LOCUS       NM_001030987             823 bp    mRNA    linear   VRT 24-SEP-2023
DEFINITION  Gallus gallus homeobox A6 (HOXA6), transcript variant 1, mRNA.
ACCESSION   NM_001030987 XM_418729
VERSION     NM_001030987.4
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 823)
  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 823)
  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 823)
  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.
            
            On Dec 14, 2021 this sequence version replaced NM_001030987.3.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BU422323.1, AY307380.1 [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
            1-527               JAENSK010000037.1  1559093-1559619     c
            528-823             JAENSK010000037.1  1557598-1557893     c
FEATURES             Location/Qualifiers
     source          1..823
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="2"
                     /map="2"
     gene            1..823
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="homeobox A6"
                     /db_xref="CGNC:51307"
                     /db_xref="GeneID:420630"
     exon            1..527
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    23..25
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="upstream in-frame stop codon"
     CDS             92..787
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="isoform 1 is encoded by transcript variant 1;
                     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 1"
                     /protein_id="NP_001026158.1"
                     /db_xref="CGNC:51307"
                     /db_xref="GeneID:420630"
                     /translation="

MSSYFVNPTFPGSLPAGQDSFLGQIPLYPAGYDALRHFPTSYGASSLQDKTYTSPCFYQQSNTVIACNRASYEYGASCFYSDKEISSASPSGSGKQRGQGDYLHFSPEQQYKSNGVQSKIVNDEGTDRKYTSPVYPWMQRMNSCAGTVYGAHGRRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIANALCLTERQIKIWFQNRRMKWKKENKFINSTQPGSDETEEKSGE"

     misc_feature    491..508
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="propagated from UniProtKB/Swiss-Prot (Q5YLH5.1);
                     Region: Antp-type hexapeptide"
     misc_feature    order(551..565,569..571,620..622,638..640,677..679,
                     683..688,695..700,704..712,716..721)
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(557..559,566..568,686..688,695..700,707..709)
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    560..718
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    725..784
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="propagated from UniProtKB/Swiss-Prot (Q5YLH5.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            528..823
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

atccagaaacaaaccacttcgatgactactaatagttatagccagatgtactaatacacaacaaatcacggtccgggagaggggagagcaaatgagttcctatttcgtgaatcccactttccccgggagcctgcccgctggccaggactccttcctcgggcagatccccctgtacccggcgggctatgatgctctgaggcattttccgacttcgtacggggcgagcagcctgcaggacaagacctacacctcaccttgtttctatcaacagtccaacaccgtcattgcttgcaatcgggcttcctatgagtacggagcctcctgtttctattcagacaaggaaattagtagcgcctctccctccggcagtggcaagcagaggggacaaggggactatctgcacttttctcccgagcaacaatacaaatccaacggcgtgcaaagcaaaatcgtgaatgacgaaggcaccgaccggaagtacacgagccctgtttacccctggatgcagcggatgaactcctgtgccggtacagtatatggagctcatgggagacgagggaggcagacttacacccgctaccaaacgctagagttagagaaggagttccattttaacagatacttaacccgaagacgacgcattgagattgcgaacgctctctgccttaccgagcgccagattaaaatatggtttcaaaacaggcggatgaaatggaaaaaggaaaacaaattcataaattccacccagcccggcagcgacgaaacagaggaaaagtcaggggagtagaaccgtgtttaataaacgctaccaggcccgtcctta

//