LOCUS       NM_197982               1659 bp    mRNA    linear   ROD 12-NOV-2024
DEFINITION  Mus musculus DEAD box helicase 39a (Ddx39a), transcript variant 2,
            mRNA.
ACCESSION   NM_197982
VERSION     NM_197982.3
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 1659)
  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 1659)
  AUTHORS   Cesari,E., Farini,D., Medici,V., Ehrmann,I., Guerra,M., Testa,E.,
            Naro,C., Geloso,M.C., Pagliarini,V., La Barbera,L., D'Amelio,M.,
            Orsini,T., Vecchioli,S.F., Tamagnone,L., Fort,P., Viscomi,M.T.,
            Elliott,D.J. and Sette,C.
  TITLE     Differential expression of paralog RNA binding proteins establishes
            a dynamic splicing program required for normal cerebral cortex
            development
  JOURNAL   Nucleic Acids Res 52 (8), 4167-4184 (2024)
   PUBMED   38324473
REFERENCE   3  (bases 1 to 1659)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   4  (bases 1 to 1659)
  AUTHORS   Bedogni,F. and Hevner,R.F.
  TITLE     Cell-Type-Specific Gene Expression in Developing Mouse Neocortex:
            Intermediate Progenitors Implicated in Axon Development
  JOURNAL   Front Mol Neurosci 14, 686034 (2021)
   PUBMED   34321999
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1659)
  AUTHORS   Brandsma,I., Sato,K., van Rossum-Fikkert,S.E., van Vliet,N.,
            Sleddens,E., Reuter,M., Odijk,H., van den Tempel,N.,
            Dekkers,D.H.W., Bezstarosti,K., Demmers,J.A.A., Maas,A.,
            Lebbink,J., Wyman,C., Essers,J., van Gent,D.C., Baarends,W.M.,
            Knipscheer,P., Kanaar,R. and Zelensky,A.N.
  TITLE     HSF2BP Interacts with a Conserved Domain of BRCA2 and Is Required
            for Mouse Spermatogenesis
  JOURNAL   Cell Rep 27 (13), 3790-3798 (2019)
   PUBMED   31242413
REFERENCE   6  (bases 1 to 1659)
  AUTHORS   Kuramitsu,Y., Suenaga,S., Wang,Y., Tokuda,K., Kitagawa,T.,
            Tanaka,T., Akada,J., Maehara,S., Maehara,Y. and Nakamura,K.
  TITLE     Up-regulation of DDX39 in human pancreatic cancer cells with
            acquired gemcitabine resistance compared to gemcitabine-sensitive
            parental cells
  JOURNAL   Anticancer Res 33 (8), 3133-3136 (2013)
   PUBMED   23898070
  REMARK    GeneRIF: The expression of DDX39 in gemcitabine-sensitive KLM1 and
            -resistant KLM1-R cells was compared.
REFERENCE   7  (bases 1 to 1659)
  AUTHORS   Wisskirchen,C., Ludersdorfer,T.H., Muller,D.A., Moritz,E. and
            Pavlovic,J.
  TITLE     Interferon-induced antiviral protein MxA interacts with the
            cellular RNA helicases UAP56 and URH49
  JOURNAL   J Biol Chem 286 (40), 34743-34751 (2011)
   PUBMED   21859714
  REMARK    GeneRIF: Mx proteins exert their antiviral activity against IAV by
            interfering with the function of the RNA helicases UAP56 and URH49
REFERENCE   8  (bases 1 to 1659)
  AUTHORS   McKee,A.E., Minet,E., Stern,C., Riahi,S., Stiles,C.D. and
            Silver,P.A.
  TITLE     A genome-wide in situ hybridization map of RNA-binding proteins
            reveals anatomically restricted expression in the developing mouse
            brain
  JOURNAL   BMC Dev Biol 5, 14 (2005)
   PUBMED   16033648
  REMARK    Publication Status: Online-Only
REFERENCE   9  (bases 1 to 1659)
  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   10 (bases 1 to 1659)
  AUTHORS   Piao,Y., Ko,N.T., Lim,M.K. and Ko,M.S.
  TITLE     Construction of long-transcript enriched cDNA libraries from
            submicrogram amounts of total RNAs by a universal PCR amplification
            method
  JOURNAL   Genome Res 11 (9), 1553-1558 (2001)
   PUBMED   11544199
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC164432.3 and AK145927.1.
            
            On Dec 12, 2010 this sequence version replaced NM_197982.2.
            
            Transcript Variant: This variant (2) differs in the 5' UTR compared
            to variant 1. Variants 1 and 2 both encode the same isoform (a).
