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RPA4 Gene

protein-coding   GIFtS: 56
GCID: GC0XP096139

Replication Protein A4, 30kDa

(Previous names: replication protein A4, 34kDa)
  See RPA4-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Replication Protein A4, 30kDa1 2     RP-A P302 3
Replication Protein A4, 34kDa1 2     HSU241862
Replication Factor A Protein 42 3     Replication Protein A 30 KDa Subunit2
RF-A Protein 42 3     Replication Protein A Complex 34 Kd Subunit Homolog Rpa42

External Ids:    HGNC: 303051   Entrez Gene: 299352   Ensembl: ENSG000002040867   OMIM: 3007675   UniProtKB: Q131563   

Export aliases for RPA4 gene to outside databases

Previous GC identifers: GC0XP095945 GC0XP085939


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RPA4 Gene:
This gene encodes a single-stranded DNA-binding protein that is the 30-kDa subunit of the replication protein A
complex. Replication protein A is an essential factor for DNA double-strand break repair and cell cycle
checkpoint activation. The encoded protein localizes to DNA repair foci and may be involved in the cellular DNA
damage response. This protein may also play a role in inhibiting viral replication.(provided by RefSeq, Apr 2010)

GeneCards Summary for RPA4 Gene:
RPA4 (replication protein A4, 30kDa) is a protein-coding gene. Diseases associated with RPA4 include babesiosis, and lung cancer susceptibility. GO annotations related to this gene include single-stranded DNA binding. An important paralog of this gene is RPA2.

UniProtKB/Swiss-Prot: RFA4_HUMAN, Q13156
Function: Functions as component of the alternative replication protein A complex (aRPA). aRPA binds
single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and
cell cycle progression through S-phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha
but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual
incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange

Gene Wiki entry for RPA4 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000023.10  NC_018934.2  NT_011651.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the RPA4 gene promoter:
         TBP   HFH-3   MEF-2   FOXL1   FOXI1   MEF-2A   POU2F1   POU2F1a   Sox9   aMEF-2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for RPA4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RPA4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xq21.33   Ensembl cytogenetic band:  Xq21.33   HGNC cytogenetic band: Xq21

RPA4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RPA4 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP096139:  view genomic region     (about GC identifiers)

Start:
96,138,907 bp from pter      End:
96,140,466 bp from pter
Size:
1,560 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: RFA4_HUMAN, Q13156 (See protein sequence)
Recommended Name: Replication protein A 30 kDa subunit  
Size: 261 amino acids; 28868 Da
Subunit: Component of the alternative replication protein A complex (aRPA) composed of RPA1, RPA3 and RPA4.
Interacts with RPA1 and RPA3
Secondary accessions: Q3SY03

Explore the universe of human proteins at neXtProt for RPA4: NX_Q13156

Explore proteomics data for RPA4 at MOPED


See RPA4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_037479.1  
ENSEMBL proteins: 
 ENSP00000362131  
Reactome Protein details: Q13156

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antibodies-online proteins for RPA4 (4 products) 

 
antibodies-online peptides for RPA4

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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5 InterPro protein domains:
 IPR011991 WHTH_DNA-bd_dom
 IPR012340 NA-bd_OB-fold
 IPR014646 RPA32
 IPR004365 NA-bd_OB_tRNA
 IPR014892 RPA_C

Graphical View of Domain Structure for InterPro Entry Q13156

ProtoNet protein and cluster: Q13156

1 Blocks protein domain: IPB004365 OB-fold nucleic acid binding domain


Find genes that share domains with RPA4           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: RFA4_HUMAN, Q13156
Function: Functions as component of the alternative replication protein A complex (aRPA). aRPA binds
single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and
cell cycle progression through S-phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha
but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual
incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange

     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003676nucleic acid binding ----
GO:0003697single-stranded DNA binding TAS7760808
     
Find genes that share ontologies with RPA4           About GenesLikeMe


Animal Models:
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SwitchGear 3'UTR luciferase reporter plasmidRPA4 3' UTR sequence
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
RFA4_HUMAN, Q13156: Nucleus. Note=Localizes to DNA repair foci after DNA damage
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus5
cytosol2

