LOCUS       NM_001126445            1247 bp    mRNA    linear   VRT 03-APR-2024
DEFINITION  Danio rerio homeobox D4a (hoxd4a), mRNA.
ACCESSION   NM_001126445 NM_130757
VERSION     NM_001126445.2
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 1247)
  AUTHORS   Zhang,W., Scerbo,P., Delagrange,M., Candat,V., Mayr,V., Vriz,S.,
            Distel,M., Ducos,B. and Bensimon,D.
  TITLE     Fgf8 dynamics and critical slowing down may account for the
            temperature independence of somitogenesis
  JOURNAL   Commun Biol 5 (1), 113 (2022)
   PUBMED   35132142
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1247)
  AUTHORS   Franke,M., De la Calle-Mustienes,E., Neto,A., Almuedo-Castillo,M.,
            Irastorza-Azcarate,I., Acemel,R.D., Tena,J.J., Santos-Pereira,J.M.
            and Gomez-Skarmeta,J.L.
  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   3  (bases 1 to 1247)
  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   4  (bases 1 to 1247)
  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   5  (bases 1 to 1247)
  AUTHORS   Matharu,N.K., Yadav,S., Kumar,M. and Mishra,R.K.
  TITLE     Role of vertebrate GAGA associated factor (vGAF) in early
            development of zebrafish
  JOURNAL   Cells Dev 166, 203682 (2021)
   PUBMED   33994355
REFERENCE   6  (bases 1 to 1247)
  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   7  (bases 1 to 1247)
  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   8  (bases 1 to 1247)
  AUTHORS   Nolte,C., Amores,A., Nagy Kovacs,E., Postlethwait,J. and
            Featherstone,M.
  TITLE     The role of a retinoic acid response element in establishing the
            anterior neural expression border of Hoxd4 transgenes
  JOURNAL   Mech Dev 120 (3), 325-335 (2003)
   PUBMED   12591602
  REMARK    GeneRIF: The sequence of regulatory elements, including a DR5 type
            retinoic acid response element (RARE) required for Hoxd4 neural
            enhancer activity, are highly conserved, zebrafish and mouse neural
            enhancers function identically in transgenic mouse embryos.
REFERENCE   9  (bases 1 to 1247)
  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
REFERENCE   10 (bases 1 to 1247)
  AUTHORS   Wang,J.M., Prefontaine,G.G., Lemieux,M.E., Pope,L., Akimenko,M.A.
            and Hache,R.J.
  TITLE     Developmental effects of ectopic expression of the glucocorticoid
            receptor DNA binding domain are alleviated by an amino acid
            substitution that interferes with homeodomain binding
  JOURNAL   Mol Cell Biol 19 (10), 7106-7122 (1999)
   PUBMED   10490647
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC162966.1.
            
            On or before May 16, 2009 this sequence version replaced
            NM_130757.1, NM_001126445.1.
            
            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 :: BC162966.1, Y14548.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA4476732, SAMEA4476745
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1247
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="9"
                     /map="9"
     gene            1..1247
                     /gene="hoxd4a"
                     /gene_synonym="etID309823.9; etID37000.9; fb36c05; hoxd4;
                     wu:fb36c05"
                     /note="homeobox D4a"
                     /db_xref="GeneID:30329"
                     /db_xref="ZFIN:ZDB-GENE-980526-214"
     exon            1..697
                     /gene="hoxd4a"
                     /gene_synonym="etID309823.9; etID37000.9; fb36c05; hoxd4;
                     wu:fb36c05"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    217..219
                     /gene="hoxd4a"
                     /gene_synonym="etID309823.9; etID37000.9; fb36c05; hoxd4;
                     wu:fb36c05"
                     /note="upstream in-frame stop codon"
     CDS             229..999
                     /gene="hoxd4a"
                     /gene_synonym="etID309823.9; etID37000.9; fb36c05; hoxd4;
                     wu:fb36c05"
                     /note="hox-D4; homeobox gene D-4; homeo box D4a"
                     /codon_start=1
                     /product="homeobox protein Hox-D4a"
                     /protein_id="NP_001119917.1"
                     /db_xref="GeneID:30329"
                     /db_xref="ZFIN:ZDB-GENE-980526-214"
                     /translation="

MEGGKKDNSRKISISYLQKLMAMSSYMVNSKYVDPKFPPCEEYSQNSYIPEQSPGYYSPSQDTDFQHPGIYSRSNYSEQPYSCSTVQGSSVQPRGHVQDQASTPSPFPAQTEQCPAVQISGSRTGGQQQNTKTQNGIPTKQPAVVYPWMKKVHVTTVNPDYTGPEPKRSRTAYTRQQVLELEKEFHFNRYLTRRRRIEIAHTLCLSERQIKIWFQNRRMKWKKDHKLPNTKGRSASVGNQHAQHAQKDSQTEITTL"

     misc_feature    727..897
                     /gene="hoxd4a"
                     /gene_synonym="etID309823.9; etID37000.9; fb36c05; hoxd4;
                     wu:fb36c05"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     exon            698..1247
                     /gene="hoxd4a"
                     /gene_synonym="etID309823.9; etID37000.9; fb36c05; hoxd4;
                     wu:fb36c05"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

cccagcactgctttcctccttgtctctttcttttatatgggtatttaatcaataaaattttatattgtgttatttccatcctaattgagagataatgtgaagtttgtaaaaatcactactaggtgtgcacagcttcttctcggttgatgaagtccctccacctcgattggccaagctggtcacatggtaggctaactttattcagttgacagcaagtaggagggctttatggagggaggaaaaaaagacaactcgagaaaaattagtatttcctaccttcagaaattaatggccatgagttcgtacatggtgaactccaagtatgtggatcccaaatttcctccttgcgaggaatattctcagaacagctatatacctgaacagagcccaggctactacagtccgtcgcaggacactgatttccagcatcccggaatctattcacggtcaaactactctgaacagccttacagttgtagcactgtccagggctcgtcggtgcagccgcggggtcatgtgcaggatcaagccagcacccctagccctttccctgcacagacagagcagtgtcccgcggtccagatttccggatcgaggactggtggacaacaacaaaacacaaagacccagaacgggataccaacgaagcagcctgctgtagtttacccgtggatgaagaaagtgcacgttactacggtgaacccggattacacaggacctgaacccaaacgttctcggacagcctacacaagacagcaggttctcgaactagagaaggagtttcattttaacaggtatctaacaagacggcgtcgcatcgagatcgcgcacacactctgtctttctgaaagacagattaaaatctggtttcagaacaggagaatgaaatggaaaaaggatcacaaactaccaaacacgaaaggaagatcggcatcagttggaaatcagcatgcacaacacgctcagaaggacagccagacagagatcacaactttataagtggatatctctccctcccttcagatgtacagatgaactgtatgtaatagacaatgcttaatttgacattgcatggtagaaaatcatgacatgttgggtctaagtgccaaaaactgagaagctgaagcacacaccatgacttaatgcagcgtaaaagctgctttgcgttacaattcccaatatttcaaatattgtaaccctttgtatgagaggcaaagaggatatgaggcatcgaatgatggttcaca

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