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DEPDC4 DEP domain containing 4 [ Homo sapiens (human) ]

Gene ID: 120863, updated on 3-Apr-2024

Summary

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Official Symbol
DEPDC4provided by HGNC
Official Full Name
DEP domain containing 4provided by HGNC
Primary source
HGNC:HGNC:22952
See related
Ensembl:ENSG00000166153 AllianceGenome:HGNC:22952
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
DEP.4
Summary
Predicted to be involved in intracellular signal transduction. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 1.0), kidney (RPKM 0.3) and 22 other tissues See more
Orthologs
all
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Genomic context

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See DEPDC4 in Genome Data Viewer
Location:
12q23.1
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (100231635..100281972, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (100192869..100243198, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (100625413..100660857, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4764 Neighboring gene Sharpr-MPRA regulatory region 7946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:100595701-100596388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:100596389-100597074 Neighboring gene microRNA 1827 Neighboring gene actin related protein 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4765 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6858 Neighboring gene MPRA-validated peak1911 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:100688535-100689176 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:100689177-100689817 Neighboring gene Sharpr-MPRA regulatory region 7724 Neighboring gene SCY1 like pseudokinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6859 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:100724514-100724735 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:100750302-100750802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:100750803-100751303 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr12:100766477-100767226 Neighboring gene solute carrier family 17 member 8 Neighboring gene small nucleolar RNA U13 Neighboring gene MPRA-validated peak1912 silencer Neighboring gene nuclear receptor subfamily 1 group H member 4 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22518 Neighboring gene MPRA-validated peak1913 silencer

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. DEP domains: structurally similar but functionally different. Consonni SV, et al. Nat Rev Mol Cell Biol, 2014 May. PMID 24739740
  2. Association mapping of the high-grade myopia MYP3 locus reveals novel candidates UHRF1BP1L, PTPRR, and PPFIA2. Hawthorne F, et al. Invest Ophthalmol Vis Sci, 2013 Mar 21. PMID 23422819, Free PMC Article
  3. Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Dias Neto E, et al. Proc Natl Acad Sci U S A, 2000 Mar 28. PMID 10737800, Free PMC Article
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

GeneRIFs: Gene References Into Functions

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

General gene information

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Markers

Homology

Clone Names

  • FLJ33505

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in intracellular signal transduction IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
DEP domain-containing protein 4

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_001319310.2 → NP_001306239.1  DEP domain-containing protein 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC026110
    UniProtKB/TrEMBL
    H0YIL0
    Related
    ENSP00000449590.1, ENST00000551642.1
    Conserved Domains (2) summary
    cd04446
    Location:64 → 159
    DEP_DEPDC4; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.
    cl02570
    Location:233 → 284
    RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...

  2. NM_001319311.2 → NP_001306240.1  DEP domain-containing protein 4 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC026110
    Conserved Domains (2) summary
    cd04405
    Location:247 → 475
    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 ...
    cd04446
    Location:64 → 159
    DEP_DEPDC4; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.

  3. NM_001364818.2 → NP_001351747.1  DEP domain-containing protein 4 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5), as well as variant 9, encodes isoform 4.
    Source sequence(s)
    AC026110
    Consensus CDS
    CCDS91741.1
    UniProtKB/TrEMBL
    E9PGM3
    Related
    ENSP00000448385.2, ENST00000550587.6
    Conserved Domains (2) summary
    cd04405
    Location:233 → 462
    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 and an N-terminal ...
    cd04446
    Location:64 → 159
    DEP_DEPDC4; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.

  4. NM_001387201.1 → NP_001374130.1  DEP domain-containing protein 4 isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) encodes the longest isoform (5).
    Source sequence(s)
    AC026110
    Conserved Domains (2) summary
    cd04405
    Location:247 → 475
    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 and an N-terminal ...
    cd04446
    Location:64 → 159
    DEP_DEPDC4; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.

  5. NM_001387205.1 → NP_001374134.1  DEP domain-containing protein 4 isoform 6

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7), as well as variant 8, encodes isoform 6.
    Source sequence(s)
    AC026110
    Conserved Domains (2) summary
    cd04405
    Location:233 → 462
    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 and an N-terminal ...
    cd04446
    Location:64 → 159
    DEP_DEPDC4; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.

  6. NM_001387206.1 → NP_001374135.1  DEP domain-containing protein 4 isoform 6

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8), as well as variant 7, encodes isoform 6.
    Source sequence(s)
    AC026110
    Conserved Domains (2) summary
    cd04405
    Location:233 → 462
    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 and an N-terminal ...
    cd04446
    Location:64 → 159
    DEP_DEPDC4; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.

