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DDX31 DEAD-box helicase 31 [ Homo sapiens (human) ]

Gene ID: 64794, updated on 3-Apr-2024

Summary

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Official Symbol
DDX31provided by HGNC
Official Full Name
DEAD-box helicase 31provided by HGNC
Primary source
HGNC:HGNC:16715
See related
Ensembl:ENSG00000125485 MIM:616533; AllianceGenome:HGNC:16715
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
PPP1R25
Summary
DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a member of this family. The function of this member has not been determined. Alternative splicing of this gene generates multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2016]
Expression
Ubiquitous expression in thyroid (RPKM 4.3), ovary (RPKM 2.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
9q34.13
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (132592997..132669983, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (144804196..144881203, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (135468384..135545370, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene cilia and flagella associated protein 77 Neighboring gene uncharacterized LOC124902293 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:135406706-135406978 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20434 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135462359-135463211 Neighboring gene NANOG hESC enhancer GRCh37_chr9:135467821-135468322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135486212-135486944 Neighboring gene BarH like homeobox 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135545227-135546094 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29221 Neighboring gene general transcription factor IIIC subunit 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135597764-135598270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135599285-135599790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135608498-135608998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135608999-135609499 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:135620695-135621194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29222 Neighboring gene Sharpr-MPRA regulatory region 7884 Neighboring gene adenylate kinase 8 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:135683689-135684190 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:135711155-135711317 Neighboring gene U6 spliceosomal RNA

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A DDX31/Mutant-p53/EGFR Axis Promotes Multistep Progression of Muscle-Invasive Bladder Cancer. Daizumoto K, et al. Cancer Res, 2018 May 1. PMID 29440146
  2. The human DDX and DHX gene families of putative RNA helicases. Abdelhaleem M, et al. Genomics, 2003 Jun. PMID 12782131
  3. DDX31 regulates the p53-HDM2 pathway and rRNA gene transcription through its interaction with NPM1 in renal cell carcinomas. Fukawa T, et al. Cancer Res, 2012 Nov 15. PMID 23019224
  4. LRF maintains genome integrity by regulating the non-homologous end joining pathway of DNA repair. Liu XS, et al. Nat Commun, 2015 Oct 8. PMID 26446488, Free PMC Article
  5. Functional proteomic analysis of human nucleolus. Scherl A, et al. Mol Biol Cell, 2002 Nov. PMID 12429849, Free PMC Article

See all (55) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. DDX31 cooperates with mutp53 and EGFR to promote progression of muscle invasive bladder cancer.
    Title: A DDX31/Mutant-p53/EGFR Axis Promotes Multistep Progression of Muscle-Invasive Bladder Cancer.
  2. Findings define a mechanism through which control of the DDX31-NPM1 complex is likely to play critical roles in renal carcinogenesis.
    Title: DDX31 regulates the p53-HDM2 pathway and rRNA gene transcription through its interaction with NPM1 in renal cell carcinomas.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ13633, FLJ14578, FLJ23349

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding HDA PubMed 
enables RNA helicase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in ribosome biogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ribosome biogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
probable ATP-dependent RNA helicase DDX31
Names
DEAD (Asp-Glu-Ala-Asp) box polypeptide 31
DEAD box protein 31
DEAD/DEXH helicase DDX31
DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31
G2 helicase
helicain
protein phosphatase 1, regulatory subunit 25
NP_001309269.2
NP_001309270.1
NP_001309271.1
NP_001309272.1
NP_001309273.2
NP_073616.7
NP_619526.2
XP_011517223.2
XP_011517224.2
XP_047279689.1
XP_047279690.1
XP_047279691.1
XP_047279692.1
XP_047279693.1
XP_047279694.1
XP_047279695.1
XP_054219531.1
XP_054219532.1
XP_054219533.1
XP_054219534.1
XP_054219535.1
XP_054219536.1
XP_054219537.1
XP_054219538.1
XP_054219539.1

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)

  1. NM_001322340.2 → NP_001309269.2  probable ATP-dependent RNA helicase DDX31 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL160165, AL354735
    UniProtKB/TrEMBL
    B4DYZ1
    Conserved Domains (2) summary
    PRK01297
    Location:21 → 507
    PRK01297; ATP-dependent RNA helicase RhlB; Provisional
    cd17949
    Location:136 → 339
    DEADc_DDX31; DEAD-box helicase domain of DEAD box protein 31

  2. NM_001322341.2 → NP_001309270.1  probable ATP-dependent RNA helicase DDX31 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL160165, AL354735
    UniProtKB/TrEMBL
    B4DYZ1
    Conserved Domains (4) summary
    PRK01297
    Location:37 → 570
    PRK01297; ATP-dependent RNA helicase RhlB; Provisional
    cd00268
    Location:136 → 348
    DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
    pfam00271
    Location:405 → 527
    Helicase_C; Helicase conserved C-terminal domain
    pfam13959
    Location:597 → 658
    DUF4217; Domain of unknown function (DUF4217)

