Human Gene ARPC1A (uc003upx.2)
  Description: Homo sapiens actin related protein 2/3 complex, subunit 1A, 41kDa (ARPC1A), transcript variant 1, mRNA.
RefSeq Summary (NM_006409): This gene encodes one of seven subunits of the human Arp2/3 protein complex. This subunit is a member of the SOP2 family of proteins and is most similar to the protein encoded by gene ARPC1B. The similarity between these two proteins suggests that they both may function as p41 subunit of the human Arp2/3 complex that has been implicated in the control of actin polymerization in cells. It is possible that the p41 subunit is involved in assembling and maintaining the structure of the Arp2/3 complex. Multiple versions of the p41 subunit may adapt the functions of the complex to different cell types or developmental stages. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010].
Transcript (Including UTRs)
   Position: hg19 chr7:98,923,496-98,963,885 Size: 40,390 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr7:98,930,977-98,963,552 Size: 32,576 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:98,923,496-98,963,885)mRNA (may differ from genome)Protein (370 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ARC1A_HUMAN
DESCRIPTION: RecName: Full=Actin-related protein 2/3 complex subunit 1A; AltName: Full=SOP2-like protein;
FUNCTION: Probably functions as component of the Arp2/3 complex which is involved in regulation of actin polymerization and together with an activating nucleation-promoting factor (NPF) mediates the formation of branched actin networks.
SUBUNIT: Probable component of the Arp2/3 complex in which it may replace ARPC1B.
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton (Probable).
SIMILARITY: Belongs to the WD repeat ARPC1 family.
SIMILARITY: Contains 6 WD repeats.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ARPC1A
CDC HuGE Published Literature: ARPC1A
Positive Disease Associations: Dehydroepiandrosterone Sulfate
Related Studies:
  1. Dehydroepiandrosterone Sulfate
    Guangju Zhai et al. PLoS genetics 2011, Eight common genetic variants associated with serum DHEAS levels suggest a key role in ageing mechanisms., PLoS genetics. [PubMed 21533175]

-  MalaCards Disease Associations
  MalaCards Gene Search: ARPC1A
Diseases sorted by gene-association score: tomato allergy (3), radial neuropathy (2), boomerang dysplasia (2), atelosteogenesis (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 59.49 RPKM in Esophagus - Mucosa
Total median expression: 2019.74 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -50.10161-0.311 Picture PostScript Text
3' UTR -86.40333-0.259 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017383 - ARPC2/3_su1
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF00400 - WD domain, G-beta repeat

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Prolyl oligopeptidase, N-terminal domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - Dipeptidyl peptidase IV/CD26, N-terminal domain

ModBase Predicted Comparative 3D Structure on Q92747
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0051015 actin filament binding

Biological Process:
GO:0030036 actin cytoskeleton organization
GO:0030833 regulation of actin filament polymerization
GO:0034314 Arp2/3 complex-mediated actin nucleation
GO:0038096 Fc-gamma receptor signaling pathway involved in phagocytosis
GO:0048013 ephrin receptor signaling pathway
GO:0061024 membrane organization