  7. NM_001387207.1 → NP_001374136.1  DEP domain-containing protein 4 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (9), as well as variant 5, encodes isoform 4.
    Source sequence(s)
    AC026110
    Consensus CDS
    CCDS91741.1
    UniProtKB/TrEMBL
    E9PGM3
    Conserved Domains (2) summary
    cd04405
    Location:233 → 462
    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 and an N-terminal ...
    cd04446
    Location:64 → 159
    DEP_DEPDC4; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.

  8. NM_001387208.1 → NP_001374137.1  DEP domain-containing protein 4 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC026110
    Conserved Domains (2) summary
    cd04405
    Location:233 → 462
    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 and an N-terminal ...
    cd04446
    Location:64 → 159
    DEP_DEPDC4; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.

  9. NM_001387209.1 → NP_001374138.1  DEP domain-containing protein 4 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC026110
    Conserved Domains (2) summary
    cd04405
    Location:166 → 395
    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 and an N-terminal ...
    cl02442
    Location:50 → 92
    DEP; DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is ...

  10. NM_001387210.1 → NP_001374139.1  DEP domain-containing protein 4 isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC026110
    Conserved Domains (1) summary
    cd04405
    Location:53 → 281
    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 and an N-terminal ...

  11. NM_001387211.1 → NP_001374140.1  DEP domain-containing protein 4 isoform 10

    Status: VALIDATED

    Source sequence(s)
    AC026110
    Conserved Domains (1) summary
    cd04405
    Location:53 → 281
    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 and an N-terminal ...

  12. NM_001387212.1 → NP_001374141.1  DEP domain-containing protein 4 isoform 11

    Status: VALIDATED

    Source sequence(s)
    AC026110
    Conserved Domains (1) summary
    cd04405
    Location:58 → 286
    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 and an N-terminal ...

  13. NM_001387213.1 → NP_001374142.1  DEP domain-containing protein 4 isoform 12

    Status: VALIDATED

    Source sequence(s)
    AC026110
    Conserved Domains (1) summary
    cd04405
    Location:44 → 273
    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 and an N-terminal ...

  14. NM_152317.4 → NP_689530.1  DEP domain-containing protein 4 isoform 1

    See identical proteins and their annotated locations for NP_689530.1

    Status: VALIDATED

    Source sequence(s)
    AC026110, AK090824, BC015117, BI023188
    Consensus CDS
    CCDS9075.1
    UniProtKB/Swiss-Prot
    Q496C8, Q8N2C3, Q96BW0
    UniProtKB/TrEMBL
    H0YIL0
    Related
    ENSP00000396234.1, ENST00000416321.5
    Conserved Domains (2) summary
    cd04446
    Location:64 → 159
    DEP_DEPDC4; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.
    cl02570
    Location:233 → 284
    RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...

RNA

  1. NR_170594.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC026110

  2. NR_170595.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC026110

  3. NR_170596.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC026110

  4. NR_170597.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC026110

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    100231635..100281972 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017018783.2 → XP_016874272.1  DEP domain-containing protein 4 isoform X4

  2. XM_047428275.1 → XP_047284231.1  DEP domain-containing protein 4 isoform X3

  3. XM_017018782.3 → XP_016874271.2  DEP domain-containing protein 4 isoform X2

  4. XM_017018779.3 → XP_016874268.3  DEP domain-containing protein 4 isoform X1

  5. XM_017018785.3 → XP_016874274.3  DEP domain-containing protein 4 isoform X5

RNA

  1. XR_944493.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    100192869..100243198 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054371047.1 → XP_054227022.1  DEP domain-containing protein 4 isoform X4

  2. XM_054371046.1 → XP_054227021.1  DEP domain-containing protein 4 isoform X3

  3. XM_054371045.1 → XP_054227020.1  DEP domain-containing protein 4 isoform X2

  4. XM_054371044.1 → XP_054227019.1  DEP domain-containing protein 4 isoform X1

  5. XM_054371048.1 → XP_054227023.1  DEP domain-containing protein 4 isoform X5

RNA

  1. XR_008488523.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_135073.1: Suppressed sequence

    Description
    NR_135073.1: This RefSeq was removed because currently there is insufficient support for the transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N2C3.1 GenPept UniProtKB/Swiss-Prot:Q8N2C3

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