DDX39B DExD-box helicase 39B [Homo sapiens (human)] - Gene

Summary

Official Symbol: DDX39Bprovided by HGNC
Official Full Name: DExD-box helicase 39Bprovided by HGNC
Primary source: HGNC:HGNC:13917
See related: Ensembl:ENSG00000198563 MIM:142560; AllianceGenome:HGNC:13917
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: BAT1; UAP56; D6S81E
Summary: This gene encodes a member of the DEAD box family of RNA-dependent ATPases that mediate ATP hydrolysis during pre-mRNA splicing. The encoded protein is an essential splicing factor required for association of U2 small nuclear ribonucleoprotein with pre-mRNA, and it also plays an important role in mRNA export from the nucleus to the cytoplasm. This gene belongs to a cluster of genes localized in the vicinity of the genes encoding tumor necrosis factor alpha and tumor necrosis factor beta. These genes are all within the human major histocompatibility complex class III region. Mutations in this gene may be associated with rheumatoid arthritis. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on both chromosomes 6 and 11. Read-through transcription also occurs between this gene and the upstream ATP6V1G2 (ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2) gene. [provided by RefSeq, Feb 2011]
Expression: Ubiquitous expression in endometrium (RPKM 76.9), ovary (RPKM 76.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.33

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (31530226..31542003, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (31383322..31395095, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (31498003..31509780, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Parsing the roles of DExD-box proteins DDX39A and DDX39B in alternative RNA splicing.
Title: Parsing the roles of DExD-box proteins DDX39A and DDX39B in alternative RNA splicing.
Terminal regions of UAP56 and URH49 are required for their distinct complex formation functioning to an essential role in mRNA processing and export.
Title: Terminal regions of UAP56 and URH49 are required for their distinct complex formation functioning to an essential role in mRNA processing and export.
Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes.
Title: Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes.
DDX39B facilitates the malignant progression of hepatocellular carcinoma via activation of SREBP1-mediated de novo lipid synthesis.
Title: DDX39B facilitates the malignant progression of hepatocellular carcinoma via activation of SREBP1-mediated de novo lipid synthesis.
Structural basis for high-order complex of SARNP and DDX39B to facilitate mRNP assembly.
Title: Structural basis for high-order complex of SARNP and DDX39B to facilitate mRNP assembly.
RETSAT associates with DDX39B to promote fork restarting and resistance to gemcitabine based chemotherapy in pancreatic ductal adenocarcinoma.
Title: RETSAT associates with DDX39B to promote fork restarting and resistance to gemcitabine based chemotherapy in pancreatic ductal adenocarcinoma.
DDX39B drives colorectal cancer progression by promoting the stability and nuclear translocation of PKM2.
Title: DDX39B drives colorectal cancer progression by promoting the stability and nuclear translocation of PKM2.
DDX39B Predicts Poor Survival and Associated with Clinical Benefit of Anti-PD-L1 Therapy in ccRCC.
Title: DDX39B Predicts Poor Survival and Associated with Clinical Benefit of Anti-PD-L1 Therapy in ccRCC.
The DDX39B/FUT3/TGFbetaR-I axis promotes tumor metastasis and EMT in colorectal cancer.
Title: The DDX39B/FUT3/TGFβR-I axis promotes tumor metastasis and EMT in colorectal cancer.
Suppression of DDX39B sensitizes ovarian cancer cells to DNA-damaging chemotherapeutic agents via destabilizing BRCA1 mRNA.
Title: Suppression of DDX39B sensitizes ovarian cancer cells to DNA-damaging chemotherapeutic agents via destabilizing BRCA1 mRNA.

