Human Gene DDX3Y (ENST00000336079.8_4) from GENCODE V47lift37
  Description: DEAD-box helicase 3 Y-linked, transcript variant 13 (from RefSeq NR_136724.1)
Gencode Transcript: ENST00000336079.8_4
Gencode Gene: ENSG00000067048.17_11
Transcript (Including UTRs)
   Position: hg19 chrY:15,016,779-15,032,390 Size: 15,612 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chrY:15,016,848-15,030,034 Size: 13,187 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrY:15,016,779-15,032,390)mRNA (may differ from genome)Protein (660 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DDX3Y_HUMAN
DESCRIPTION: RecName: Full=ATP-dependent RNA helicase DDX3Y; EC=3.6.4.13; AltName: Full=DEAD box protein 3, Y-chromosomal;
FUNCTION: Probable ATP-dependent RNA helicase. May play a role in spermatogenesis.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: May interact with TDRD3.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Shuttles between the nucleus and the cytoplasm in an XPO1-dependent manner.
TISSUE SPECIFICITY: Testis-specific. Expressed predominantly in spermatogonia.
DISEASE: Note=DDX3Y is located in the 'azoospermia factor a' (AZFa) region on chromosome Y which is deleted in Sertoli cell- only syndrome. This is an infertility disorder in which no germ cells are visible in seminiferous tubules leading to azoospermia.
SIMILARITY: Belongs to the DEAD box helicase family. DDX3/DED1 subfamily.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/DDX3Y";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: DDX3Y
Diseases sorted by gene-association score: male infertility (20), sertoli cell-only syndrome (19), azoospermia (16), partial deletion of y* (12), infertility (11), y chromosome infertility (10), male reproductive system disease (6), spermatocytoma (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 36.20 RPKM in Testis
Total median expression: 681.05 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -12.1069-0.175 Picture PostScript Text
3' UTR -576.602356-0.245 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011545 - DNA/RNA_helicase_DEAD/DEAH_N
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR000629 - RNA-helicase_DEAD-box_CS
IPR014014 - RNA_helicase_DEAD_Q_motif

Pfam Domains:
PF00270 - DEAD/DEAH box helicase
PF00271 - Helicase conserved C-terminal domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
103515 - Autotransporter

ModBase Predicted Comparative 3D Structure on O15523
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0004004 ATP-dependent RNA helicase activity
GO:0004386 helicase activity
GO:0005524 ATP binding
GO:0016787 hydrolase activity

Biological Process:
GO:0006413 translational initiation
GO:0007059 chromosome segregation
GO:0010468 regulation of gene expression
GO:0010501 RNA secondary structure unwinding

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0036464 cytoplasmic ribonucleoprotein granule


-  Descriptions from all associated GenBank mRNAs
  BC034942 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked, mRNA (cDNA clone MGC:25989 IMAGE:4826417), complete cds.
AK303638 - Homo sapiens cDNA FLJ53122 complete cds, highly similar to ATP-dependent RNA helicase DDX3Y (EC 3.6.1.-).
AK303176 - Homo sapiens cDNA FLJ53946 complete cds, highly similar to ATP-dependent RNA helicase DDX3Y (EC 3.6.1.-).
AK307884 - Homo sapiens cDNA, FLJ97832.
BC011022 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked, mRNA (cDNA clone IMAGE:4272736), with apparent retained intron.
AF000985 - Homo sapiens dead box, Y isoform (DBY) mRNA, alternative transcript 1, complete cds.
AF000984 - Homo sapiens dead box, Y isoform (DBY) mRNA, alternative transcript 2, complete cds.
JD500348 - Sequence 481372 from Patent EP1572962.
AK310382 - Homo sapiens cDNA, FLJ17424.
AK296366 - Homo sapiens cDNA FLJ59914 complete cds, highly similar to ATP-dependent RNA helicase DDX3Y (EC 3.6.1.-).
DL492087 - Novel nucleic acids.
DL490631 - Novel nucleic acids.
AK302172 - Homo sapiens cDNA FLJ50912 complete cds, highly similar to ATP-dependent RNA helicase DDX3Y (EC 3.6.1.-).
DQ574619 - Homo sapiens piRNA piR-42731, complete sequence.
JD046532 - Sequence 27556 from Patent EP1572962.
JD398911 - Sequence 379935 from Patent EP1572962.
JD562421 - Sequence 543445 from Patent EP1572962.
JD562804 - Sequence 543828 from Patent EP1572962.
JD564923 - Sequence 545947 from Patent EP1572962.
JD186210 - Sequence 167234 from Patent EP1572962.
JD559187 - Sequence 540211 from Patent EP1572962.
JD247420 - Sequence 228444 from Patent EP1572962.
JD468318 - Sequence 449342 from Patent EP1572962.
JD237906 - Sequence 218930 from Patent EP1572962.
JD495393 - Sequence 476417 from Patent EP1572962.
JD527281 - Sequence 508305 from Patent EP1572962.
JD455163 - Sequence 436187 from Patent EP1572962.
JD564861 - Sequence 545885 from Patent EP1572962.
JD080341 - Sequence 61365 from Patent EP1572962.
JD357070 - Sequence 338094 from Patent EP1572962.
JD490116 - Sequence 471140 from Patent EP1572962.
JD374793 - Sequence 355817 from Patent EP1572962.
JD298469 - Sequence 279493 from Patent EP1572962.
JD280150 - Sequence 261174 from Patent EP1572962.
JD449544 - Sequence 430568 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DK29, B4DXX7, DBY , DDX3Y_HUMAN, ENST00000336079.1, ENST00000336079.2, ENST00000336079.3, ENST00000336079.4, ENST00000336079.5, ENST00000336079.6, ENST00000336079.7, NR_136724, O15523, Q8IYV7, uc317ukw.1, uc317ukw.2
UCSC ID: ENST00000336079.8_4
RefSeq Accession: NM_004660.5
Protein: O15523 (aka DDX3Y_HUMAN or DDXY_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene DDX3Y:
yci (Y Chromosome Infertility)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.