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DEPDC1B DEP domain containing 1B [ Homo sapiens (human) ]

Gene ID: 55789, updated on 3-Apr-2024

Summary

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Official Symbol
DEPDC1Bprovided by HGNC
Official Full Name
DEP domain containing 1Bprovided by HGNC
Primary source
HGNC:HGNC:24902
See related
Ensembl:ENSG00000035499 MIM:616073; AllianceGenome:HGNC:24902
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
XTP1; BRCC3
Summary
Predicted to enable GTPase activator activity. Involved in cell migration and positive regulation of Wnt signaling pathway. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in gall bladder (RPKM 6.2), testis (RPKM 3.3) and 14 other tissues See more
Orthologs
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Genomic context

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Location:
5q12.1
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (60596912..60700166, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (61415059..61518602, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (59892739..59995993, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene phosphodiesterase 4D Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22586 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22587 Neighboring gene Sharpr-MPRA regulatory region 9229 Neighboring gene SET pseudogene 21 Neighboring gene Sharpr-MPRA regulatory region 1909 Neighboring gene prostate androgen-regulated transcript 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16038 Neighboring gene uncharacterized LOC124900982 Neighboring gene calcium binding protein 39 pseudogene 1 Neighboring gene keratin 8 pseudogene 31

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. Aberrantly high DEPDC1B expression leads to poor prognosis in patients with lower-grade gliomas. Liu ZD, et al. Eur Rev Med Pharmacol Sci, 2022 Nov. PMID 36394729
  2. DEPDC1B promotes colorectal cancer via facilitating cell proliferation and migration while inhibiting apoptosis. Han F, et al. Cell Cycle, 2023 Jan. PMID 36016512, Free PMC Article
  3. DEPDC1B knockdown inhibits the development of malignant melanoma through suppressing cell proliferation and inducing cell apoptosis. Xu Y, et al. Exp Cell Res, 2019 Jun 1. PMID 30880030
  4. DEPDC1B is involved in the proliferation, metastasis, cell cycle arrest and apoptosis of colon cancer cells by regulating NUP37. Xiong H, et al. Mol Med Rep, 2023 Jun. PMID 37203403, Free PMC Article
  5. DEP domain containing 1B (DEPDC1B) exerts the tumor promoter in hepatocellular carcinoma through activating p53 signaling pathway via kinesin family member 23 (KIF23). Shen E, et al. Bioengineered, 2022 Jan. PMID 34983303, Free PMC Article

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. DEPDC1B enhances malignant phenotypes of multiple myeloma through upregulating CCNB1 and inhibiting p53 signaling pathway.
    Title: DEPDC1B enhances malignant phenotypes of multiple myeloma through upregulating CCNB1 and inhibiting p53 signaling pathway.
  2. DEPDC1B-mediated USP5 deubiquitination of beta-catenin promotes breast cancer metastasis by activating the wnt/beta-catenin pathway.
    Title: DEPDC1B-mediated USP5 deubiquitination of β-catenin promotes breast cancer metastasis by activating the wnt/β-catenin pathway.
  3. Circ_0005276 Promotes Prostate Cancer Progression Through the Crosstalk of miR-128-3p/DEPDC1B Axis.
    Title: Circ_0005276 Promotes Prostate Cancer Progression Through the Crosstalk of miR-128-3p/DEPDC1B Axis.
  4. DEPDC1B is involved in the proliferation, metastasis, cell cycle arrest and apoptosis of colon cancer cells by regulating NUP37.
    Title: DEPDC1B is involved in the proliferation, metastasis, cell cycle arrest and apoptosis of colon cancer cells by regulating NUP37.
  5. DEPDC1B promotes colorectal cancer via facilitating cell proliferation and migration while inhibiting apoptosis.
    Title: DEPDC1B promotes colorectal cancer via facilitating cell proliferation and migration while inhibiting apoptosis.
  6. Aberrantly high DEPDC1B expression leads to poor prognosis in patients with lower-grade gliomas.
    Title: Aberrantly high DEPDC1B expression leads to poor prognosis in patients with lower-grade gliomas.
  7. DEPDC1B Promotes Melanoma Angiogenesis and Metastasis through Sequestration of Ubiquitin Ligase CDC16 to Stabilize Secreted SCUBE3.
    Title: DEPDC1B Promotes Melanoma Angiogenesis and Metastasis through Sequestration of Ubiquitin Ligase CDC16 to Stabilize Secreted SCUBE3.
  8. DEP domain containing 1B (DEPDC1B) exerts the tumor promoter in hepatocellular carcinoma through activating p53 signaling pathway via kinesin family member 23 (KIF23).
    Title: DEP domain containing 1B (DEPDC1B) exerts the tumor promoter in hepatocellular carcinoma through activating p53 signaling pathway via kinesin family member 23 (KIF23).
  9. DEPDC1B regulates the progression of human chordoma through UBE2T-mediated ubiquitination of BIRC5.
    Title: DEPDC1B regulates the progression of human chordoma through UBE2T-mediated ubiquitination of BIRC5.
  10. Overexpressed DEPDC1B contributes to the progression of hepatocellular carcinoma by CDK1.
    Title: Overexpressed DEPDC1B contributes to the progression of hepatocellular carcinoma by CDK1.
Submit: New GeneRIF Correction See all GeneRIFs (19)

