LOCUS       NM_001396999            2138 bp    mRNA    linear   VRT 12-JUN-2024
DEFINITION  Gallus gallus homeobox D9 (HOXD9), transcript variant 1, mRNA.
ACCESSION   NM_001396999 XM_025152481 XM_040675619
VERSION     NM_001396999.1
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 2138)
  AUTHORS   Tang,H., Finn,R.D. and Thomas,P.D.
  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 2138)
  AUTHORS   Burge,S., Kelly,E., Lonsdale,D., Mutowo-Muellenet,P., McAnulla,C.,
            Mitchell,A., Sangrador-Vegas,A., Yong,S.Y., 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 2138)
  AUTHORS   Izpisua-Belmonte,J.C., 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
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000236.1.
            
            On or before Oct 29, 2021 this sequence version replaced
            XM_025152481.2, XM_040675619.1.
            
            Transcript Variant: This variant (1) has four exons.
            
            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.
            
            ##Evidence-Data-START##
            CDS exon combination :: SRR13267654.117223.1, SRR13267649.269673.1
                                    [ECO:0000331]
            RNAseq introns       :: single sample supports all introns
                                    SAMEA103992604 [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-136               JAENSK010000236.1  8559814-8559949     c
            137-269             JAENSK010000236.1  8559032-8559164     c
            270-1099            JAENSK010000236.1  8557959-8558788     c
            1100-2138           JAENSK010000236.1  8556523-8557561     c
FEATURES             Location/Qualifiers
     source          1..2138
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="7"
                     /map="7"
     gene            1..2138
                     /gene="HOXD9"
                     /note="homeobox D9"
                     /db_xref="CGNC:56606"
                     /db_xref="GeneID:771214"
     exon            1..136
                     /gene="HOXD9"
                     /inference="alignment:Splign:2.1.0"
     exon            137..269
                     /gene="HOXD9"
                     /inference="alignment:Splign:2.1.0"
     exon            270..1099
                     /gene="HOXD9"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    421..423
                     /gene="HOXD9"
                     /note="upstream in-frame stop codon"
     CDS             442..1341
                     /gene="HOXD9"
                     /note="chox-4.4; homeobox protein Hox-4.4"
                     /codon_start=1
                     /product="homeobox protein Hox-D9"
                     /protein_id="NP_001383928.1"
                     /db_xref="CGNC:56606"
                     /db_xref="GeneID:771214"
                     /translation="

MSSSGTISNYYVDSLIGHESEEVYGSRFVQGGHSATSRPSGVAESSDFSSCSFAPKSTVFSTSWSTVHPQPPAAMTGIYHPYMHQPHLGAADAGRYVRSWIEPFPGFPGGGGGSGGGGGGSASGSGSGSSAGRHYGIKPETGAAASSSSSSSSSSSKRTECSSSRESQGIAVPEYTCGTFLPEPREKAAAGSAKEPAACSHSPGPGGEPKEEKQQQLDPNNPAANWIHARSTRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARILNLTERQVKIWFQNRRMKMKKMNKEKGNKGD"

     misc_feature    442..1098
                     /gene="HOXD9"
                     /note="Hox9 activation region; Region: Hox9_act;
                     pfam04617"
                     /db_xref="CDD:461369"
     misc_feature    1138..1284
                     /gene="HOXD9"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     exon            1100..2138
                     /gene="HOXD9"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gtgttttcgcagtgctgttgtttgtgtcctcagcgggccgtgctgcgggctccactctaactgtgtgcgttttctccagattccgacacagcaccttccctctctcggaggagcagaaaggcgcagcacggcgcgggcaagaatccccccttcccagcgggtttcctcggcagctcggagtgtgattagcaagccaaggccgttggatgtatttaaacaccctgcctctcattgattaagaaatgaatggcagaaatcactcggaggagcagccccagtttagcggattgatttactcgcagtattggtaaatatgatcacgtgggctccgcaaccaatggttgagggttgcagtctgcaaaatactacgattgttctcagggagggtatcatatacagttaacagtgtaaccttttatatgagtaagaggggagcctaaaatgtcgtctagtggcaccataagtaactattatgtcgattctctcataggccatgaaagcgaagaagtttacgggagtagattcgtccaggggggtcacagtgcgacctccaggccatcaggtgtggcagagagttccgatttttcctcctgtagctttgcaccaaaatccaccgtgttctccacctcctggtccacggttcacccgcagccgcccgcggccatgaccgggatctaccacccctacatgcaccagccccacttaggggcagccgacgccggccgctacgtgcgctcctggatcgagcccttcccgggcttcccgggcggcggcggcggcagcggcggcggcggcggcggctccgcgtccggctcgggctcgggctcctccgccgggcgccactacgggataaagccggagacgggagcagccgcctcctcttcttcctcctcctcctcctcctcctccaaaaggactgagtgctcctcgtcccgagagtcccaggggatcgccgtgcccgaatacacgtgcggcactttcctgccggagccccgagagaaggcggccgccggcagcgccaaggagcccgccgcctgcagccacagccccggccccggcggagagccgaaggaggagaagcagcagcaacttgacccaaataaccccgcggcaaactggatccacgctcgttcgacgaggaaaaagcgttgcccctacactaagtatcaaactctggaactggagaaggagtttctctttaacatgtacctcacccgcgaccgccgctacgaagtagctaggattctaaatctcaccgagagacaggtcaaaatctggtttcagaacagacggatgaaaatgaaaaagatgaacaaggagaaaggcaataaaggagactaacgccggggtgggaacgcggccggggagcgcagctctggggctgaggttggggctgtggttttttctttttcttttattattatttgtatttttattttcggttcgctcgggttttatgcttcccctgccccctcggccccgcgtgcgtctctcctccccccccccctcccgccccccgcgcccccgccccaggatcgttaaatcaatccggtcttttttaggtagaagtgaaacgtggtctgtgtcaggtatttggggaaatgttgtcttgctcgccgacgtgtttgcagagtcgcttccccccccccccctctcctcccccccgggccgttcggtcggtggtgttgtgagtgcacgttagcttcggggactttagctgatgttaagtgttcgacatgtctcttacaagtgatgtagttaggtagttcctttgccaaaataaaggtaaggaaagtaattataataacgataacaaactatatattaaatcacagtggcttcgatcgacggcagcgctgcgtcgtccgcgattcattgagaggaaatctcgccccaacctctgctttctaggtctaaattttttgcaatagatgccaccgcgaggccacgggatgccccctccaccccacccccttagtgcactgttaggaggtcgtctccgattcgaagccatttgcaataggcctcacgtttcccgagctccggcccggtaaatgctgtgcgcgctcccacgtccctaactgccgacctgctgtatctgtgtccgttctaacacaataaaggctgtcgtgaccgaa

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