LOCUS       NM_001139568            1506 bp    mRNA    linear   VRT 21-DEC-2022
DEFINITION  Salmo salar homeobox A5a (hoxa5a), mRNA.
ACCESSION   NM_001139568
VERSION     NM_001139568.1
KEYWORDS    RefSeq.
SOURCE      Salmo salar (Atlantic salmon)
  ORGANISM  Salmo salar
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Actinopterygii; Neopterygii; Teleostei; Protacanthopterygii;
            Salmoniformes; Salmonidae; Salmoninae; Salmo.
REFERENCE   1  (bases 1 to 1506)
  AUTHORS   Ramberg S, Hoyheim B, Ostbye TK and Andreassen R.
  TITLE     A de novo Full-Length mRNA Transcriptome Generated From
            Hybrid-Corrected PacBio Long-Reads Improves the Transcript
            Annotation and Identifies Thousands of Novel Splice Variants in
            Atlantic Salmon
  JOURNAL   Front Genet 12, 656334 (2021)
   PUBMED   33986770
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1506)
  AUTHORS   Mungpakdee S, Seo HC, Angotzi AR, Dong X, Akalin A and Chourrout D.
  TITLE     Differential evolution of the 13 Atlantic salmon Hox clusters
  JOURNAL   Mol Biol Evol 25 (7), 1333-1343 (2008)
   PUBMED   18424774
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from EU025695.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: EF695315.1, DW575599.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00779696, SAMN02597926
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1506
                     /organism="Salmo salar"
                     /mol_type="mRNA"
                     /db_xref="taxon:8030"
                     /chromosome="ssa14"
                     /map="ssa14"
     gene            1..1506
                     /gene="hoxa5a"
                     /gene_synonym="hoxa5; hoxa5ab; S12-B"
                     /note="homeobox A5a"
                     /db_xref="GeneID:100194478"
     exon            1..1130
                     /gene="hoxa5a"
                     /gene_synonym="hoxa5; hoxa5ab; S12-B"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    482..484
                     /gene="hoxa5a"
                     /gene_synonym="hoxa5; hoxa5ab; S12-B"
                     /note="upstream in-frame stop codon"
     CDS             530..1387
                     /gene="hoxa5a"
                     /gene_synonym="hoxa5; hoxa5ab; S12-B"
                     /note="homeobox protein HoxA5ab"
                     /codon_start=1
                     /product="homeobox protein Hox-A5"
                     /protein_id="NP_001133040.1"
                     /db_xref="GeneID:100194478"
                     /translation="

MSSYFVNSFCGRYPNGADFQLHNYGDHSSANDQYRDSTTMHSSRHGYGYNGMDLTVGRGNGHFVANERAQGYSPNQSAAATTSSVEPSRVHPVRERHWDGAPLALHLTRFPCSSSVTSSSPVSESQPQHRAIKNSITIPCASPSSSSNGGTLLNQECVSKASPLLEEEKPAGREQTTSQHFTDGAQPQIYPWMRKLHISHDSLTGPEGKRARTAYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLSERQIKIWFQNRRMKWKKDNKLKSMSMAAAGGVGYHRP"

     misc_feature    order(1154..1168,1172..1174,1223..1225,1241..1243,
                     1280..1282,1286..1291,1298..1303,1307..1315,1319..1324)
                     /gene="hoxa5a"
                     /gene_synonym="hoxa5; hoxa5ab; S12-B"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(1160..1162,1169..1171,1289..1291,1298..1303,
                     1310..1312)
                     /gene="hoxa5a"
                     /gene_synonym="hoxa5; hoxa5ab; S12-B"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    1163..1321
                     /gene="hoxa5a"
                     /gene_synonym="hoxa5; hoxa5ab; S12-B"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     exon            1131..1506
                     /gene="hoxa5a"
                     /gene_synonym="hoxa5; hoxa5ab; S12-B"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

ggttgcatattcactattcagtgcgtttcttgttgtattgtttgggaaagcgatgcgtttgccgcaacggtcgttaacctctgaacgaccctgttcagaggccacgcctcaaagcccgtcgcaggcagtgccagattgtgtccggaggatggcgcgcaaggacaatccaagagacgcaacccgggccccgcgagcgccctgcccaggcgcactctcaggcgcgcgccactaaaatcccacccagatttcctacttgtgcacgagtttacctctggaggtcatcaagcaggatttacgactggtcaacaaaagcacgtgattctcagccgtaacccatatttgggtgcctacgtaagagagaatcaagtacacgttctactcatttccctaattcatcataaattgtgcaagggtgctatagaagaagcaaaagcatcaagagccacaaatcaagcacacacgttactattttatccaaaaataaaaacaacaaatacctgctaaacaacagtatttgaatagtcaatcaatgagctcctattttgtaaactcattctgcggtcgctatcccaatggcgccgacttccagttacataattatggagatcacagctcagcaaacgaccaatacagggactcaacgaccatgcattccagcaggcacggttatggctacaacgggatggacctcactgtcggtcgcggtaacgggcactttgtggccaacgagcgggcacagggctactccccgaaccagtcggcggcggcaacaacgtcttctgtcgagccatccagggtacacccagtccgcgagcgccactgggacggcgcccctctcgccctgcacctgacccgcttcccgtgctcctcctctgtcacaagctcgtctccggtcagcgagtctcaacctcaacaccgagccataaagaactccataactatcccctgcgcgagcccgagctcgagttcgaacggaggcacgctgttgaaccaggagtgtgtgtccaaagcctcccccctcctcgaggaagagaagcccgctggaagagagcagacaacttcccaacatttcaccgacggtgcccagcctcagatctacccctggatgaggaaactgcacataagtcatgacagtctcactggaccagaggggaagagggcgaggacagcatacacgcgctaccagaccctggagctcgagaaagagttccatttcaaccggtatctgacccgcagacggaggatcgagatagcgcacgcgctctgcctatcagaacgccagatcaaaatctggttccagaacagaaggatgaagtggaaaaaggacaacaaactgaaaagcatgagcatggcagcggcagggggtgtagggtaccaccgtccctgatatttggttccccgatgagctctaataaaataatacaaagcttgggagaacttccattcatttttacattgcgaaagactgttttgggacagtgaacatgcagttgtccatactccggc

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