  3. NM_001322342.1 → NP_001309271.1  probable ATP-dependent RNA helicase DDX31 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL160165, AL354735
    UniProtKB/TrEMBL
    B4DYZ1
    Conserved Domains (4) summary
    smart00487
    Location:77 → 274
    DEXDc; DEAD-like helicases superfamily
    cd00268
    Location:55 → 267
    DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
    pfam00271
    Location:324 → 446
    Helicase_C; Helicase conserved C-terminal domain
    pfam13959
    Location:516 → 577
    DUF4217; Domain of unknown function (DUF4217)

  4. NM_001322343.1 → NP_001309272.1  probable ATP-dependent RNA helicase DDX31 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AL160165, AL354735
    UniProtKB/TrEMBL
    B4DYZ1
    Conserved Domains (4) summary
    PRK01297
    Location:1 → 537
    PRK01297; ATP-dependent RNA helicase RhlB; Provisional
    cd00268
    Location:103 → 315
    DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
    pfam00271
    Location:372 → 494
    Helicase_C; Helicase conserved C-terminal domain
    pfam13959
    Location:564 → 625
    DUF4217; Domain of unknown function (DUF4217)

  5. NM_001322344.2 → NP_001309273.2  probable ATP-dependent RNA helicase DDX31 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AL160165
    Consensus CDS
    CCDS83433.2
    Related
    ENSP00000479697.2, ENST00000480876.3
    Conserved Domains (2) summary
    PRK01297
    Location:28 → 189
    PRK01297; ATP-dependent RNA helicase RhlB; Provisional
    cl28899
    Location:136 → 196
    DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

  6. NM_022779.9 → NP_073616.7  probable ATP-dependent RNA helicase DDX31 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AL160165, AL354735
    Consensus CDS
    CCDS6951.2
    UniProtKB/TrEMBL
    B4DYZ1
    Related
    ENSP00000361232.4, ENST00000372159.8
    Conserved Domains (3) summary
    COG0513
    Location:123 → 617
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    cd17949
    Location:136 → 339
    DEADc_DDX31; DEAD-box helicase domain of DEAD box protein 31
    pfam13959
    Location:589 → 649
    DUF4217; Domain of unknown function (DUF4217)

  7. NM_138620.2 → NP_619526.2  probable ATP-dependent RNA helicase DDX31 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has a shorter and alternate 3' region, as compared to variant 1. Since the first 3 nt of the alternate region is just an in-frame translation stop codon, this variant encodes a C-terminal truncated isoform (2) compared to isoform 1.
    Source sequence(s)
    AL160165
    Consensus CDS
    CCDS6952.2
    Related
    ENSP00000310539.2, ENST00000310532.7
    Conserved Domains (2) summary
    cd17949
    Location:136 → 339
    DEADc_DDX31; DEAD-box helicase domain of DEAD box protein 31
    cl38915
    Location:376 → 480
    DEAD-like_helicase_C; C-terminal helicase domain of the DEAD-like helicases

RNA

  1. NR_136309.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL160165, AL354735

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    132592997..132669983 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423735.1 → XP_047279691.1  probable ATP-dependent RNA helicase DDX31 isoform X5

  2. XM_047423739.1 → XP_047279695.1  probable ATP-dependent RNA helicase DDX31 isoform X9

  3. XM_011518922.4 → XP_011517224.2  probable ATP-dependent RNA helicase DDX31 isoform X4

  4. XM_047423734.1 → XP_047279690.1  probable ATP-dependent RNA helicase DDX31 isoform X3

  5. XM_011518921.4 → XP_011517223.2  probable ATP-dependent RNA helicase DDX31 isoform X1

  6. XM_047423733.1 → XP_047279689.1  probable ATP-dependent RNA helicase DDX31 isoform X2

  7. XM_047423738.1 → XP_047279694.1  probable ATP-dependent RNA helicase DDX31 isoform X8

  8. XM_047423736.1 → XP_047279692.1  probable ATP-dependent RNA helicase DDX31 isoform X6

  9. XM_047423737.1 → XP_047279693.1  probable ATP-dependent RNA helicase DDX31 isoform X7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    144804196..144881203 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054363560.1 → XP_054219535.1  probable ATP-dependent RNA helicase DDX31 isoform X5

  2. XM_054363564.1 → XP_054219539.1  probable ATP-dependent RNA helicase DDX31 isoform X9

  3. XM_054363559.1 → XP_054219534.1  probable ATP-dependent RNA helicase DDX31 isoform X4

  4. XM_054363558.1 → XP_054219533.1  probable ATP-dependent RNA helicase DDX31 isoform X3

  5. XM_054363556.1 → XP_054219531.1  probable ATP-dependent RNA helicase DDX31 isoform X1

  6. XM_054363557.1 → XP_054219532.1  probable ATP-dependent RNA helicase DDX31 isoform X2

  7. XM_054363563.1 → XP_054219538.1  probable ATP-dependent RNA helicase DDX31 isoform X8

  8. XM_054363561.1 → XP_054219536.1  probable ATP-dependent RNA helicase DDX31 isoform X6

  9. XM_054363562.1 → XP_054219537.1  probable ATP-dependent RNA helicase DDX31 isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H8H2.2 GenPept UniProtKB/Swiss-Prot:Q9H8H2

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