LOCUS       NM_005804               1498 bp    mRNA    linear   PRI 12-NOV-2024
DEFINITION  Homo sapiens DExD-box helicase 39A (DDX39A), transcript variant 1,
            mRNA.
ACCESSION   NM_005804
VERSION     NM_005804.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1498)
  AUTHORS   Nai,S., Wang,M., Yang,J., Ling,B., Dong,Q., Yang,X., Du,X., Lu,M.,
            Liu,L., Yu,Z. and Chen,L.
  TITLE     Novel role for Ddx39 in differentiation and telomere length
            regulation of embryonic stem cells
  JOURNAL   Cell Death Differ 31 (11), 1534-1544 (2024)
   PUBMED   39107495
  REMARK    GeneRIF: Novel role for Ddx39 in differentiation and telomere
            length regulation of embryonic stem cells.
REFERENCE   2  (bases 1 to 1498)
  AUTHORS   Chang,C., Li,L., Su,L., Yang,F., Zha,Q., Sun,M., Tao,L., Wang,M.,
            Song,K., Jiang,L., Gao,H., Liang,Y., Xu,C., Yong,C., Wang,M.,
            Huang,J., Liu,J., Jin,W., Lv,W., Dong,H., Li,Q., Bu,F., Yan,S.,
            Qi,H., Zhao,S., Zhu,Y., Wang,Y., Shi,J., Qiao,Y., Xu,J., Chabot,B.
            and Chen,J.
  TITLE     Intron Retention of DDX39A Driven by SNRPD2 is a Crucial Splicing
            Axis for Oncogenic MYC/Spliceosome Program in Hepatocellular
            Carcinoma
  JOURNAL   Adv Sci (Weinh) 11 (35), e2403387 (2024)
   PUBMED   39018261
  REMARK    GeneRIF: Intron Retention of DDX39A Driven by SNRPD2 is a Crucial
            Splicing Axis for Oncogenic MYC/Spliceosome Program in
            Hepatocellular Carcinoma.
REFERENCE   3  (bases 1 to 1498)
  AUTHORS   Banerjee,S., Nagasawa,C.K., Widen,S.G. and Garcia-Blanco,M.A.
  TITLE     Parsing the roles of DExD-box proteins DDX39A and DDX39B in
            alternative RNA splicing
  JOURNAL   Nucleic Acids Res 52 (14), 8534-8551 (2024)
   PUBMED   38801080
  REMARK    GeneRIF: Parsing the roles of DExD-box proteins DDX39A and DDX39B
            in alternative RNA splicing.
REFERENCE   4  (bases 1 to 1498)
  AUTHORS   Fujita,K.I., Yamazaki,T., Mayeda,A. and Masuda,S.
  TITLE     Terminal regions of UAP56 and URH49 are required for their distinct
            complex formation functioning to an essential role in mRNA
            processing and export
  JOURNAL   Biochem Biophys Res Commun 703, 149682 (2024)
   PUBMED   38377942
  REMARK    GeneRIF: Terminal regions of UAP56 and URH49 are required for their
            distinct complex formation functioning to an essential role in mRNA
            processing and export.
REFERENCE   5  (bases 1 to 1498)
  AUTHORS   Kikuta,K., Kubota,D., Saito,T., Orita,H., Yoshida,A., Tsuda,H.,
            Suehara,Y., Katai,H., Shimada,Y., Toyama,Y., Sato,K., Yao,T.,
            Kaneko,K., Beppu,Y., Murakami,Y., Kawai,A. and Kondo,T.
  TITLE     Clinical proteomics identified ATP-dependent RNA helicase DDX39 as
            a novel biomarker to predict poor prognosis of patients with
            gastrointestinal stromal tumor
  JOURNAL   J Proteomics 75 (4), 1089-1098 (2012)
   PUBMED   22119546
  REMARK    GeneRIF: -dependent RNA helicase DDX39 has a role in poor prognosis
            of patients with gastrointestinal stromal tumor
REFERENCE   6  (bases 1 to 1498)
  AUTHORS   Yamazaki,T., Fujiwara,N., Yukinaga,H., Ebisuya,M., Shiki,T.,
            Kurihara,T., Kioka,N., Kambe,T., Nagao,M., Nishida,E. and Masuda,S.
