LOCUS       NM_004660               4408 bp    mRNA    linear   PRI 04-OCT-2024
DEFINITION  Homo sapiens DEAD-box helicase 3 Y-linked (DDX3Y), transcript
            variant 2, mRNA.
ACCESSION   NM_004660
VERSION     NM_004660.5
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 4408)
  AUTHORS   Xiu,L., Ma,B. and Ding,L.
  TITLE     Antioncogenic roles of USP9Y and DDX3Y in lung cancer: USP9Y
            stabilizes DDX3Y by preventing its degradation through
            deubiquitination
  JOURNAL   Acta Histochem 126 (1), 152132 (2024)
   PUBMED   38217953
  REMARK    GeneRIF: Antioncogenic roles of USP9Y and DDX3Y in lung cancer:
            USP9Y stabilizes DDX3Y by preventing its degradation through
            deubiquitination.
REFERENCE   2  (bases 1 to 4408)
  AUTHORS   Umino,K., Morita,K., Ikeda,T., Kawaguchi,S.I., Nagayama,T., Ito,S.,
            Minakata,D., Ashizawa,M., Yamamoto,C., Hatano,K., Sato,K.,
            Ohmine,K., Fujiwara,S.I., Kimura,S.I., Kako,S., Doki,N., Ozawa,Y.,
            Mori,Y., Eto,T., Hiramoto,N., Nakamae,H., Kanda,J., Ichinohe,T.,
            Atsuta,Y., Nakasone,H., Morishima,S. and Kanda,Y.
  TITLE     Antibody-mediated pathogenesis of chronic GVHD through DBY/HLA
            class II complexes and induction of a GVL effect
  JOURNAL   Blood 142 (11), 1008-1021 (2023)
   PUBMED   37363859
  REMARK    GeneRIF: Antibody-mediated pathogenesis of chronic GVHD through
            DBY/HLA class II complexes and induction of a GVL effect.
REFERENCE   3  (bases 1 to 4408)
  AUTHORS   Dicke,A.K., Pilatz,A., Wyrwoll,M.J., Punab,M., Ruckert,C.,
            Nagirnaja,L., Aston,K.I., Conrad,D.F., Di Persio,S., Neuhaus,N.,
            Fietz,D., Laan,M., Stallmeyer,B. and Tuttelmann,F.
  TITLE     DDX3Y is likely the key spermatogenic factor in the AZFa region
            that contributes to human non-obstructive azoospermia
  JOURNAL   Commun Biol 6 (1), 350 (2023)
   PUBMED   36997603
  REMARK    GeneRIF: DDX3Y is likely the key spermatogenic factor in the AZFa
            region that contributes to human non-obstructive azoospermia.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 4408)
  AUTHORS   Rosner,A. and Rinkevich,B.
  TITLE     The DDX3 subfamily of the DEAD box helicases: divergent roles as
            unveiled by studying different organisms and in vitro assays
  JOURNAL   Curr Med Chem 14 (23), 2517-2525 (2007)
   PUBMED   17979704
  REMARK    Review article
REFERENCE   5  (bases 1 to 4408)
  AUTHORS   Ditton,H.J., Zimmer,J., Kamp,C., Rajpert-De Meyts,E. and Vogt,P.H.
  TITLE     The AZFa gene DBY (DDX3Y) is widely transcribed but the protein is
            limited to the male germ cells by translation control
  JOURNAL   Hum Mol Genet 13 (19), 2333-2341 (2004)
   PUBMED   15294876
REFERENCE   6  (bases 1 to 4408)
  AUTHORS   Session,D.R., Lee,G.S. and Wolgemuth,D.J.
  TITLE     Characterization of D1Pas1, a mouse autosomal homologue of the
            human AZFa region DBY, as a nuclear protein in spermatogenic cells
  JOURNAL   Fertil Steril 76 (4), 804-811 (2001)
   PUBMED   11591417
REFERENCE   7  (bases 1 to 4408)
  AUTHORS   Shen,P., Wang,F., Underhill,P.A., Franco,C., Yang,W.H., Roxas,A.,
            Sung,R., Lin,A.A., Hyman,R.W., Vollrath,D., Davis,R.W.,
            Cavalli-Sforza,L.L. and Oefner,P.J.
  TITLE     Population genetic implications from sequence variation in four Y
            chromosome genes
  JOURNAL   Proc Natl Acad Sci U S A 97 (13), 7354-7359 (2000)
   PUBMED   10861003
REFERENCE   8  (bases 1 to 4408)
  AUTHORS   Foresta,C., Ferlin,A. and Moro,E.
