LOCUS       NM_001318419            1677 bp    mRNA    linear   VRT 23-SEP-2023
DEFINITION  Gallus gallus homeobox A5 (HOXA5), mRNA.
ACCESSION   NM_001318419 XM_003640699
VERSION     NM_001318419.2
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 1677)
  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 1677)
  AUTHORS   Chen JW, Zahid S, Shilts MH, Weaver SJ, Leskowitz RM, Habbsa S,
            Aronowitz D, Rokins KP, Chang Y, Pinnella Z, Holloway L and
            Mansfield JH.
  TITLE     Hoxa-5 acts in segmented somites to regulate cervical vertebral
            morphology
  JOURNAL   Mech Dev 130 (4-5), 226-240 (2013)
   PUBMED   23462683
  REMARK    GeneRIF: The role of Hoxa-5 in after somite segmentation in chick,
            was investigated.
REFERENCE   3  (bases 1 to 1677)
  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     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from
            JAENSK010000037.1.
            
            On Sep 23, 2021 this sequence version replaced NM_001318419.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AY686640.1, HAEL01011593.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA103992290, SAMEA103992323
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-640               JAENSK010000037.1  1554961-1555600     c
            641-1677            JAENSK010000037.1  1553054-1554090     c
FEATURES             Location/Qualifiers
     source          1..1677
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="2"
                     /map="2"
     gene            1..1677
                     /gene="HOXA5"
                     /gene_synonym="HOX1.3; HOX1C"
                     /note="homeobox A5"
                     /db_xref="CGNC:66000"
                     /db_xref="GeneID:100858404"
     exon            1..640
                     /gene="HOXA5"
                     /gene_synonym="HOX1.3; HOX1C"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    25..27
                     /gene="HOXA5"
                     /gene_synonym="HOX1.3; HOX1C"
                     /note="upstream in-frame stop codon"
     CDS             79..891
                     /gene="HOXA5"
                     /gene_synonym="HOX1.3; HOX1C"
                     /note="homeo box 1C; homeo box A5; homeobox protein HOXA5;
                     homeobox protein Hox-1C"
                     /codon_start=1
                     /product="homeobox protein Hox-A5"
                     /protein_id="NP_001305348.1"
                     /db_xref="CGNC:66000"
                     /db_xref="GeneID:100858404"
                     /translation="

MSSYFVNSFCGRYPNGPDYQLHNYGDHSSVSEQYRDSASMHSGRYGYGYNGMDLSVGRSASTHFGASERARTYPANSTSASTEPRYSQSAAASHSPPPDPLPCTAVAASPVSESHHGVKNSLGNSSSTSSNSSSSTHISRDGVGTSSGTEEDTPASSEQASAPSDQSTAQPSQPQIYPWMRKLHISHDNIGGPEGKRARTAYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLSERQIKIWFQNRRMKWKKDNKLKSMSMAAAGGAFRP"

     misc_feature    277..597
                     /gene="HOXA5"
                     /gene_synonym="HOX1.3; HOX1C"
                     /note="propagated from UniProtKB/Swiss-Prot (Q6B3N0.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    538..>858
                     /gene="HOXA5"
                     /gene_synonym="HOX1.3; HOX1C"
                     /note="Homeodomain-containing transcription factor
                     [Transcription]; Region: COG5576"
                     /db_xref="CDD:227863"
     misc_feature    604..621
                     /gene="HOXA5"
                     /gene_synonym="HOX1.3; HOX1C"
                     /note="propagated from UniProtKB/Swiss-Prot (Q6B3N0.1);
                     Region: Antp-type hexapeptide"
     misc_feature    order(664..678,682..684,733..735,751..753,790..792,
                     796..801,808..813,817..825,829..834)
                     /gene="HOXA5"
                     /gene_synonym="HOX1.3; HOX1C"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(670..672,679..681,799..801,808..813,820..822)
                     /gene="HOXA5"
                     /gene_synonym="HOX1.3; HOX1C"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    673..831
                     /gene="HOXA5"
                     /gene_synonym="HOX1.3; HOX1C"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     exon            641..1677
                     /gene="HOXA5"
                     /gene_synonym="HOX1.3; HOX1C"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

atcataaattgtgcaagggtgctatagacgcacaaaacgaccaagagccacaaatcaagcacacatatcaaaaaacaaatgagctcttattttgtaaactcattttgcggtcgctatccaaatggcccggactaccagttacataattatggagatcacagctcggtgagcgagcaatacagggactccgccagcatgcactccggcaggtacggatacggctacaatggcatggacctcagcgtcgggcgctccgcttccacccactttggtgccagcgagagagcccgcacctacccggccaacagcacctctgcctcgacagagcccaggtacagccagtccgcggccgcttcccactcgcctccccccgaccccctgccctgcaccgccgtggccgcttcgcccgtcagcgagagtcaccacggggtgaaaaactccctgggcaactccagcagcacttcgtccaattccagcagcagcacgcacatcagcagggacggggttggcacctcgtccggcaccgaggaagacactccggcgagcagcgagcaggcaagtgccccgagcgaccaaagcacagcacagccttcccagccccagatctacccttggatgcgaaagctgcacataagtcatgacaacatagggggaccagaagggaaaagggctcggactgcttacacccggtatcagaccttggagctggaaaaggaatttcacttcaatagatacctgacccgcagaagaaggattgaaatagcacacgctctttgcctctcagagagacaaataaagatctggttccaaaacaggagaatgaaatggaaaaaggataataagctgaaaagtatgagcatggcagctgcagggggggcattccgtccctaagcgtttgatcaattaaaagtactgagcagtattagctgaccctgcgtctcatgtcagtactaagttgactttctaaaacttccttgtgttacttctgtgaagaaaccctgttcttgtcgcccttattcatcttttaatcatgagcctgtttattaccattctctcgcgtgtataagtagatctgcttttatcgtacatttctttgtcttgaatggctttgtcttgaaaaaaaataatagatgttttaacttatttatatgaagcgagctgtgttacttgaagtaactgttaaaaaaaaaagaagcaaaaggaaaaaaaaaagaacaaaaaggaaaggaaagaaaagggaaaaaaagagagagagagaaagaaaccctcccccggtttagtacaaatgttatgtgttgcactcaacctgcttaactgtgcatgtgtggtcaagtgttaatgtccgtatagctccaagctgttacaaatatttttattcaaactacctatataatttctgtgtaattaatgctgtcgtagaggtgaaatgatgaaatcaactgaacttgtcctacgtgtagtgaatagtgaatctgtgacgaaaactgtgattccaagcagtatgtccttgctgtgcctttgtatatgactctttgcacgaactcttagaagtggctcttattaagcgcagcttctgtgatgtatgtttgggttggttttttttttttggtatatattttttttttcggtggacagagttacaaatatagtcaaagtctggctgtttgagcaaactgt

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