Gene Ontology (GO): 3 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IDA19942684
GO:0005654nucleoplasm TAS--
GO:0005662DNA replication factor A complex IDA19116208

Find genes that share ontologies with RPA4           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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SuperPaths for RPA4 About   (see all 9)  
See pathways by source

SuperPathContained pathways About
1Activation of the pre-replicative complex
Activation of the pre-replicative complex0.66
DNA Replication0.66
2CDK-mediated phosphorylation and removal of Cdc6
DNA Replication0.92
DNA Replication Pre-Initiation0.81
M/G1 Transition0.81
3Cell Cycle, Mitotic
Cell Cycle, Mitotic0.90
Cell Cycle0.90
4E2F mediated regulation of DNA replication
G1/S Transition0.81
Mitotic G1-G1/S phases0.81
5Global Genomic NER (GG-NER)
Nucleotide excision repair0.69


Find genes that share SuperPaths with RPA4           About GenesLikeMe

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways


1 BioSystems Pathway for RPA4
    DNA Replication


1 Reactome Pathway for RPA4
    Activation of the pre-replicative complex


5 Kegg Pathways  (Kegg details for RPA4):
    DNA replication
Nucleotide excision repair
Mismatch repair
Homologous recombination
Fanconi anemia pathway

    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RPA4
Interactions:

    Search GeneGlobe Interaction Network for RPA4

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for RPA4 (Q131563 ENSP000003621314) via UniProtKB, MINT, STRING, and/or I2D (see all 54)
InteractantInteraction Details
GeneCardExternal ID(s)
RPA3P352443, ENSP000002231294I2D: score=2 STRING: ENSP00000223129
MSH2P432463, ENSP000002331464I2D: score=1 STRING: ENSP00000233146
MSH3P205853, ENSP000002650814I2D: score=1 STRING: ENSP00000265081
MUTYHQ9UIF73, ENSP000004081764I2D: score=1 STRING: ENSP00000408176
RPA2P159273, ENSP000003630214I2D: score=1 STRING: ENSP00000363021
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Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000077DNA damage checkpoint IDA19942684
GO:0000082G1/S transition of mitotic cell cycle TAS--
GO:0000278mitotic cell cycle TAS--
GO:0006270DNA replication initiation TAS7760808
GO:0006289nucleotide-excision repair IDA19996105

Find genes that share ontologies with RPA4           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for RPA4 (RFA4)

1 Novoseek inferred chemical compound relationship for RPA4 gene    About this table
Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
rpa 2 85.3 6 19996105 (1), 7760808 (1), 20012581 (1), 19116208 (1)



Find genes that share compounds with RPA4           About GenesLikeMe



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for RPA4 gene: 
NM_013347.4  

Unigene Cluster for RPA4:

Replication protein A4, 30kDa
Hs.659349  [show with all ESTs]
Unigene Representative Sequence: NM_013347
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000373040(uc004efv.4)
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hsa-miR-138-1* hsa-miR-3671 hsa-miR-505 hsa-miR-607 hsa-miR-330-3p hsa-miR-421
SwitchGear 3'UTR luciferase reporter plasmidRPA4 3' UTR sequence
Inhib. RNA
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  QuantiFast Probe-based Assays in human, mouse, rat RPA4

Additional mRNA sequence: 

BC069791.1 BC069808.1 BC069824.1 BC104013.2 BC104014.2 U24186.2 

1 DOTS entry:

DT.102842451 

6 AceView cDNA sequences:

BC069808 BC069824 BC069791 U24186 NM_013347 BE891049 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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RPA4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ATTTTCGGGG
RPA4 Expression
About this image

RPA4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

RPA4 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.659349

UniProtKB/Swiss-Prot: RFA4_HUMAN, Q13156
Tissue specificity: Preferentially expressed in placental and colon mucosa. Widely expressed at intermediate or
lower levels

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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals and fungi.