Submit: New GeneRIF Correction See all GeneRIFs (51)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A whole-genome association study of major determinants for allopurinol-related Stevens-Johnson syndrome and toxic epidermal necrolysis in Japanese patients. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies identifies three new risk loci for atopic dermatitis. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (DDX39B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (DDX39B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (DDX39B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (DDX39B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Rev	rev	HIV-1 Rev specifically inhibits the association of ALY/REF and UAP56 with spliced RRE-containing RNA	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH1521 (e-PCR)
- UniSTS:91914

CH241-100F12_SP6 (e-PCR)
- UniSTS:505626

D17H6S81E-1 (e-PCR), detects polymorphism
- UniSTS:142121

SHGC-172533 (e-PCR)
- UniSTS:184443

Readthrough ATP6V1G2-DDX39B

Readthrough gene: ATP6V1G2-DDX39B, Included gene: ATP6V1G2

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	EXP Inferred from Experiment more info	PubMed
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent activity, acting on RNA	IDA Inferred from Direct Assay more info	PubMed
enables ATP-dependent protein binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables RNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables U4 snRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables U6 snRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA export from nucleus	TAS Traceable Author Statement more info
involved_in RNA secondary structure unwinding	IDA Inferred from Direct Assay more info	PubMed
involved_in RNA splicing	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in mRNA export from nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA export from nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA export from nucleus	IGI Inferred from Genetic Interaction more info	PubMed
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	IGI Inferred from Genetic Interaction more info	PubMed
involved_in spliceosomal complex assembly	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of U4 snRNP	IDA Inferred from Direct Assay more info	PubMed
part_of U6 snRNP	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear speck	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of spliceosomal complex	IDA Inferred from Direct Assay more info	PubMed
part_of transcription export complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: spliceosome RNA helicase DDX39B

Names: 56 kDa U2AF65-associated protein; ATP-dependent RNA helicase p47; DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B; DEAD-box helicase 39B; HLA-B-associated transcript 1 protein; nuclear RNA helicase (DEAD family); spliceosome RNA helicase BAT1

NP_004631.1

EC 3.6.4.13

NP_542165.1

EC 3.6.4.13

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_004640.7 → NP_004631.1 spliceosome RNA helicase DDX39B

See identical proteins and their annotated locations for NP_004631.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Both variants 1 and 2 encode the same protein.

Source sequence(s)

BM993499, DA272922, Z37166

Consensus CDS

CCDS4697.1

UniProtKB/Swiss-Prot

B0S8C0, O43496, Q0EFA1, Q13838, Q2L6F9, Q53GL9, Q5RJ64, Q5RJ66, Q5ST94, Q5STB4, Q5STB5, Q5STB7, Q5STB8, Q5STU4, Q5STU5, Q5STU6, Q5STU8, Q71V76

UniProtKB/TrEMBL

A0A024RCM3, Q5HYT9, Q5RJ68, Q5STU3

Related

ENSP00000379475.1, ENST00000396172.6

Conserved Domains (2) summary

cd18787
Location:262 → 391

SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases

cd17950
Location:44 → 251

DEADc_DDX39; DEAD-box helicase domain of DEAD box protein 39
NM_080598.6 → NP_542165.1 spliceosome RNA helicase DDX39B

See identical proteins and their annotated locations for NP_542165.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternative splice site in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same protein.

Source sequence(s)

AL662801, BC000361, BM993499, DA272922

Consensus CDS

CCDS4697.1

UniProtKB/Swiss-Prot

B0S8C0, O43496, Q0EFA1, Q13838, Q2L6F9, Q53GL9, Q5RJ64, Q5RJ66, Q5ST94, Q5STB4, Q5STB5, Q5STB7, Q5STB8, Q5STU4, Q5STU5, Q5STU6, Q5STU8, Q71V76

UniProtKB/TrEMBL

A0A024RCM3, Q5HYT9, Q5RJ68, Q5STU3

Related

ENSP00000416269.1, ENST00000458640.5

Conserved Domains (2) summary

cd18787
Location:262 → 391

SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases

cd17950
Location:44 → 251

DEADc_DDX39; DEAD-box helicase domain of DEAD box protein 39

RNA

NR_037852.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK298194, BM993499, DA272922