LOCUS       NM_001397002            2589 bp    mRNA    linear   VRT 23-SEP-2023
DEFINITION  Gallus gallus homeobox D1 (HOXD1), mRNA.
ACCESSION   NM_001397002 XM_004942724
VERSION     NM_001397002.2
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 2589)
  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 2589)
  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 2589)
  AUTHORS   Rangini Z, Frumkin A, Shani G, Guttmann M, Eyal-Giladi H, Gruenbaum
            Y and Fainsod A.
  TITLE     The chicken homeo box genes CHox1 and CHox3: cloning, sequencing
            and expression during embryogenesis
  JOURNAL   Gene 76 (1), 61-74 (1989)
   PUBMED   2568317
COMMENT     INFERRED REFSEQ: This record is predicted by genome sequence
            analysis and is not yet supported by experimental evidence. The
            reference sequence was derived from JAENSK010000236.1.
            
            On Dec 15, 2021 this sequence version replaced NM_001397002.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR13267649.68398.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3109051, SAMN02738219
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-709               JAENSK010000236.1  8515153-8515861     c
            710-2589            JAENSK010000236.1  8513137-8515016     c
FEATURES             Location/Qualifiers
     source          1..2589
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="7"
                     /map="7"
     gene            1..2589
                     /gene="HOXD1"
                     /note="homeobox D1"
                     /db_xref="CGNC:7040"
                     /db_xref="GeneID:101750316"
     exon            1..709
                     /gene="HOXD1"
                     /inference="alignment:Splign:2.1.0"
     CDS             331..966
                     /gene="HOXD1"
                     /note="homeobox protein CHOX-1"
                     /codon_start=1
                     /product="homeobox protein Hox-D1"
                     /protein_id="NP_001383931.1"
                     /db_xref="CGNC:7040"
                     /db_xref="GeneID:101750316"
                     /translation="

MDLGFFPIVLPSGLCHGTPPLPYSRRGLDAFPALSTAASSAHPPSAAGVGAAGYAAVPAANCQQPPGAACPGEAPPRPAASPCTGSGRPTSPEPERAFSCCPTPGAAPAKPRAFEWMRMKRSTPGRSDAAPPAFSLRTSFSTRQLTELEKEFHFSRYLSRARRLEVARSLRLRDAQVKVWFQNRRMKQKKREREALPDPTAAPRAAPGDTA"

     misc_feature    order(739..744,748..750,799..801,817..819,856..858,
                     862..867,874..879,883..891,895..900)
                     /gene="HOXD1"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    739..897
                     /gene="HOXD1"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(745..747,865..867,874..879,886..888)
                     /gene="HOXD1"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            710..2589
                     /gene="HOXD1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

ggcagcggcggctccggcaagtgggggatcccgagcggtcccgggagagctgagaagagaacagccacccggttccaggaaccgtcccatccgtcccagggccaggccgctgtggggttacgcctgggagctcaaggtgcgctgcctacgcatctaccacgggcagcagggagcgggcagggtaacggcggcgcccgggatacccggtgcgggctgcccccaccgggctcccattggccgcggggcgggacgtgcctccgctccggccctatatcagggcaatattaccccgtcgggggtgggggtaggtgtggtgctgtccgcgcaggcatggacttgggttttttccccatcgtcctcccgtccgggctgtgtcacgggaccccgccgctcccctactcccggcgagggctcgacgccttcccagcgctgagcaccgcggccagctctgcgcatcctccgtcggctgctggcgtgggggcggcgggctacgcggccgtcccggccgccaactgtcagcagccccccggggccgcgtgtccgggtgaggctccgccgcgtcccgccgcgtccccctgcaccgggagcggccgcccgacgtcgccggagcccgaacgggcattctcctgctgtccgaccccgggggcggctccggccaagccccgcgccttcgaatggatgcggatgaagcggagcacgcccggcagaagcgacgcggcaccccccgccttctccctgcgcaccagtttcagcacccggcagctcacggagctagagaaggagtttcacttcagccgctacctgtcgcgggcccgtcgcctcgaggtggcccgctcgctgcgcctccgcgacgcccaggtgaaggtgtggttccagaatcgccgcatgaagcagaagaagcgcgagcgggaggcgctgcccgaccccaccgcagcgccccgcgcagccccgggcgacaccgcctgagcccgtcgccacggcgcgctgcgaggatgccgcgagcggctccgcgctcctcttcgctccgccgctgctttactccctttgtattgatgaggatgatcggggagagctgtcgctccgaagcgccgccgctcaacttcgtcgttttgcgaggggacgaaagagccagaggagagcctcgtagagccgcaccgcggggtcgactcggagctgggggcgggcaggaccgcagcccccggcctgggctccctagggccgcccccatctggggccatagcgctgccccgccgcctccccgagccgtgtccggtgcctcggccgggtcggggagcagcggggtccgggcccgctcacagccgtcggggcgggggtgtcgggcagaggaggagcagaaaccccagcggggcaaagcagaacaggacaatgctcccctcgcaagaaaagagacgatgtataccattagcaagtgtagcagaaatccctttttagaaaagtaccctcgtcttcctcccttcctgtgcaaaattgctataaagagagcttacttgtactcatccctcacttgttcccctcccctttcgtgatgtggctgatttagtctgaaaaaatctgtgaaggaaaccttgaacaaacagtccatcaggagaaaggctgccctacgtgccctctgcagggccagtgcccactccgctgcctcccagtgtgtgggcaaggacagtgtagagtctctcatagcacgggggctctcctaggctttactctatctaatgtttaaagaaaagtaccatattaagccagtttgctaagagctgttaaagagcataaagatgtttgggtttgactgcagacctctgtcagtgagaccatgcgagttcctgggtctctcccctcccagagaaccagttctaaagcagtgacaaccccagctactccactgaagtgcaacactcaccagcaatcctcacttccccagattccatcttttccagaggtaaaacaatggtatcaaagtggacagagaagctggattcagaggtttttctggacctgactgatgactgggaatgtataaatggcagcacagatagggaggccacccggatttaggggacgaaagagctggcagtttgctttggatttcactcaggtgaaagaaaaacatagcactgggagagggatctccaggacctggaagcgtggatccacacctggaaagcagcccctgctaccaacagctgctgagatctagtcacacaccataccctgggcagaggctcatggccttgctcgcacacagagactttcaggtttcgtgcacagtgttacagctcacttccaaagagctgatgcacttcacgagttaaaaaacgaaacaacataaattcccagggtggagctgcttatatgaaatttgtacgaaaatacaaacatccaaaataaggggtgggcagttccttgttaaagcgctgaccccaaacaagctttcattctccttatcatttattaaagaacagaaaatagtatttctgccaactgtttttgaggagaggctatttagaataaagcaagatgtggaaagattcatagaaattacttttcatgtgattattaaaagcaaatcaattg

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