LOCUS       NM_001398309             880 bp    mRNA    linear   VRT 23-SEP-2023
DEFINITION  Gallus gallus homeobox A6 (HOXA6), transcript variant 2, mRNA.
ACCESSION   NM_001398309
VERSION     NM_001398309.1
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 880)
  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 880)
  AUTHORS   Attia L, Yelin R and Schultheiss TM.
  TITLE     Analysis of nephric duct specification in the avian embryo
  JOURNAL   Development 139 (22), 4143-4151 (2012)
   PUBMED   23034630
  REMARK    GeneRIF: In the primitive streak, expression of the gene HoxB4 is
            associated with prospective duct IM, whereas expression of the more
            posterior Hox gene HoxA6 is associated with more posterior,
            non-duct-forming IM.
REFERENCE   3  (bases 1 to 880)
  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
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000037.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR13267647.12816.1, HAEL01011072.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA103992290, SAMEA103992323
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-328               JAENSK010000037.1  1563382-1563709     c
            329-584             JAENSK010000037.1  1559093-1559348     c
            585-880             JAENSK010000037.1  1557598-1557893     c
FEATURES             Location/Qualifiers
     source          1..880
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="2"
                     /map="2"
     gene            1..880
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="homeobox A6"
                     /db_xref="CGNC:51307"
                     /db_xref="GeneID:420630"
     exon            1..328
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    323..325
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="upstream in-frame stop codon"
     exon            329..584
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /inference="alignment:Splign:2.1.0"
     CDS             560..844
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="isoform 2 is encoded by transcript variant 2;
                     homeobox protein Hox-A6; homeo box A6; homeo box 1B;
                     homeobox protein HOXA6; homeobox protein Hox-1B"
                     /codon_start=1
                     /product="homeobox protein Hox-A6 isoform 2"
                     /protein_id="NP_001385238.1"
                     /db_xref="CGNC:51307"
                     /db_xref="GeneID:420630"
                     /translation="

MQRMNSCAGTVYGAHGRRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIANALCLTERQIKIWFQNRRMKWKKENKFINSTQPGSDETEEKSGE"

     misc_feature    order(608..622,626..628,677..679,695..697,734..736,
                     740..745,752..757,761..769,773..778)
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(614..616,623..625,743..745,752..757,764..766)
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    617..775
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     exon            585..880
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

attcttttgctgagctctgtcctgcttcggatctctctggctttcaatccccatttcatttgctctttgtaaggctatagtgaacaaagtgtgcggaggttcggcataagcagccgcctagaacacagatccgggatggcaatttccagttcccccgctggaaggtgtggcatattggattcaaagcactggcgtggcagattttcaacttgcaacctggctaatttcctgcttcttctggcaccaaaaggagggcgattcgtctcctgtgcagccaaagcgacagctgtcaaagtcgcaggggctcctgcgagccagaacctaaaagtccaacaccgtcattgcttgcaatcgggcttcctatgagtacggagcctcctgtttctattcagacaaggaaattagtagcgcctctccctccggcagtggcaagcagaggggacaaggggactatctgcacttttctcccgagcaacaatacaaatccaacggcgtgcaaagcaaaatcgtgaatgacgaaggcaccgaccggaagtacacgagccctgtttacccctggatgcagcggatgaactcctgtgccggtacagtatatggagctcatgggagacgagggaggcagacttacacccgctaccaaacgctagagttagagaaggagttccattttaacagatacttaacccgaagacgacgcattgagattgcgaacgctctctgccttaccgagcgccagattaaaatatggtttcaaaacaggcggatgaaatggaaaaaggaaaacaaattcataaattccacccagcccggcagcgacgaaacagaggaaaagtcaggggagtagaaccgtgtttaataaacgctaccaggcccgtcctta

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