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ARPC4 actin related protein 2/3 complex subunit 4 [ Homo sapiens (human) ]

Gene ID: 10093, updated on 3-Nov-2024

Summary

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Official Symbol
ARPC4provided by HGNC
Official Full Name
actin related protein 2/3 complex subunit 4provided by HGNC
Primary source
HGNC:HGNC:707
See related
Ensembl:ENSG00000241553 MIM:604226; AllianceGenome:HGNC:707
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
ARC20; DEVLO; P20-ARC
Summary
This gene encodes one of seven subunits of the human Arp2/3 protein complex. This complex controls actin polymerization in cells and has been conserved throughout eukaryotic evolution. This gene encodes the p20 subunit, which is necessary for actin nucleation and high-affinity binding to F-actin. Alternative splicing results in multiple transcript variants. Naturally occurring read-through transcription exists between this gene and the downstream tubulin tyrosine ligase-like family, member 3 (TTLL3), which results in the production of a fusion protein. [provided by RefSeq, Nov 2010]
Expression
Ubiquitous expression in lymph node (RPKM 63.0), appendix (RPKM 61.6) and 25 other tissues See more
Orthologs
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Genomic context

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See ARPC4 in Genome Data Viewer
Location:
3p25.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (9792518..9807101)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (9784472..9799053)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (9834202..9848785)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14038 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14039 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9773975-9774534 Neighboring gene bromodomain and PHD finger containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19407 Neighboring gene 8-oxoguanine DNA glycosylase Neighboring gene calcium/calmodulin dependent protein kinase I Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14040 Neighboring gene Sharpr-MPRA regulatory region 4794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14041 Neighboring gene transcriptional adaptor 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9832484-9832984 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9834089-9834615 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14042 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9834616-9835142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19409 Neighboring gene ARPC4-TTLL3 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14044 Neighboring gene tubulin tyrosine ligase like 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:9866222-9866442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9867034-9867534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9867535-9868035 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9868869-9869369 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9876763-9877262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19411 Neighboring gene RNA pseudouridine synthase D3

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 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ARPC4 promotes bladder cancer cell invasion and is associated with lymph node metastasis.
    Title: ARPC4 promotes bladder cancer cell invasion and is associated with lymph node metastasis.
  2. Expression of the ARPC4 severely affects mycobacterium tuberculosis growth and suppresses immunogenic response in murine macrophages
    Title: Expression of the ARPC4 subunit of human Arp2/3 severely affects mycobacterium tuberculosis growth and suppresses immunogenic response in murine macrophages.
  3. we show cell line-specific differences in ARP2/3 complex subunit dependency on cell migratory potential, and suggest ARPC4 to be one of the key members of the ARP2/3 complex in pancreatic cancer.
    Title: Silencing of the ARP2/3 complex disturbs pancreatic cancer cell migration.
  4. We show that coronin 3 similar to other coronins interacts with the Arp2/3-complex and cofilin indicating that this family in general is involved in regulating Arp2/3-mediated events.
    Title: Coronin 3 involvement in F-actin-dependent processes at the cell cortex.
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

Associated conditions

Description Tests
Developmental delay, language impairment, and ocular abnormalities
MedGen: C5774262 OMIM: 620141 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify 20kDa subunit 4 of actin related protein 2/3 complex (ARPC4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify 20kDa subunit 4 of actin related protein 2/3 complex (ARPC4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify 20kDa subunit 4 of actin related protein 2/3 complex (ARPC4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify 20kDa subunit 4 of actin related protein 2/3 complex (ARPC4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Readthrough ARPC4-TTLL3

Readthrough gene: ARPC4-TTLL3, Included gene: TTLL3

Homology

Clone Names

  • MGC13544

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to actin filament binding IDA
Inferred from Direct Assay
more info
 PubMed 
contributes_to actin filament binding NAS
Non-traceable Author Statement
more info
 PubMed 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
contributes_to protein-macromolecule adaptor activity IPI
Inferred from Physical Interaction
more info
 PubMed 
enables structural constituent of cytoskeleton IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in Arp2/3 complex-mediated actin nucleation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in Arp2/3 complex-mediated actin nucleation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in actin filament polymerization IEA
Inferred from Electronic Annotation
more info
  
involved_in actin nucleation NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of Arp2/3 protein complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Arp2/3 protein complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Arp2/3 protein complex TAS
Traceable Author Statement
more info
 PubMed 
located_in cell projection IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in site of double-strand break ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
actin-related protein 2/3 complex subunit 4
Names
actin related protein 2/3 complex, subunit 4, 20kDa
arp2/3 complex 20 kDa subunit
arp2/3 protein complex subunit p20

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_001024959.3 → NP_001020130.1  actin-related protein 2/3 complex subunit 4 isoform b

    See identical proteins and their annotated locations for NP_001020130.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and uses a downstream start codon, compared to variant 1. The resulting isoform (b) is shorter at the N-terminus, compared to isoform a. Both variants 2 and 3 encode isoform b.
    Source sequence(s)
    AC022382, AI612891, BQ688329, DB060690
    Consensus CDS
    CCDS46743.1
    UniProtKB/Swiss-Prot
    P59998
    Related
    ENSP00000432235.1, ENST00000498623.6
    Conserved Domains (1) summary
    cl05433
    Location:1 → 76
    ARPC4; ARP2/3 complex 20 kDa subunit (ARPC4)

  2. NM_001024960.3 → NP_001020131.1  actin-related protein 2/3 complex subunit 4 isoform b

    See identical proteins and their annotated locations for NP_001020131.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and uses a downstream start codon, compared to variant 1. The resulting isoform (b) is shorter at the N-terminus, compared to isoform a. Both variants 2 and 3 encode isoform b.
    Source sequence(s)
    AC022382, AI612891, BG938423
    Consensus CDS
    CCDS46743.1
    UniProtKB/Swiss-Prot
    P59998
    Related
    ENSP00000473435.1, ENST00000485273.1
    Conserved Domains (1) summary
    cl05433
    Location:1 → 76
    ARPC4; ARP2/3 complex 20 kDa subunit (ARPC4)

  3. NM_001198780.3 → NP_001185709.1  actin-related protein 2/3 complex subunit 4 isoform c

    See identical proteins and their annotated locations for NP_001185709.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The resulting isoform (c) is longer than isoform a.
    Source sequence(s)
    AC022382, AI612891, BX419672
    Consensus CDS
    CCDS56238.1
    UniProtKB/TrEMBL
    F8WCF6
    Related
    ENSP00000388169.1, ENST00000433034.1
    Conserved Domains (1) summary
    pfam05856
    Location:21 → 185
    ARPC4; ARP2/3 complex 20 kDa subunit (ARPC4)

  4. NM_005718.5 → NP_005709.1  actin-related protein 2/3 complex subunit 4 isoform a

    See identical proteins and their annotated locations for NP_005709.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform a.
    Source sequence(s)
    AC022382, AF006087, AI612891, DA909066
    Consensus CDS
    CCDS43047.1
    UniProtKB/Swiss-Prot
    C9JWM7, E7ETI0, F6TTL5, O15509, P59998, Q6P0W5, Q96QJ3
    UniProtKB/TrEMBL
    F8WCF6
    Related
    ENSP00000380431.2, ENST00000397261.8
    Conserved Domains (1) summary
    pfam05856
    Location:1 → 166
    ARPC4; ARP2/3 complex 20 kDa subunit (ARPC4)

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    9792518..9807101
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    9784472..9799053
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P59998.3 GenPept UniProtKB/Swiss-Prot:P59998

Gene LinkOut

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