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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
    mouse all
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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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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