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

  • FLJ11252

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTPase activator activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cell migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in intracellular signal transduction IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of Wnt signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of Wnt signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
DEP domain-containing protein 1B
Names
HBV X-transactivated gene 8 protein
HBV XAg-transactivated protein 8
HBxAg transactivated protein 1
breast cancer cell 3

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_001145208.2 → NP_001138680.1  DEP domain-containing protein 1B isoform 2

    See identical proteins and their annotated locations for NP_001138680.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 3' coding region compared to variant 1. The resulting isoform (2) is shorter but has the same N- and C-termini compared to isoform 1.
    Source sequence(s)
    AA830503, AK300782, BC010904, DC299445
    Consensus CDS
    CCDS47214.1
    UniProtKB/TrEMBL
    B4DRG1
    Related
    ENSP00000389101.2, ENST00000453022.6
    Conserved Domains (2) summary
    cd04405
    Location:177 → 400
    RhoGAP_BRCC3-like; RhoGAP_BRCC3-like: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of BRCC3-like proteins. This subgroup also contains two groups of closely related proteins, BRCC3 and DEPDC7, which both contain a C-terminal RhoGAP-like domain ...
    cd04447
    Location:15 → 106
    DEP_BRCC3; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in BBRC3-like proteins. BBRC3, also known as DEPDC1B, is a DEP containing protein of unknown function.

  2. NM_018369.3 → NP_060839.2  DEP domain-containing protein 1B isoform 1

    See identical proteins and their annotated locations for NP_060839.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AA830503, AK290684, BC010904, DC299445
    Consensus CDS
    CCDS3977.1
    UniProtKB/Swiss-Prot
    A8K3R9, B4DUT4, Q86WJ3, Q8IZY6, Q8WUY9, Q9NUN3, Q9NW57
    UniProtKB/TrEMBL
    A0A2X0SFC1
    Related
    ENSP00000265036.5, ENST00000265036.10
    Conserved Domains (2) summary
    cd04405
    Location:177 → 400
    RhoGAP_BRCC3-like; RhoGAP_BRCC3-like: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of BRCC3-like proteins. This subgroup also contains two groups of closely related proteins, BRCC3 and DEPDC7, which both contain a C-terminal RhoGAP-like domain ...
    cd04447
    Location:15 → 106
    DEP_BRCC3; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in BBRC3-like proteins. BBRC3, also known as DEPDC1B, is a DEP containing protein of unknown function.

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    60596912..60700166 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011543509.3 → XP_011541811.1  DEP domain-containing protein 1B isoform X1

    UniProtKB/TrEMBL
    A0A2X0SFC1
    Conserved Domains (2) summary
    cd04405
    Location:162 → 385
    RhoGAP_BRCC3-like; RhoGAP_BRCC3-like: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of BRCC3-like proteins. This subgroup also contains two groups of closely related proteins, BRCC3 and DEPDC7, which both contain a C-terminal RhoGAP-like domain ...
    cd04447
    Location:1 → 91
    DEP_BRCC3; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in BBRC3-like proteins. BBRC3, also known as DEPDC1B, is a DEP containing protein of unknown function.

  2. XM_047417369.1 → XP_047273325.1  DEP domain-containing protein 1B isoform X2

  3. XM_011543510.4 → XP_011541812.1  DEP domain-containing protein 1B isoform X3

    Conserved Domains (2) summary
    cd04405
    Location:177 → 301
    RhoGAP_BRCC3-like; RhoGAP_BRCC3-like: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of BRCC3-like proteins. This subgroup also contains two groups of closely related proteins, BRCC3 and DEPDC7, which both contain a C-terminal RhoGAP-like domain ...
    cd04447
    Location:15 → 106
    DEP_BRCC3; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in BBRC3-like proteins. BBRC3, also known as DEPDC1B, is a DEP containing protein of unknown function.

  4. XM_047417370.1 → XP_047273326.1  DEP domain-containing protein 1B isoform X4

RNA

  1. XR_007058609.1 RNA Sequence

  2. XR_948274.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    61415059..61518602 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054352912.1 → XP_054208887.1  DEP domain-containing protein 1B isoform X1

  2. XM_054352913.1 → XP_054208888.1  DEP domain-containing protein 1B isoform X2

RNA

  1. XR_008487130.1 RNA Sequence

  2. XR_008487131.1 RNA Sequence

  3. XR_008487132.1 RNA Sequence

  4. XR_008487133.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WUY9.2 GenPept UniProtKB/Swiss-Prot:Q8WUY9

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