Orthologs for RPA4 gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
dog
(Canis familiaris)
Mammalia RPA46
replication protein A4, 30kDa
49(a)
1 ↔ 1
X(70256422-70257176)
chicken
(Gallus gallus)
Aves RPA26
Gallus gallus replication protein A2, 32kDa (RPA2)...
38(a)
1 → many
23(1455974-1459771)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
37(a)
1 → many
GL343743.1(52034-61000)
zebrafish
(Danio rerio)
Actinopterygii rpa26
replication protein A2
35(a)
1 → many
16(5691316-5714695) ENSDARG00000037188
fruit fly
(Drosophila melanogaster)
Insecta RPA26
Replication protein A2
21(a)
1 → many
2L(20924975-20926147)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RFA26
Subunit of heterotrimeric Replication Protein A (R...
19(a)
1 → many
XIV(48287-49216) YNL312W


ENSEMBL Gene Tree for RPA4 (if available)
TreeFam Gene Tree for RPA4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for RPA4 gene
RPA22  
1 SIMAP similar gene for RPA4 using alignment to 1 protein entry:     RFA4_HUMAN:
RPA2

Find genes that share paralogs with RPA4           About GenesLikeMe



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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1 SNPs for RPA4    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr X posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs26422191,2,4
----see VAR_0191702 mis40--------

HapMap Linkage Disequilibrium report for RPA4 (96138907 - 96140466 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for RPA4:    About this table    
Variant IDTypeSubtypePubMed ID
dgv520n21CNV Gain19592680

Human Gene Mutation Database (HGMD): RPA4
Locus Specific Mutation Databases (LSDB): RPA4

Site Specific Mutation Identification with PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 300767    OMIM disorders: --

3 diseases for RPA4:    
About MalaCards
babesiosis    lung cancer susceptibility    lung cancer

1 disease from the University of Copenhagen DISEASES database for RPA4:
Babesiosis

Find genes that share disorders with RPA4           About GenesLikeMe

Genetic Association Database (GAD): RPA4
Human Genome Epidemiology (HuGE) Navigator: RPA4 (3 documents)

Export disorders for RPA4 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for RPA4 gene, integrated from 10 sources (see all 27):
(articles sorted by number of sources associating them with RPA4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Rpa4, a homolog of the 34-kilodalton subunit of the replication protein A complex. (PubMed id 7760808)1, 2, 3, 9 Keshav K.F.... Dutta A. (Mol. Cell. Biol. 1995)
  2. An alternative form of replication protein a expressed in normal human tissues supports DNA repair. (PubMed id 19996105)1, 2, 9 Kemp M.G.... Wold M.S. (J. Biol. Chem. 2010)
  3. An alternative form of replication protein a prevents viral replication in vitro. (PubMed id 19116208)1, 2, 9 Mason A.C....Wold M.S. (J. Biol. Chem. 2009)
  4. A naturally occurring human RPA subunit homolog does not support DNA replication or cell-cycle progression. (PubMed id 19942684)1, 2, 9 Haring S.J.... Wold M.S. (Nucleic Acids Res. 2010)
  5. Genetic susceptibility to distinct bladder cancer subphenotypes. (PubMed id 19692168)1, 4 Guey L.T....Malats N. (Eur. Urol. 2010)
  6. Polymorphisms in innate immunity genes and lung cancer risk in Xuanwei, China. (PubMed id 19170196)1, 4 Shen M....Lan Q. (Environ. Mol. Mutagen. 2009)
  7. Pathway-based evaluation of 380 candidate genes and lung cancer susceptibility suggests the importance of the cell cycle pathway. (PubMed id 18676680)1, 4 Hosgood H.D....Lan Q. (Carcinogenesis 2008)
  8. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
  9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  10. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 29935 HGNC: 30305 AceView: RPA4 Ensembl:ENSG00000204086 euGenes: HUgn29935
ECgene: RPA4 Kegg: 29935 H-InvDB: RPA4

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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PharmGKB entry for RPA4 Pharmacogenomics, SNPs, Pathways
NIEHS-SNPshttp://egp.gs.washington.edu/data/hsu24186/

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for RPA4 gene:
Search GeneIP for patents involving RPA4

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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