LOCUS       NM_001012293            1296 bp    mRNA    linear   VRT 24-SEP-2023
DEFINITION  Gallus gallus homeobox D4 (HOXD4), mRNA.
ACCESSION   NM_001012293 XM_421990
VERSION     NM_001012293.3
KEYWORDS    RefSeq.
SOURCE      Gallus gallus (chicken)
  ORGANISM  Gallus gallus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
            Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes;
            Phasianidae; Phasianinae; Gallus.
REFERENCE   1  (bases 1 to 1296)
  AUTHORS   Tang H, Finn RD and Thomas PD.
  TITLE     TreeGrafter: phylogenetic tree-based annotation of proteins with
            Gene Ontology terms and other annotations
  JOURNAL   Bioinformatics 35 (3), 518-520 (2019)
   PUBMED   30032202
REFERENCE   2  (bases 1 to 1296)
  AUTHORS   Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C,
            Mitchell A, Sangrador-Vegas A, Yong SY, Mulder N and Hunter S.
  TITLE     Manual GO annotation of predictive protein signatures: the InterPro
            approach to GO curation
  JOURNAL   Database (Oxford) 2012, bar068 (2012)
   PUBMED   22301074
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1296)
  AUTHORS   Sasaki H, Yokoyama E and Kuroiwa A.
  TITLE     Specific DNA binding of the two chicken Deformed family homeodomain
            proteins, Chox-1.4 and Chox-a
  JOURNAL   Nucleic Acids Res 18 (7), 1739-1747 (1990)
   PUBMED   1970866
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000236.1.
            
            On Dec 14, 2021 this sequence version replaced NM_001012293.2.
            
            Sequence Note: This RefSeq record was created from genomic sequence
            data because no single transcript from the same breed was available
            for the full length of the gene. The extent of this transcript is
            supported by transcript alignments and orthologous data.
            
            ##Evidence-Data-START##
            Transcript exon combination :: HAEL01003354.1, SRR13267657.13720.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN06140854 [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-706               JAENSK010000236.1  8537213-8537918     c
            707-1296            JAENSK010000236.1  8536325-8536914     c
FEATURES             Location/Qualifiers
     source          1..1296
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="7"
                     /map="7"
     gene            1..1296
                     /gene="HOXD4"
                     /gene_synonym="Chox-a"
                     /note="homeobox D4"
                     /db_xref="CGNC:52136"
                     /db_xref="GeneID:424139"
     exon            1..706
                     /gene="HOXD4"
                     /gene_synonym="Chox-a"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    217..219
                     /gene="HOXD4"
                     /gene_synonym="Chox-a"
                     /note="upstream in-frame stop codon"
     CDS             298..1011
                     /gene="HOXD4"
                     /gene_synonym="Chox-a"
                     /note="homeobox protein Hox-A"
                     /codon_start=1
                     /product="homeobox protein Hox-D4"
                     /protein_id="NP_001012293.1"
                     /db_xref="CGNC:52136"
                     /db_xref="GeneID:424139"
                     /translation="

MAMSSYMVNSKYVDPKFPPCEEYLQSSYLGEQGAEYYGASQGSDFQHQGLYPRSNYSEQPFGCAGAQGSAVQPRGHGQEQSAPPSHFPGQAEHCPPPPMSNSRACGQQPALKAPHGSAVKQPAVVYPWMKKVHVNSVNPNYSGGEPKRSRTAYTRQQVLELEKEFHFNRYLTRRRRIEIAHTLCLSERQIKIWFQNRRMKWKKDHKLPNTKGRSSSSASNPHLQTVPKDHQTDLTTL"

     misc_feature    535..>798
                     /gene="HOXD4"
                     /gene_synonym="Chox-a"
                     /note="superantigen-like protein SSL4; Reviewed; Region:
                     PRK13042"
                     /db_xref="CDD:183854"
     misc_feature    order(736..750,754..756,805..807,823..825,862..864,
                     868..873,880..885,889..897,901..906)
                     /gene="HOXD4"
                     /gene_synonym="Chox-a"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    742..903
                     /gene="HOXD4"
                     /gene_synonym="Chox-a"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(742..744,751..753,871..873,880..885,892..894)
                     /gene="HOXD4"
                     /gene_synonym="Chox-a"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            707..1296
                     /gene="HOXD4"
                     /gene_synonym="Chox-a"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gcacctgggggcagggaggcggccgcacgcggggaatggccccaaaactccgggatcggccccggagggcgaagcccgccgcggaggggtcgctcagctccgcgtatattatttagttaaattcgtggaaattctgaggcgcacacaaatccggtgatcggctccccgcctccccattggccgggccggtcacatgcacgcctaactttattcagttgacagcaagtaggagggctctatggaaggagaaaaaaagacaacacgagaaaaattagtattttctaccttccgaaattaatggccatgagttcgtatatggtgaactctaagtatgtggatcccaaatttcctccttgcgaggaatatttgcagagcagctacctaggcgagcagggggccgagtattacggggcctcgcagggctccgatttccagcaccaggggctctacccacggtcaaactacagcgagcagccctttggctgcgccggtgcccagggctctgccgtgcagccgcggggtcacggacaggagcagtccgcccctccgagccacttccccggccaagccgagcattgtcctccgcctccaatgtccaactcccgagcctgcggccagcagccagccctcaaagccccccacgggtcagcagttaagcagccagcagtagtttatccctggatgaagaaagtccatgttaactcggtgaaccccaattacagcggaggggaacctaagcgctcccgaacagcttacaccaggcagcaagtcctagaactggaaaaagaatttcattttaacaggtacctgacccggcgccgccgtatcgagatagcgcacactttgtgtctctctgagcgccagatcaagatctggtttcagaacagaagaatgaagtggaaaaaagaccacaaactgcccaacactaagggcaggtcttcctcctccgcttctaacccccacttacagactgttcccaaggaccatcagactgacttgacaactttatagaagaggtgaaattttccatttcatccttcgattctgaccagtactgtacataagtgacactatccaagcagaacctgcgtgtagcagccaaggactcgagaaactgccatctctccgtaaggtactgtggtacaaaggagactgaatgacgctactccggactttattttatttgcctctcgctagcacagaaagaaagggggggaaaaaaagcatcatacaggcagtaggaattgggaaagtcttaaacgagaccttctgtccataaaaagtaataaatcattg

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