Human Gene DDX41 (ENST00000330503.12_7) from GENCODE V47lift37
  Description: DEAD-box helicase 41, transcript variant 1 (from RefSeq NM_016222.4)
Gencode Transcript: ENST00000330503.12_7
Gencode Gene: ENSG00000183258.12_12
Transcript (Including UTRs)
   Position: hg19 chr5:176,938,578-176,943,962 Size: 5,385 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr5:176,938,792-176,943,946 Size: 5,155 Coding Exon Count: 17 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:176,938,578-176,943,962)mRNA (may differ from genome)Protein (622 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DDX41_HUMAN
DESCRIPTION: RecName: Full=Probable ATP-dependent RNA helicase DDX41; EC=3.6.4.13; AltName: Full=DEAD box protein 41; AltName: Full=DEAD box protein abstrakt homolog;
FUNCTION: Probable ATP-dependent RNA helicase. Is required during post-transcriptional gene expression. May be involved in pre-mRNA splicing.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Identified in the spliceosome C complex.
SUBCELLULAR LOCATION: Nucleus (Potential).
SIMILARITY: Belongs to the DEAD box helicase family. DDX41 subfamily.
SIMILARITY: Contains 1 CCHC-type zinc finger.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.
SEQUENCE CAUTION: Sequence=CAE46035.1; Type=Miscellaneous discrepancy; Note=Intron retention;

-  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: DDX41
Diseases sorted by gene-association score: myeloproliferative/lymphoproliferative neoplasms, familial* (1305), ddx41-related susceptibility to familial myeloproliferative/lymphoproliferative neoplasms* (525), cardiovascular syphilis (15), late congenital syphilis (11), focal chorioretinitis (10), tertiary syphilis (9), latent syphilis (7), primary syphilis (7), acute myeloid leukemia, flt3-related (7), tertiary neurosyphilis (7), von economo's disease (6), congenital syphilis (6), heart block, congenital (6), autoimmune neuropathy (6), autoimmune disease of endocrine system (6), secondary syphilis (6), autoimmune disease of central nervous system (5), robinow syndrome, autosomal dominant 1 (5), tabes dorsalis (5), eumycotic mycetoma (5), leukemia, acute myeloid (5), fish allergy (5), cd3gamma deficiency (5), cercarial dermatitis (5), retinitis pigmentosa 30 (5), hypersensitivity reaction disease (4), retinitis pigmentosa 42 (4), asymptomatic neurosyphilis (4), neuromuscular junction disease (4), herpes gestationis (4), bartter syndrome, type 3 (4), tonsil cancer (4), immune system disease (1), primary bacterial infectious disease (1)
* = 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: 38.21 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1027.08 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 -2.4016-0.150 Picture PostScript Text
3' UTR -52.50214-0.245 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
IPR014014 - RNA_helicase_DEAD_Q_motif
IPR001878 - Znf_CCHC

Pfam Domains:
PF00098 - Zinc knuckle
PF00270 - DEAD/DEAH box helicase
PF00271 - Helicase conserved C-terminal domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
57756 - Retrovirus zinc finger-like domains

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2P6N - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9UJV9
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 orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  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:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0006915 apoptotic process
GO:0008283 cell proliferation
GO:0008380 RNA splicing
GO:0010501 RNA secondary structure unwinding
GO:0030154 cell differentiation
GO:0032481 positive regulation of type I interferon production
GO:0035458 cellular response to interferon-beta
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0051607 defense response to virus

Cellular Component:
GO:0005634 nucleus
GO:0005681 spliceosomal complex
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol
GO:0016020 membrane
GO:0071013 catalytic step 2 spliceosome


