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

    Gene ID: 120863, updated on 10-Dec-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, Dec 2024]
    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_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (100231635..100281972, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (100192869..100243198, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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)

    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_2024_08

    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

      UniProtKB/TrEMBL
      H0YIL0

    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

      UniProtKB/TrEMBL
      H0YIL0

    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

    Gene LinkOut

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

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