Ddx39b DExD-box helicase 39B [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ddx39bprovided by RGD
Official Full Name: DExD-box helicase 39Bprovided by RGD
Primary source: RGD:70923
See related: EnsemblRapid:ENSRNOG00000000841 AllianceGenome:RGD:70923
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: p47; Bat1; Bat1a
Summary: Predicted to enable several functions, including ATP hydrolysis activity; ATP-dependent protein binding activity; and RNA binding activity. Involved in several processes, including positive regulation of cell growth involved in cardiac muscle cell development; positive regulation of macromolecule biosynthetic process; and positive regulation of vascular associated smooth muscle cell proliferation. Located in nuclear matrix. Part of protein-containing complex. Human ortholog(s) of this gene implicated in type 1 diabetes mellitus. Orthologous to human DDX39B (DExD-box helicase 39B). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 912.2), Spleen (RPKM 608.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20p12

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (3577200..3589651, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (3547702..3585064, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (4806103..4818600, complement)

Chromosome 20 - NC_086038.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

These findings suggest that UAP56 is a regulator of VSMC proliferation and identify UAP56 as a target for preventing vascular proliferative disease.
Title: UAP56 is an important mediator of angiotensin II/platelet derived growth factor induced vascular smooth muscle cell DNA synthesis and proliferation.
To determine whether the rat possesses an H2-D orthologue, we sequenced a cosmid clone that contains rat Bat1 and an adjacent class I gene, RT1.46 (l).
Title: Does the rat have an H2-D orthologue next to Bat1?

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Bat1_microsatellite (e-PCR)
- UniSTS:240926

D20Yum47 (e-PCR)
- UniSTS:526137

RH126881 (e-PCR)
- UniSTS:209757

RH144334 (e-PCR)
- UniSTS:233579

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
enables ATP-dependent protein binding	IEA Inferred from Electronic Annotation more info
enables ATP-dependent protein binding	ISO Inferred from Sequence Orthology more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables U4 snRNA binding	IEA Inferred from Electronic Annotation more info
enables U4 snRNA binding	ISO Inferred from Sequence Orthology more info
enables U6 snRNA binding	IEA Inferred from Electronic Annotation more info
enables U6 snRNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA secondary structure unwinding	IEA Inferred from Electronic Annotation more info
involved_in RNA secondary structure unwinding	ISO Inferred from Sequence Orthology more info
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in RNA splicing	ISO Inferred from Sequence Orthology more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in liver development	IEP Inferred from Expression Pattern more info	PubMed
involved_in mRNA export from nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA export from nucleus	IEA Inferred from Electronic Annotation more info
involved_in mRNA export from nucleus	ISO Inferred from Sequence Orthology more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in mRNA transport	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell growth involved in cardiac muscle cell development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of translation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of vascular associated smooth muscle cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spliceosomal complex assembly	IEA Inferred from Electronic Annotation more info
involved_in spliceosomal complex assembly	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of U4 snRNP	IEA Inferred from Electronic Annotation more info
part_of U4 snRNP	ISO Inferred from Sequence Orthology more info
part_of U6 snRNP	IEA Inferred from Electronic Annotation more info
part_of U6 snRNP	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in nuclear matrix	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of spliceosomal complex	IEA Inferred from Electronic Annotation more info
part_of spliceosomal complex	ISO Inferred from Sequence Orthology more info
part_of transcription export complex	IEA Inferred from Electronic Annotation more info
part_of transcription export complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: spliceosome RNA helicase Ddx39b

Names: 56 kDa U2AF65-associated protein; ATP-dependent RNA helicase p47; D17H6S81E-1; D20H6S81e; DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B; DEAD box protein UAP56; DEAD-box helicase 39B; HLA-B associated transcript 1; HLA-B-associated transcript 1A; Nuclear RNA helicase; spliceosome RNA helicase Bat1

NP_579834.2

EC 3.6.4.13

XP_063134999.1

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_133300.3 → NP_579834.2 spliceosome RNA helicase Ddx39b

See identical proteins and their annotated locations for NP_579834.2

Status: VALIDATED

Source sequence(s)

BC080243, DY309526

UniProtKB/Swiss-Prot

Q63413, Q811A6, Q8R2G9

UniProtKB/TrEMBL

A0A8I6A103, A6KTX4

Related

ENSRNOP00000001115.4, ENSRNOT00000001115.8

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