LOCUS       NM_204620               1528 bp    mRNA    linear   VRT 23-SEP-2023
DEFINITION  Gallus gallus homeobox D11 (HOXD11), mRNA.
ACCESSION   NM_204620 XM_001234561
VERSION     NM_204620.2
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 1528)
  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 1528)
  AUTHORS   Kamiyama N, Seki R, Yokoyama H and Tamura K.
  TITLE     Heterochronically early decline of Hox expression prior to
            cartilage formation in the avian hindlimb zeugopod
  JOURNAL   Dev Growth Differ 54 (6), 619-632 (2012)
   PUBMED   22708793
  REMARK    GeneRIF: Expression of Hoxd11/Hoxd12 in the chick hindlimb
            decreased and disappeared from the presumptive zeugopod region
            before cartilage formation.
REFERENCE   3  (bases 1 to 1528)
  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   4  (bases 1 to 1528)
  AUTHORS   Rogina B, Coelho CN, Kosher RA and Upholt WB.
  TITLE     The pattern of expression of the chicken homolog of HOX1I in the
            developing limb suggests a possible role in the ectodermal
            inhibition of chondrogenesis
  JOURNAL   Dev Dyn 193 (1), 92-101 (1992)
   PUBMED   1347239
REFERENCE   5  (bases 1 to 1528)
  AUTHORS   Izpisua-Belmonte JC, Tickle C, Dolle P, Wolpert L and Duboule D.
  TITLE     Expression of the homeobox Hox-4 genes and the specification of
            position in chick wing development
  JOURNAL   Nature 350 (6319), 585-589 (1991)
   PUBMED   1673231
REFERENCE   6  (bases 1 to 1528)
  AUTHORS   Nohno T, Noji S, Koyama E, Ohyama K, Myokai F, Kuroiwa A, Saito T
            and Taniguchi S.
  TITLE     Involvement of the Chox-4 chicken homeobox genes in determination
            of anteroposterior axial polarity during limb development
  JOURNAL   Cell 64 (6), 1197-1205 (1991)
   PUBMED   1672266
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from
            JAENSK010000236.1.
            
            On Sep 23, 2021 this sequence version replaced NM_204620.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: M81249.1, JF317542.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA103992290, SAMEA103992428
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-680               JAENSK010000236.1  8573238-8573917     c
            681-1528            JAENSK010000236.1  8571791-8572638     c
FEATURES             Location/Qualifiers
     source          1..1528
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="7"
                     /map="7"
     gene            1..1528
                     /gene="HOXD11"
                     /gene_synonym="GHOX4.6"
                     /note="homeobox D11"
                     /db_xref="CGNC:7045"
                     /db_xref="GeneID:395328"
     exon            1..680
                     /gene="HOXD11"
                     /gene_synonym="GHOX4.6"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    35..37
                     /gene="HOXD11"
                     /gene_synonym="GHOX4.6"
                     /note="upstream in-frame stop codon"
     CDS             74..916
                     /gene="HOXD11"
                     /gene_synonym="GHOX4.6"
                     /note="homeodomain-containing protein; homeo box D11;
                     chox-4E; chox-4.6; ghox-4.6; homeobox protein Hox-4E;
                     homeobox protein Hox-4.6; Hox D11"
                     /codon_start=1
                     /product="homeobox protein Hox-D11"
                     /protein_id="NP_989951.1"
                     /db_xref="CGNC:7045"
                     /db_xref="GeneID:395328"
                     /translation="

MTEFDDCSHGASNMYLPGCAYYVSPSDFSTKPSFLSQSSSCQMTFPYSSNLPHVQPVREVAFREYGLERGKWQYRGSYAPYYSAEEVMHRDFLQPANRRTEMLFKTDPVCGHHGASPAASNFYGSVGRNGILPQGFDQFYEPAPAPPYQQHSEGEGDADKGELKPQHSACSKAPSGQEKKVTTASGAASPPGEAVAEKSNSSAVPQRSRKKRCPYTKYQIRELEREFFFNVYINKEKRLQLSRMLNLTDRQVKIWFQNRRMKEKKLNRDRLQYFTGNPLF"

     misc_feature    149..520
                     /gene="HOXD11"
                     /gene_synonym="GHOX4.6"
                     /note="Protein of unknown function (DUF3528); Region:
                     DUF3528; pfam12045"
                     /db_xref="CDD:432284"
     misc_feature    476..706
                     /gene="HOXD11"
                     /gene_synonym="GHOX4.6"
                     /note="propagated from UniProtKB/Swiss-Prot (P24342.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    order(698..712,716..718,767..769,785..787,824..826,
                     830..835,842..847,851..859,863..868)
                     /gene="HOXD11"
                     /gene_synonym="GHOX4.6"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    704..865
                     /gene="HOXD11"
                     /gene_synonym="GHOX4.6"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(704..706,713..715,833..835,842..847,854..856)
                     /gene="HOXD11"
                     /gene_synonym="GHOX4.6"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            681..1528
                     /gene="HOXD11"
                     /gene_synonym="GHOX4.6"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

ctcttgtgcaatagatggatctcgttcaacgcattgaagcctcccggtcgctcgcaatcgcgaaaaggaagacatgaccgagtttgacgattgcagtcacggcgcatccaatatgtatctgccagggtgcgcttattacgtctcgccctcagacttctcgacgaaaccctcttttttgtcgcaatcgtcttcctgtcaaatgacttttccttattcttctaatttacctcatgtccaacctgtgcgcgaagtggcattcagggaatacggattagagcgcggcaaatggcagtacaggggcagttacgctccctattactcagctgaagaggtgatgcacagagactttctgcagcccgcgaacaggaggacggaaatgctattcaaaacggaccccgtgtgcggccaccacggagcgtcccccgccgcctccaacttctacggctcggtggggaggaacggcatcctgccgcagggcttcgaccagttctacgagccggcccccgcgcccccgtaccagcagcactccgagggcgagggggacgcggacaagggcgagctgaagccccagcacagcgcctgcagcaaggcaccttccggccaggagaagaaagtgacaacggcgagcggcgccgcttcccctcccggtgaggctgttgcagagaagagcaacagttcagcagttcctcagcgatcgaggaaaaagaggtgtccctataccaaatatcagataagagaactggaacgtgagtttttcttcaacgtgtacataaacaaagagaaaagactgcagttgtccagaatgctcaacctcactgaccggcaagttaaaatctggttccagaatcgaaggatgaaagaaaagaaactgaacagagatcgactccaatacttcactggaaatcccttgttttgaggaggaaaaaaagaaagaaaaaaaaaagaaaggaaaaaaaaaagaaaggaaaaaatgtaaaaaaaaaaaaaatcgaaagagaaagagaaaaggaagaaagaagaagaagcaaagaatccctcggtcagtgtgacctgccatccgaatgccaagtgaatgggtttacatgacacagccgccctgcggaactcaaagtttcatttccatgcgcagctccacacgctgaatggccacaggagatttcggggcttggcggagcagattcctgctaagggaacctagagtaaagccagctgtctattctcaagtggttctcgccaaaggtgcttttttttttctcctctcctctcccacagtaccagcaatggacctgcagtgtgtctggtagtttttgcttacgattcattgagttcggggggggctatgttgttgcttttgagttagggtaacactttcctcccctcaagtgaatgcggtttatttaagagatggtaaatgtacgttcgctatatataaaatatatatatatatatgtttctattgtcatccaaaagcatgggccactgtctttttcatgtgaataaatggtttctagtaaagctaaggttataa

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