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005885 Arp2/3 protein complex
GO:0015629 actin cytoskeleton
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  EU668326 - Homo sapiens epididymis luminal protein 68 (HEL-68) mRNA, complete cds.
AK297111 - Homo sapiens cDNA FLJ57124 complete cds, highly similar to Actin-related protein 2/3 complex subunit 1A.
BC039594 - Homo sapiens actin related protein 2/3 complex, subunit 1A, 41kDa, mRNA (cDNA clone MGC:48820 IMAGE:6018804), complete cds.
BC006445 - Homo sapiens cDNA clone IMAGE:3537492, containing frame-shift errors.
AB209059 - Homo sapiens mRNA for actin related protein 2/3 complex subunit 1A variant protein.
BC047889 - Homo sapiens actin related protein 2/3 complex, subunit 1A, 41kDa, mRNA (cDNA clone MGC:57658 IMAGE:6473050), complete cds.
BC054027 - Homo sapiens actin related protein 2/3 complex, subunit 1A, 41kDa, mRNA (cDNA clone MGC:64823 IMAGE:6514889), complete cds.
Y08999 - H.sapiens mRNA for Sop2p-like protein.
EU832206 - Synthetic construct Homo sapiens clone HAIB:100067235; DKFZo004C0226 actin related protein 2/3 complex, subunit 1A, 41kDa protein (ARPC1A) gene, encodes complete protein.
JF432387 - Synthetic construct Homo sapiens clone IMAGE:100073589 actin related protein 2/3 complex, subunit 1A, 41kDa (ARPC1A) gene, encodes complete protein.
KJ893072 - Synthetic construct Homo sapiens clone ccsbBroadEn_02466 ARPC1A gene, encodes complete protein.
GQ891339 - Homo sapiens clone HEL-S-110d epididymis secretory sperm binding protein mRNA, complete cds.
EU832112 - Synthetic construct Homo sapiens clone HAIB:100067141; DKFZo008C0225 actin related protein 2/3 complex, subunit 1A, 41kDa protein (ARPC1A) gene, encodes complete protein.
AK223015 - Homo sapiens mRNA for actin related protein 2/3 complex subunit 1A variant, clone: HSI13986.
GQ472234 - Homo sapiens epididymis secretory protein Li 307 (HEL-S-307) mRNA, partial cds.
JD415921 - Sequence 396945 from Patent EP1572962.
JD433769 - Sequence 414793 from Patent EP1572962.
CU691736 - Synthetic construct Homo sapiens gateway clone IMAGE:100021107 5' read ARPC1A mRNA.
JD020873 - Sequence 1897 from Patent EP1572962.
JD031794 - Sequence 12818 from Patent EP1572962.
DQ587708 - Homo sapiens piRNA piR-54820, complete sequence.
JD024620 - Sequence 5644 from Patent EP1572962.
JD028191 - Sequence 9215 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04666 - Fc gamma R-mediated phagocytosis
hsa04810 - Regulation of actin cytoskeleton
hsa05100 - Bacterial invasion of epithelial cells
hsa05130 - Pathogenic Escherichia coli infection
hsa05131 - Shigellosis

Reactome (by CSHL, EBI, and GO)

Protein Q92747 (Reactome details) participates in the following event(s):

R-HSA-442592 WASPs or WAVEs activate the ARP2/3 complex
R-HSA-3928595 N-WASP binds ARP2/3 and G-actin
R-HSA-8868230 SNX9 recruits components of the actin polymerizing machinery
R-HSA-2029466 Attachment of preexisting mother filament and initiation of branching
R-HSA-1861595 Extension of pseudopodia by myosin-X in a PI3K dependent manner
R-HSA-2197690 Detachment of WASP/WAVE
R-HSA-8868236 BAR domain proteins recruit dynamin
R-HSA-8871194 RAB5 and GAPVD1 bind AP-2
R-HSA-8868658 HSPA8-mediated ATP hydrolysis promotes vesicle uncoating
R-HSA-8868659 Clathrin recruits auxilins to the clathrin-coated vesicle
R-HSA-8868661 Dynamin-mediated GTP hydrolysis promotes vesicle scission
R-HSA-8868660 Auxilin recruits HSPA8:ATP to the clathrin-coated vesicle
R-HSA-8868648 SYNJ hydrolyze PI(4,5)P2 to PI(4)P
R-HSA-8868651 Endophilins recruit synaptojanins to the clathrin-coated pit
R-HSA-2029482 Regulation of actin dynamics for phagocytic cup formation
R-HSA-5663213 RHO GTPases Activate WASPs and WAVEs
R-HSA-3928662 EPHB-mediated forward signaling
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-2029480 Fcgamma receptor (FCGR) dependent phagocytosis
R-HSA-195258 RHO GTPase Effectors
R-HSA-2682334 EPH-Ephrin signaling
R-HSA-199991 Membrane Trafficking
R-HSA-168249 Innate Immune System
R-HSA-194315 Signaling by Rho GTPases
R-HSA-422475 Axon guidance
R-HSA-5653656 Vesicle-mediated transport
R-HSA-168256 Immune System
R-HSA-162582 Signal Transduction
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: A4D276, ARC1A_HUMAN, D6W5S1, NM_006409, NP_006400, Q7Z5U8, Q86WU5, Q8IXQ0, Q92747, SOP2L
UCSC ID: uc003upx.2
RefSeq Accession: NM_006409
Protein: Q92747 (aka ARC1A_HUMAN)
CCDS: CCDS5660.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006409.3
exon count: 10CDS single in 3' UTR: no RNA size: 1623
ORF size: 1113CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2329.00frame shift in genome: no % Coverage: 99.01
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.