  TITLE     The closely related RNA helicases, UAP56 and URH49, preferentially
            form distinct mRNA export machineries and coordinately regulate
            mitotic progression
  JOURNAL   Mol Biol Cell 21 (16), 2953-2965 (2010)
   PUBMED   20573985
  REMARK    GeneRIF: Data show that the two closely related RNA helicases UAP56
            and URH49 have evolved to form distinct mRNA export machineries,
            which regulate mitosis at different steps.
REFERENCE   7  (bases 1 to 1498)
  AUTHORS   Leaw,C.L., Ren,E.C. and Choong,M.L.
  TITLE     Hcc-1 is a novel component of the nuclear matrix with growth
            inhibitory function
  JOURNAL   Cell Mol Life Sci 61 (17), 2264-2273 (2004)
   PUBMED   15338056
REFERENCE   8  (bases 1 to 1498)
  AUTHORS   Pryor,A., Tung,L., Yang,Z., Kapadia,F., Chang,T.H. and Johnson,L.F.
  TITLE     Growth-regulated expression and G0-specific turnover of the mRNA
            that encodes URH49, a mammalian DExH/D box protein that is highly
            related to the mRNA export protein UAP56
  JOURNAL   Nucleic Acids Res 32 (6), 1857-1865 (2004)
   PUBMED   15047853
  REMARK    GeneRIF: Regulation of URH49 mRNA expression and comparison with
            the related UAP56 RNA helicase.
            Publication Status: Online-Only
REFERENCE   9  (bases 1 to 1498)
  AUTHORS   Lehner,B., Semple,J.I., Brown,S.E., Counsell,D., Campbell,R.D. and
            Sanderson,C.M.
  TITLE     Analysis of a high-throughput yeast two-hybrid system and its use
            to predict the function of intracellular proteins encoded within
            the human MHC class III region
  JOURNAL   Genomics 83 (1), 153-167 (2004)
   PUBMED   14667819
REFERENCE   10 (bases 1 to 1498)
  AUTHORS   Peelman,L.J., Chardon,P., Nunes,M., Renard,C., Geffrotin,C.,
            Vaiman,M., Van Zeveren,A., Coppieters,W., van de Weghe,A.,
            Bouquet,Y. et al.
  TITLE     The BAT1 gene in the MHC encodes an evolutionarily conserved
            putative nuclear RNA helicase of the DEAD family
  JOURNAL   Genomics 26 (2), 210-218 (1995)
   PUBMED   7601445
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA432925.1, BC001009.2 and
            BM792110.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On May 17, 2019 this sequence version replaced NM_005804.3.
            
            Summary: This gene encodes a member of the DEAD box protein family.
            These proteins are characterized by the conserved motif
            Asp-Glu-Ala-Asp (DEAD) and are putative RNA helicases. They are
            implicated in a number of cellular processes involving alteration
            of RNA secondary structure, such as translation initiation, nuclear
            and mitochondrial splicing, and ribosome and spliceosome assembly.
            Based on their distribution patterns, some members of the DEAD box
            protein family are believed to be involved in embryogenesis,
            spermatogenesis, and cellular growth and division. This gene is
            thought to play a role in the prognosis of patients with
            gastrointestinal stromal tumors. A pseudogene of this gene is
            present on chromosome 13. Alternate splicing results in multiple
            transcript variants. Additional alternatively spliced transcript
            variants of this gene have been described, but their full-length
            nature is not known. [provided by RefSeq, Sep 2013].