  TITLE     Deletion and expression analysis of AZFa genes on the human Y
            chromosome revealed a major role for DBY in male infertility
  JOURNAL   Hum Mol Genet 9 (8), 1161-1169 (2000)
   PUBMED   10767340
REFERENCE   9  (bases 1 to 4408)
  AUTHORS   Lahn,B.T. and Page,D.C.
  TITLE     Functional coherence of the human Y chromosome
  JOURNAL   Science 278 (5338), 675-680 (1997)
   PUBMED   9381176
REFERENCE   10 (bases 1 to 4408)
  AUTHORS   Fan,Y. and Silber,S.J.
  TITLE     Y Chromosome Infertility
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301513
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DC394594.1, BC034942.2,
            CR981580.1, CX783434.1, BQ718381.1, DR421958.1, BM055220.1 and
            BM995760.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_004660.4.
            
            Summary: The protein encoded by this gene is a member of the
            DEAD-box RNA helicase family, characterized by nine conserved
            motifs, included the conserved Asp-Glu-Ala-Asp (DEAD) motif. These
            motifs are thought to be involved in ATP binding, hydrolysis, RNA
            binding, and in the formation of intramolecular interactions. This
            protein shares high similarity to DDX3X, on the X chromosome, but a
            deletion of this gene is not complemented by DDX3X. Mutations in
            this gene result in male infertility, a reduction in germ cell
            numbers, and can result in Sertoli-cell only sydrome. Pseudogenes
            sharing similarity to both this gene and the DDX3X paralog are
            found on chromosome 4 and the X chromosome. Alternative splicing
            results in multiple transcript variants encoding different
            isoforms. [provided by RefSeq, Oct 2014].
            
            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 :: AF000984.1, SRR1803614.58260.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1966682, SAMEA1968832
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000336079.8/ ENSP00000336725.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-492               DC394594.1         83-574
            493-2457            BC034942.2         733-2697
            2458-2547           CR981580.1         484-573
            2548-3015           CX783434.1         5-472
            3016-3397           BQ718381.1         1-382
            3398-3741           DR421958.1         65-408
            3742-4156           BM055220.1         4-418
            4157-4408           BM995760.1         19-270              c
FEATURES             Location/Qualifiers
     source          1..4408
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="Y"
                     /map="Yq11.221"
     gene            1..4408
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /note="DEAD-box helicase 3 Y-linked"
                     /db_xref="GeneID:8653"
                     /db_xref="HGNC:HGNC:2699"
                     /db_xref="MIM:400010"
     exon            1..114
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     CDS             70..2052
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /EC_number="3.6.4.13"
                     /note="isoform 1 is encoded by transcript variant 2;
                     DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide, Y
                     chromosome; ATP-dependent RNA helicase DDX3Y; DEAD box
                     protein 3, Y-chromosomal; DEAD (Asp-Glu-Ala-Asp) box
                     polypeptide 3, Y-linked; DEAD (Asp-Glu-Ala-Asp) box
                     helicase 3, Y-linked"
                     /codon_start=1
                     /product="ATP-dependent RNA helicase DDX3Y isoform 1"
                     /protein_id="NP_004651.2"
                     /db_xref="CCDS:CCDS14782.1"
                     /db_xref="GeneID:8653"
                     /db_xref="HGNC:HGNC:2699"
                     /db_xref="MIM:400010"
                     /translation="MSHVVVKNDPELDQQLANLDLNSEKQSGGASTASKGRYIPPHLR