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: AK145927.1, BC020134.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            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
            1-61                AC164432.3         53292-53352         c
            62-1647             AK145927.1         5-1590
            1648-1659           AC164432.3         45178-45189         c
FEATURES             Location/Qualifiers
     source          1..1659
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="8"
                     /map="8 40.22 cM"
     gene            1..1659
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /note="DEAD box helicase 39a"
                     /db_xref="GeneID:68278"
                     /db_xref="MGI:MGI:1915528"
     exon            1..161
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            162..373
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     CDS             166..1449
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /EC_number="3.6.4.13"
                     /note="isoform a is encoded by transcript variant 2;
                     DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 39;
                     UAP56-related helicase, 49 kDa; ATP-dependent RNA helicase
                     DDX39; ATP-dependent RNA helicase DDX39A; DEAD box protein
                     39; DEAD (Asp-Glu-Ala-Asp) box polypeptide 39"
                     /codon_start=1
                     /product="ATP-dependent RNA helicase DDX39A isoform a"
                     /protein_id="NP_932099.2"
                     /db_xref="CCDS:CCDS22460.1"
                     /db_xref="GeneID:68278"
                     /db_xref="MGI:MGI:1915528"
                     /translation="MAEQDVENELLDYDEDEEPQAPQESTPAPPKKDVKGSYVSIHSS
                     GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLAT
                     LQQIEPVNGQVSVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLSIKKDEDVL
                     KKNCPHVVVGTPGRILALVRSRSLNLRNVKHFVLDECDKMLEQLDMRRDVQEIFRLTP
                     HEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKLTLHGLQQYYVKLKDSEKNRK
                     LFDLLDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKD
                     FQRRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAVTFVSD
                     ENDAKILNDVQDRFEVNVAELPEEIDISTYIEQSR"
     exon            374..501
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            502..594
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            595..778
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            779..897
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            898..1029
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            1030..1139
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            1140..1284
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            1285..1432
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     exon            1433..1659
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1567..1572
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /note="hexamer: AATAAA"
     polyA_site      1582
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /note="major polyA site"
     polyA_site      1585
                     /gene="Ddx39a"
                     /gene_synonym="2610307C23Rik; BAT1; Ddx39; DDXL; URH49"
                     /note="major polyA site"
ORIGIN      
        1 aaccatcatc ctttcctctg ttgagtgata agccagctat ccagtgagcg agactcgagt
       61 tgggctccag gcaggaagca ctgtagcgcg cgtccagggt cgcggcgtag aaccggacgg
      121 gtggctctct ttgcagctcg cggaggcgaa ccgggcggca gtgccatggc agaacaggat
      181 gtggaaaatg aacttttgga ttatgatgaa gatgaagagc cccaggcacc ccaggagagc
      241 actccagctc ccccgaagaa agatgtcaaa ggatcttatg tctccatcca cagttctggc
      301 ttccgggact ttctactgaa gccagagctc ctgagagcta tagttgactg tggctttgag
      361 catccttcag aggtccagca tgagtgtatt ccccaggcca ttctgggtat ggatgtcctg
      421 tgccaggcca agtctgggat gggcaagaca gctgtgtttg tgctggccac cctgcagcag
      481 attgagcctg tcaatggcca ggtatcagtc ctggtcatgt gccacacgag ggagctggcc
      541 ttccagatca gcaaggagta tgagcgcttc tctaagtaca tgcccagtgt taaggtttct
      601 gtgttctttg gaggcctctc cattaagaag gatgaagatg tgttgaagaa gaactgtcct
      661 catgttgtgg tggggacacc aggccggatc ctggcacttg tgcggagcag gagcctcaac
      721 ctgaggaatg tgaagcactt tgtgctagat gaatgtgaca agatgctgga acagctggac
      781 atgcgccggg atgtacagga gatctttcgt ctgacacccc acgagaagca gtgtatgatg
      841 ttcagcgcca ccctgagcaa ggagatccgg ccagtctgca ggaagttcat gcaggatcct
      901 atggaggtgt ttgtggacga cgagaccaag ctcacactgc atgggctgca gcagtattac
      961 gtcaagctca aggacagtga gaagaaccgt aagctcttcg acctcctcga cgtgctagag
     1021 tttaaccagg tggtgatctt tgtcaagtct gtgcaacgct gcatggccct ggcccagctc
     1081 ctagtggagc agaatttccc agctatcgct attcaccgag gcatggccca ggaggagcgc
     1141 ctgtcccgat accagcagtt caaggacttc cagcgacgaa tcctggtggc tactaatctg
     1201 tttggcagag gtatggacat tgagcgagtc aacattgtct tcaactatga catgccagag
     1261 gactcagaca cctaccttca ccgagtggct cgtgctggtc gctttggtac caagggcctg
     1321 gcagtcactt ttgtatcgga tgaaaatgat gccaaaatcc ttaatgatgt tcaggaccgg
     1381 tttgaagtga atgtagctga gcttccagag gaaatagata tctccacata cattgagcag
     1441 agccggtaac cgtatgtgta gccagggcaa catggccact ctctttccca cctgctgctt
     1501 cagaacctct ttctaggtga caaatcgatg tctcttttta ttgttccaaa gctttagtga
     1561 tgtaagaata aacttttatt gtgaatgcat ggctccagcc ccatcccttt cggtcaacat
     1621 ctcatggggt tgggtcaagc cagcaaactt ctcaccagc
//
