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2024-03-28 18:46:21, GGRNA.v2 : RefSeq release 222 (Jan, 2024)

LOCUS       NM_001139563             995 bp    mRNA    linear   VRT 28-JUN-2020
DEFINITION  Salmo salar homeobox A1a (hoxa1a), mRNA.
ACCESSION   NM_001139563
VERSION     NM_001139563.2
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 995)
  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 EF695309.1.
            
            On Apr 10, 2020 this sequence version replaced NM_001139563.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: EF695309.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN02863984, SAMN02864156
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-995               EF695309.1         2-996
FEATURES             Location/Qualifiers
     source          1..995
                     /organism="Salmo salar"
                     /mol_type="mRNA"
                     /db_xref="taxon:8030"
                     /chromosome="ssa14"
                     /map="ssa14"
     gene            1..995
                     /gene="hoxa1a"
                     /gene_synonym="hoxa1; hoxa1aa"
                     /note="homeobox A1a"
                     /db_xref="GeneID:100194473"
     exon            1..624
                     /gene="hoxa1a"
                     /gene_synonym="hoxa1; hoxa1aa"
                     /inference="alignment:Splign:2.1.0"
     CDS             9..995
                     /gene="hoxa1a"
                     /gene_synonym="hoxa1; hoxa1aa"
                     /note="homeobox protein HoxA1aa; homeobox A1"
                     /codon_start=1
                     /product="homeobox protein Hox-A1a"
                     /protein_id="NP_001133035.1"
                     /db_xref="GeneID:100194473"
                     /translation="
MSSFLDYSVMSGDGGSCSVRAFHSDHGITTFQSCAVTVNNCGADERFMPNRSSPDGIPHQTGSYQTPTGSLGLAYGAHPACGSGYGPQGFCATYNHYALNQEVESATGFPQCAPLMYSGNISSSMVPQLRQGYGGAPMGQLQYAHATYGGGHEQANLPPFSGCSNPLSPLHAAHLDSCCSPLSSESASNAQTFDWMKVKRNPPKTGRSGEYGYGGQSNTVRTNFTTKQLTELEKEFHFNKYLTRARRVEIAAALQLNETQVKIWFQNRRMKQKKREKECLLPTNAAVSDPRDSCPEKAAGSERSLSAPSTPSPASSTVSSGVDPYSSS"
     misc_feature    501..>830
                     /gene="hoxa1a"
                     /gene_synonym="hoxa1; hoxa1aa"
                     /note="Homeodomain-containing transcription factor
                     [Transcription]; Region: COG5576"
                     /db_xref="CDD:227863"
     misc_feature    order(669..674,678..680,729..731,747..749,786..788,
                     792..797,804..809,813..821,825..830)
                     /gene="hoxa1a"
                     /gene_synonym="hoxa1; hoxa1aa"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    669..827
                     /gene="hoxa1a"
                     /gene_synonym="hoxa1; hoxa1aa"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(675..677,795..797,804..809,816..818)
                     /gene="hoxa1a"
                     /gene_synonym="hoxa1; hoxa1aa"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            625..995
                     /gene="hoxa1a"
                     /gene_synonym="hoxa1; hoxa1aa"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
atgctacaatgagcagcttcttagattactctgtgatgagcggcgacggcgggtcctgctcagtcagggctttccactccgaccacggaattactacattccagtcctgtgcagtcaccgtgaacaactgtggggcggatgagcgcttcatgcccaataggtcttccccggatggcatccctcaccaaacggggtcctaccagactcctactggctctctgggtttagcctatggggcccatcctgcttgcggctcaggctatggaccccagggcttctgtgccacctacaaccattacgcactgaaccaggaagtggagtcggccacgggtttcccccagtgcgccccattaatgtactccggcaacatttcctcgtccatggtaccacagcttcgccaaggttacgggggagcgcccatgggtcagctccagtacgctcacgccacctatggtggcgggcacgagcaggcgaacctgcctcctttctctgggtgttcaaacccgctgtcacccctgcacgcggcccaccttgactcgtgctgctcgcccctgtcctccgagagcgcctccaacgcacagaccttcgattggatgaaagtgaagaggaacccgcccaagacaggcagatcaggggagtatggctatggggggcagtccaacaccgtccggaccaacttcaccaccaaacaactcaccgagcttgagaaggagttccacttcaacaagtatttgacccgcgcgcggcgcgtggagatcgcggcagcgcttcagctgaacgagactcaggtcaaaatctggttccagaaccgcaggatgaaacagaagaagcgcgagaaggaatgcctgctgcccaccaatgccgcagtgtcagacccgagggatagctgcccggaaaaagcagccggatctgagaggtccctctccgctccctccaccccgtctccagcctcttcaacagtgtcctctggggttgacccatactcctccagctaa
//

by @meso_cacase at DBCLS
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If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596. [Full Text]