                     NREASKGFHDKDSSGWSCSKDKDAYSSFGSRDSRGKPGYFSERGSGSRGRFDDRGRSD
                     YDGIGNRERPGFGRFERSGHSRWCDKSVEDDWSKPLPPSERLEQELFSGGNTGINFEK
                     YDDIPVEATGSNCPPHIENFSDIDMGEIIMGNIELTRYTRPTPVQKHAIPIIKGKRDL
                     MACAQTGSGKTAAFLLPILSQIYTDGPGEALKAVKENGRYGRRKQYPISLVLAPTREL
                     AVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKI
                     GLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLAR
                     DFLDEYIFLAVGRVGSTSENITQKVVWVEDLDKRSFLLDILGATGSDSLTLVFVETKK
                     GADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNV
                     RHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNEKNMNITKDLLDLLVEAKQEVP
                     SWLENMAYEHHYKGGSRGRSKSNRFSGGFGARDYRQSSGSSSSGFGASRGSSSRSGGG
                     GYGNSRGFGGGGYGGFYNSDGYGGNYNSQGVDWWGN"
     exon            115..172
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            173..220
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            221..350
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            351..506
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            507..606
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            607..742
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            743..828
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            829..927
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            928..1088
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            1089..1233
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            1234..1378
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            1379..1560
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            1561..1678
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            1679..1832
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            1833..1972
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     exon            1973..4408
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4390..4395
                     /regulatory_class="polyA_signal_sequence"
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /note="hexamer: AATAAA"
     polyA_site      4408
                     /gene="DDX3Y"
                     /gene_synonym="DBY"
                     /note="major polyA site"
ORIGIN      
        1 agtgtaagag ttccgctatt cggtctcaca cctacagtgg actacccgat ttttcgcttc
       61 tcttcaggga tgagtcatgt ggtggtgaaa aatgaccctg aactggacca gcagcttgct
      121 aatctggacc tgaactctga aaaacagagt ggaggagcaa gtacagcgag caaagggcgc
      181 tatatacctc ctcacttaag gaacagagaa gcatctaaag gattccatga taaagacagt
      241 tcaggttgga gttgcagcaa agataaggat gcatatagca gttttgggtc tcgagattct
      301 agaggaaagc ctggttattt cagtgaacgt ggaagtggat caaggggaag atttgatgat
      361 cgtggacgga gtgactatga tggtattggc aatcgtgaaa gacctggctt tggcagattt
      421 gaacggagtg gacatagtcg ttggtgtgac aagtcagttg aagatgattg gtcaaaacca
      481 cttccaccaa gtgaacgctt ggagcaagaa ctgttttctg gaggaaacac ggggattaac
      541 tttgagaaat atgatgatat accagtagag gcaaccggca gtaactgtcc tccacatatt
      601 gagaatttta gcgatattga catgggagaa attatcatgg ggaacattga acttactcgc
      661 tatactcgtc ctactccagt gcaaaaacat gccattccta ttattaaggg aaaaagagac
      721 ttaatggctt gtgcccaaac aggatctggg aaaactgcag catttctttt acccatactg
      781 agtcagatat atacagatgg tccaggagaa gctttgaagg ctgtgaagga aaatggaagg
      841 tatgggcgcc gcaaacaata tccaatatcc ttggttttag ccccaacaag agaattggct
      901 gtacagatct atgaggaagc cagaaaattt tcctaccgat ctagagttcg tccttgtgta
      961 gtttatggtg gtgctgatat tggtcagcag attcgggact tagaacgtgg atgccacttg
     1021 ttagtagcca ctccaggacg tctagtggat atgatggaaa gaggaaagat tggattagac
     1081 ttctgcaagt acttagtgtt ggatgaagct gataggatgc tggatatggg atttgaacct
     1141 cagatacgtc gtatagttga acaagatact atgccaccaa agggcgttcg tcacaccatg
     1201 atgtttagtg ctacttttcc taaggaaata cagatgcttg ctcgtgactt tttggatgaa