-  Descriptions from all associated GenBank mRNAs
  AL137455 - Homo sapiens mRNA; cDNA DKFZp761G089 (from clone DKFZp761G089); partial cds.
AK026117 - Homo sapiens cDNA: FLJ22464 fis, clone HRC10141, highly similar to AF195417 Homo sapiens DEAD-box protein abstrakt (ABS) mRNA.
BX641072 - Homo sapiens mRNA; cDNA DKFZp686G07210 (from clone DKFZp686G07210).
BC067902 - Homo sapiens cDNA clone IMAGE:5299215, containing frame-shift errors.
AF195417 - Homo sapiens DEAD-box protein abstrakt (ABS) mRNA, complete cds.
BC015476 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 41, mRNA (cDNA clone MGC:8828 IMAGE:3917178), complete cds.
AK001255 - Homo sapiens cDNA FLJ10393 fis, clone NT2RM4000191, weakly similar to PUTATIVE ATP-DEPENDENT RNA HELICASE PL10.
AK092585 - Homo sapiens cDNA FLJ35266 fis, clone PROST2005131, highly similar to Homo sapiens DEAD-box protein abstrakt (ABS) mRNA.
AX747613 - Sequence 1138 from Patent EP1308459.
AK027768 - Homo sapiens cDNA FLJ14862 fis, clone PLACE1001739, weakly similar to PUTATIVE ATP-DEPENDENT RNA HELICASE PL10.
AK091774 - Homo sapiens cDNA FLJ34455 fis, clone HLUNG2002648, highly similar to Probable ATP-dependent RNA helicase DDX41 (EC 3.6.1.-).
AK091545 - Homo sapiens cDNA FLJ34226 fis, clone FCBBF3023667, highly similar to Homo sapiens DEAD-box protein abstrakt (ABS) mRNA.
AX747049 - Sequence 574 from Patent EP1308459.
AK222598 - Homo sapiens mRNA for DEAD-box protein abstrakt variant, clone: CAS06147.
JD371383 - Sequence 352407 from Patent EP1572962.
JD514506 - Sequence 495530 from Patent EP1572962.
JD123051 - Sequence 104075 from Patent EP1572962.
JD494427 - Sequence 475451 from Patent EP1572962.
JD159357 - Sequence 140381 from Patent EP1572962.
JF432312 - Synthetic construct Homo sapiens clone IMAGE:100073497 DEAD (Asp-Glu-Ala-Asp) box polypeptide 41 (DDX41) gene, encodes complete protein.
KJ893910 - Synthetic construct Homo sapiens clone ccsbBroadEn_03304 DDX41 gene, encodes complete protein.
AK315491 - Homo sapiens cDNA, FLJ96554, Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 41 (DDX41),mRNA.
AB587378 - Synthetic construct DNA, clone: pF1KB5059, Homo sapiens DDX41 gene for DEAD (Asp-Glu-Ala-Asp) box polypeptide 41, without stop codon, in Flexi system.
DL492130 - Novel nucleic acids.
CU677309 - Synthetic construct Homo sapiens gateway clone IMAGE:100020371 5' read DDX41 mRNA.
AK310525 - Homo sapiens cDNA, FLJ17567.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UJV9 (Reactome details) participates in the following event(s):

R-HSA-3134822 DDX41 binds viral dsDNA
R-HSA-3134946 DDX41 ubiquitination by TRIM21
R-HSA-9013869 DDX41 binds bacterial c-di-AMP, c-di-GMP
R-HSA-1834941 STING mediated induction of host immune responses
R-HSA-3134975 Regulation of innate immune responses to cytosolic DNA
R-HSA-1834949 Cytosolic sensors of pathogen-associated DNA
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: ABS, B2RDC8, DDX41_HUMAN, ENST00000330503.1, ENST00000330503.10, ENST00000330503.11, ENST00000330503.2, ENST00000330503.3, ENST00000330503.4, ENST00000330503.5, ENST00000330503.6, ENST00000330503.7, ENST00000330503.8, ENST00000330503.9, NM_016222, Q96BK6, Q96K05, Q9NT96, Q9NW04, Q9UJV9, uc317szj.1, uc317szj.2
UCSC ID: ENST00000330503.12_7
RefSeq Accession: NM_016222.4
Protein: Q9UJV9 (aka DDX41_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene DDX41:
ddx41-mds (DDX41-Associated Familial Myelodysplastic Syndrome and Acute Myeloid Leukemia)

-  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.