     Hox gene expression reveals regionalization along the
            anteroposterior axis of the zebrafish notochord
  JOURNAL   Dev Genes Evol 208 (9), 517-522 (1998)
   PUBMED   9799433
REFERENCE   9  (bases 1 to 2320)
  AUTHORS   Prince,V.E., Joly,L., Ekker,M. and Ho,R.K.
  TITLE     Zebrafish hox genes: genomic organization and modified colinear
            expression patterns in the trunk
  JOURNAL   Development 125 (3), 407-420 (1998)
   PUBMED   9425136
REFERENCE   10 (bases 1 to 2320)
  AUTHORS   Misof,B.Y., Blanco,M.J. and Wagner,G.P.
  TITLE     PCR-survey of Hox-genes of the zebrafish: new sequence information
            and evolutionary implications
  JOURNAL   J Exp Zool 274 (3), 193-206 (1996)
   PUBMED   8882497
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC080255.1.
            
            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 :: BC080255.1, EE693846.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505370, SAMEA3505371
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..2320
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="23"
                     /map="23"
     gene            1..2320
                     /gene="hoxc8a"
                     /gene_synonym="cb341; hoxc8; z-179; zgc:91832"
                     /note="homeobox C8a"
                     /db_xref="GeneID:449648"
                     /db_xref="ZFIN:ZDB-GENE-990415-114"
     exon            1..689
                     /gene="hoxc8a"
                     /gene_synonym="cb341; hoxc8; z-179; zgc:91832"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    245..247
                     /gene="hoxc8a"
                     /gene_synonym="cb341; hoxc8; z-179; zgc:91832"
                     /note="upstream in-frame stop codon"
     CDS             254..1006
                     /gene="hoxc8a"
                     /gene_synonym="cb341; hoxc8; z-179; zgc:91832"
                     /note="homeobox gene C-8; homeo box C8a"
                     /codon_start=1
                     /product="homeobox protein Hox-C8a"
                     /protein_id="NP_001005771.1"
                     /db_xref="GeneID:449648"
                     /db_xref="ZFIN:ZDB-GENE-990415-114"
                     /translation="

MSSYFVNPLFSKYKGGETLEPTYYDCRFPQSVARSHTLVYGHGAAAPGFQHPSHHVQDFFHHGTTGISNPGYQQNPCALACHGDATKFYGYEALPRQPLYGTQQEATLAQYPDCKSSNSTNPGEGQGHLSQNSSPSLMFPWMRPHAPGRRNGRQTYSRYQTLELEKEFLFNPYLTRKRRIEVSHALSLTERQVKIWFQNRRMKWKKENNKDKFPGQRGEAEAEAEEEGNEDGEAEEGEDKETEEKEESKE"

     misc_feature    587..709
                     /gene="hoxc8a"
                     /gene_synonym="cb341; hoxc8; z-179; zgc:91832"
                     /note="propagated from UniProtKB/Swiss-Prot (Q68EH7.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    665..682
                     /gene="hoxc8a"
                     /gene_synonym="cb341; hoxc8; z-179; zgc:91832"
                     /note="propagated from UniProtKB/Swiss-Prot (Q68EH7.1);
                     Region: Antp-type hexapeptide. /evidence=ECO:0000255"
     misc_feature    701..871
                     /gene="hoxc8a"
                     /gene_synonym="cb341; hoxc8; z-179; zgc:91832"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    869..1003
                     /gene="hoxc8a"
                     /gene_synonym="cb341; hoxc8; z-179; zgc:91832"
                     /note="propagated from UniProtKB/Swiss-Prot (Q68EH7.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            690..2294
                     /gene="hoxc8a"
                     /gene_synonym="cb341; hoxc8; z-179; zgc:91832"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gtgcacgccatgatttgaggctgcaaaaggaaaggctggcgataggaagagagagagagagagactaagcgaaaggagctgaagtgggagctgcctcagattgtccgaaggggcagcatttctccatctagttccggttgctgtgtctgcgttgcatgccatttggaactgcaacaataggttgccaccattaggagaggagaatacatatattttttccaaacagactgactctttttaatgctagataaacatgagctcttattttgttaaccctcttttttccaagtacaaaggcggcgaaacattagagccaacttactacgactgcaggtttccacagagcgttgcccgaagccacacgcttgtgtacggacatggagcagctgcgccggggtttcaacacccgtcgcatcacgtacaggactttttccatcacggaaccacaggtatctccaaccctgggtatcaacagaacccctgtgcattggcatgtcacggagacgctacgaaattttatggatatgaagcccttccgaggcaaccgctttatggtacccagcaagaggccaccttagcgcaatacccagactgtaaatcgtccaatagcactaaccctggagaaggacaaggccacttaagtcaaaactcctctccgagcctcatgttcccttggatgcggcctcacgctcctgggagacgcaatggaaggcagacatacagccgataccagacattggagctggagaaagagttcctcttcaacccatacctcacacgcaagcgccgtattgaagtgtcccacgcgctaagcttaactgaacgacaggtgaagatctggtttcagaatcgccgaatgaagtggaaaaaagaaaataacaaagacaaatttccggggcagagaggagaggctgaagcagaggccgaagaagagggcaatgaagacggtgaagcggaggaaggagaagacaaggaaacggaagagaaagaggaaagcaaggagtgattttatggtcttttttatggttatatggcagatattgaagaggtctcacgaatgggaaatgaaagagaagacgcgccaattttattacaaacagttgggtcaaaaagtgagaaaatccccctccatacaaatgtacattgaaacctgcccaaagaaaaaaggcttcttttttaccaacacacgaagacttttaccattagcgaaatgtggatctgtgcattcgacaaattactcaaaagacagacctacaggaatacaataacccatcgttttatataggaaatgttagcagcatgaaaaacatattacggaatttgacattcatttcatacttgatgaatatgtctgggggttaaatggataagatgcaaccaactgaaataattgcatcagcttatcacctttaaaactattggtcttgtacataaaatcaagccacatcatgctgttacaacatacattacgaatcaaattgacagaaaaatatattatgtatttggtgtaacgttatttctacaatccgaatatggcaaaggtgtattagtgccatatacagagcaaagcgatggcaagtgtagaaaattcattctgtattacacacattatagattacttaactgttctttgttgttcttctatgtgagtgggcgaggatacagtttgtattttttcgatattttattggactcacaagagattgcaatcgtttgaaaatctcgtttgaagctacctaatcatgggaaatttgcaatatacatttctacctagagatttcatagactcttgtttttgtagtgtattaaacctaagttatgtaatttaccctttaaacacttatgattatcgagcattttgtcgtcttcggaagacacgaatagctcgaagccaatcttaactattttaaaagattgtatcacggcactacctaaaacaaagttttgctagaaagaatgaatttatttattctacgtgctgctttgttaaaaataattatacattttcccccaacaacttaaactgcctatagaaaatgcacatttatgtgtagttgaacaaacacgctgattactaccctaccttacttaaagaaagagagtcaatttatcgtgctggtgttatagcgtagattttgaattgcactgagtataatcttcatgtacgtcttgttatatcttgctgttatcaatatgctcgttttacttgtgttcctcgtgtgaatataaacaaattcgtgtgtccacgccattgttgttgaaatcaacaagaataaacaagatggctcattctaaaaaaaaaaaaaaaaaaaaaaaaaaa

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