     1261 tatatctttt tggctgtagg cagagtaggc tctacctctg agaacatcac acagaaagta
     1321 gtttgggtgg aagacttaga taaacggtca tttctactgg acattttagg tgcaacaggg
     1381 agtgattcac ttactttagt gtttgtggag accaaaaagg gagcagattc cctggaggat
     1441 ttcttatacc atgaaggata tgcttgtact agtattcatg gagaccggtc acagagagat
     1501 cgagaggagg cccttcacca gtttcgctca ggaaaaagcc caattctagt ggctacagct
     1561 gtggcagcac gaggactaga catttcaaat gtgagacatg ttatcaattt tgatttgcca
     1621 agtgatattg aagaatatgt gcatcgtatt ggccgtacag gacgtgtagg aaacctgggc
     1681 cttgccacct cattctttaa tgaaaaaaat atgaatatta caaaggattt gttggatctt
     1741 cttgtagaag ctaaacaaga agtgccttct tggttggaaa atatggctta tgaacaccac
     1801 tacaagggtg gcagtcgtgg acgatctaaa agtaatagat tcagtggagg atttggtgcc
     1861 agagactatc gacaaagtag tggttccagc agttctggct ttggtgctag tcgcggaagc
     1921 agcagccgca gtggtggagg tggttacggc aacagcagag gatttggtgg aggtggctat
     1981 ggaggcttct acaatagtga tggatatgga ggaaattata actcccaggg ggttgactgg
     2041 tggggcaact gaatctgctt tgcagcaaag tcacccttac aaagaagcta atatggaaac
     2101 cacatgtaac ttagccagac tatattgtgt agcttcaaga acttgcagta cattaccagc
     2161 tgtgattctc ctgataattc aagggagctc aaagtcacaa gaagaaaaat gaaaggaaaa
     2221 aacagcagcc ctattcagaa attggtttga agatgtaatt gctctagttt ggattaaact
     2281 cttcccctcc tgctttagtg ccaccccaaa ctgcatttat aattttgtga ctgaggatcg
     2341 tttgtttgtt aacgtactgt gactttaact ttagacaact tactactttg atgtcctgtt
     2401 ggctcagtaa tgctcacgat accaattgtt ttgacaaaat aaatttacta aacttggcct
     2461 aaaatcaaac cttggcacag aggtatgata caactttaac aggagtcatc aattcatcca
     2521 taaatataaa aagggaaaaa aacttaaggc agtagtctgc attaggactg tttgagtttt
     2581 gcagacttgg ggttgggaga acatcttaaa gcattaaagc atagtttttt gtatggccaa
     2641 ccttactaaa ttaagttctg acttgctcac tctatcctgg ataggcactt gggaacttac
     2701 actctttaag ccattccagt catgatgagg tggaatgtat cagtatacca attaatattt
     2761 ttgaaagagc tcttttaggt taatttaagt acagcaattt ctcatgtaat gtttagggag
     2821 tttattctaa cctaggcaaa cggcatgcta tcacaagaaa ggtttaaagc tttgataaaa
     2881 tgggggagat ttaatcagtt tttttaatgc ctgctataaa aatttgaaat attagaatgg
     2941 ccgaccatgg cagtgaccag gcctcactac aggcctggtt ggattctggt ctttaatgca
     3001 tgctagtgtt gatgtttttt ggtcaagaac ggtttaaaca ggaaggattg tgcagcaggc
     3061 tttaatttaa tgtagattca tactgctctg ttaaagctgc attgaaatgt taaaatggct
     3121 tacacttgca gactttgcaa atcttaagac taacaaatcc ttgaaatcac acagcttgca
     3181 aatacgtact aaactgcaca aggtgtgtgt tctatatgtg cagttttagc gtattttagt
     3241 tgcataggtt tccatggtat ttatagtctc ttgtgctaaa tttggccaaa gatgattgtc
     3301 caccactaaa aatgcctctc ccacttggaa ttctgtactg attttgtggc cagatgcaat
     3361 gatctttaaa aacaaatctt ttcaatggca taagaagttg acaaaaattt cttaaagtgc
     3421 aatagatttt caagtgtatt gtgccttgtt ctaaaacttt taagtaggtg cacttgacag
     3481 tattgaggtc atttgttaag gtgctatttc aattagtgta ggtttagact cttgtacatt
     3541 tctcccataa ctttttacaa agtattttgt tgcacattca gagaatttta tatatatatg
     3601 tcttgtgtgg gtgtcctcga ccttccaatc ttatttcgtc tcttggagat tgttgaatgc
     3661 agccagtgaa gaagtagatt cctaaatttt attggggacc atggaatggt agttgagaag
     3721 aaaactattt gcacacaaca gattttagat actttttgct gctagttgtg taatatttat
     3781 tgaacatttt gacaaatatt tatttttgta agcctaaaaa tgattctttg aaagtttaaa
     3841 gaaacttgac caaaagacag tacaaaaaac actggcactt gaatgttgaa tgtcaccgta
     3901 tgtgaaataa tatattttgg ggtagtgtga gcttttaatg ttaagtctgt taaacttgag
     3961 tcaaattaag cagacccggc attggcaatg tagctgtaat tttctgacaa aatttaagac
     4021 aaaattgtca acttgaaact aaaacatgcc aaggttttga tatacttgtc ttaagatatt
     4081 aatgaaacac ttctgaacac tgataggaag tgtccacatc cacaaagttt ctcttgagtt
     4141 ttgttatgtg ttttgttgtg tttgattttc agtgattgtc tggtatattt acagtcctca
     4201 aacatggtta tttctgtcag tgacttaaca ttcggtttta tcagccagca gtattcttca
     4261 gtaaataaag aatggaattg ctgaatgtaa tcattgaacc tcgagtcact gtaaaagttc
     4321 agtaattgct tattgtatta gttttagatg ctggcactgc atgtgctctg tttattctga
     4381 ttttactaaa ataaaaagtt caaaagtc
//