            
            Transcript Variant: This variant (1) represents the longer
            transcript.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC001009.2, U90426.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000242776.9/ ENSP00000242776.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-21                DA432925.1         44-64
            22-1477             BC001009.2         1-1456
            1478-1498           BM792110.1         653-673
FEATURES             Location/Qualifiers
     source          1..1498
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="19"
                     /map="19p13.12"
     gene            1..1498
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /note="DExD-box helicase 39A"
                     /db_xref="GeneID:10212"
                     /db_xref="HGNC:HGNC:17821"
                     /db_xref="MIM:619906"
     exon            1..72
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            73..284
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     CDS             77..1360
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /EC_number="3.6.4.13"
                     /note="DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 39;
                     DEAD (Asp-Glu-Ala-Asp) box polypeptide 39A; nuclear RNA
                     helicase, DECD variant of DEAD box family; UAP56-related
                     helicase, 49 kDa; DEAD box protein 39; nuclear RNA
                     helicase URH49; DEAD-box helicase 39A"
                     /codon_start=1
                     /product="ATP-dependent RNA helicase DDX39A"
                     /protein_id="NP_005795.2"
                     /db_xref="CCDS:CCDS12308.1"
                     /db_xref="GeneID:10212"
                     /db_xref="HGNC:HGNC:17821"
                     /db_xref="MIM:619906"
                     /translation="MAEQDVENDLLDYDEEEEPQAPQESTPAPPKKDIKGSYVSIHSS
                     GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLAT
                     LQQIEPVNGQVTVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLSIKKDEEVL
                     KKNCPHVVVGTPGRILALVRNRSFSLKNVKHFVLDECDKMLEQLDMRRDVQEIFRLTP
                     HEKQCMMFSATLSKDIRPVCRKFMQDPMEVFVDDETKLTLHGLQQYYVKLKDSEKNRK
                     LFDLLDVLEFNQVIIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKD
                     FQRRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSD
                     ENDAKILNDVQDRFEVNVAELPEEIDISTYIEQSR"
     exon            285..412
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            413..505
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            506..689
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            690..808
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            809..940
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            941..1050
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            1051..1195
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            1196..1343
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            1344..1498
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1457..1462
                     /regulatory_class="polyA_signal_sequence"
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /note="hexamer: AATAAA"
     polyA_site      1477
                     /gene="DDX39A"
                     /gene_synonym="BAT1; BAT1L; DDX39; DDXL; URH49"
                     /note="major polyA site"
ORIGIN      
        1 gtctgagcgc ccggcggaaa accgaagttg gaagtgtctc ttagcagcgc gcggagaaga
       61 acggggagcc agcatcatgg cagaacagga tgtggaaaac gatcttttgg attacgatga
      121 agaggaagag ccccaggctc ctcaagagag cacaccagct ccccctaaga aagacatcaa
      181 gggatcctac gtttccatcc acagctctgg cttccgggac tttctgctga agccggagct
      241 cctgcgggcc atcgtggact gtggctttga gcatccttct gaggtccagc atgagtgcat
      301 tccccaggcc atcctgggca tggacgtcct gtgccaggcc aagtccggga tgggcaagac
      361 agcggtcttc gtgctggcca ccctacagca gattgagcct gtcaacggac aggtgacggt
      421 cctggtcatg tgccacacga gggagctggc cttccagatc agcaaggaat atgagcgctt
      481 ttccaagtac atgcccagcg tcaaggtgtc tgtgttcttc ggtggtctct ccatcaagaa
      541 ggatgaagaa gtgttgaaga agaactgtcc ccatgtcgtg gtggggaccc cgggccgcat
      601 cctggcgctc gtgcggaata ggagcttcag cctaaagaat gtgaagcact ttgtgctgga
      661 cgagtgtgac aagatgctgg agcagctgga catgcggcgg gatgtgcagg agatcttccg
      721 cctgacacca cacgagaagc agtgcatgat gttcagcgcc accctgagca aggacatccg
      781 gcctgtgtgc aggaagttca tgcaggatcc catggaggtg tttgtggacg acgagaccaa
      841 gctcacgctg cacggcctgc agcagtacta cgtcaaactc aaagacagtg agaagaaccg
      901 caagctcttt gatctcttgg atgtgctgga gtttaaccag gtgataatct tcgtcaagtc
      961 agtgcagcgc tgcatggccc tggcccagct cctcgtggag cagaacttcc cggccatcgc
     1021 catccaccgg ggcatggccc aggaggagcg cctgtcacgc tatcagcagt tcaaggattt
     1081 ccagcggcgg atcctggtgg ccaccaatct gtttggccgg gggatggaca tcgagcgagt
     1141 caacatcgtc tttaactacg acatgcctga ggactcggac acctacctgc accgggtggc
     1201 ccgggcgggt cgctttggca ccaaaggcct agccatcact tttgtgtctg acgagaatga
     1261 tgccaaaatc ctcaatgacg tccaggaccg gtttgaagtt aatgtggcag aacttccaga
     1321 ggaaatcgac atctccacat acatcgagca gagccggtaa ccaccacgtg ccagagccgc
     1381 ccacccggag ccgcccgcat gcagcttcac ctcccctttc caggcgccac tgttgagaag
     1441 ctagagattg tatgagaata aacttgttat tatggaagcc tggctcccac cccatcta
//
