RPA4 Gene (Protein Coding)

Replication Protein A4

GC0XP096883
GIFtS:
37
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 i... See more...

Aliases for RPA4 Gene

Aliases for RPA4 Gene

  • Replication Protein A4 2 3 5
  • Replication Protein A 30 KDa Subunit 3 4
  • Replication Factor A Protein 4 3 4
  • Replication Protein A4, 34kDa 2 3
  • Replication Protein A4, 30kDa 2 3
  • RF-A Protein 4 3 4
  • HSU24186 2 3
  • RP-A P30 3 4
  • Replication Protein A Complex 34 Kd Subunit Homolog Rpa4 3
  • RPA4 5

External Ids for RPA4 Gene

Previous GeneCards Identifiers for RPA4 Gene

  • GC0XP095945
  • GC0XP096139
  • GC0XP085939

Summaries for RPA4 Gene

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) is a Protein Coding gene. Diseases associated with RPA4 include Spinal Muscular Atrophy, X-Linked 2 and Cholestasis, Intrahepatic, Of Pregnancy, 1. Among its related pathways are Cell Cycle, Mitotic and CDK-mediated phosphorylation and removal of Cdc6. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and single-stranded DNA binding. An important paralog of this gene is RPA2.

UniProtKB/Swiss-Prot Summary for RPA4 Gene

  • As part of the alternative replication protein A complex, aRPA, binds single-stranded DNA and probably plays a role in DNA repair. Compared to the RPA2-containing, canonical RPA complex, may not support chromosomal DNA replication and cell cycle progression through S-phase. The aRPA may not promote efficient priming by DNA polymerase alpha but could support 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

Additional gene information for RPA4 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RPA4 Gene

Genomics for RPA4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for RPA4 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH0XJ097021 Enhancer 0.3 Ensembl 15.4 +137.9 137892 1.2 NFE2L2 RPA4 piR-52294-155 piR-35674-563 DIAPH2 ERVFC1
GH0XJ096978 Enhancer 0.2 ENCODE 17.1 +95.5 95460 1.2 RPA4 DIAPH2 piR-52294-155 NDUFB5P2 ERVFC1
GH0XJ096905 Enhancer 0.2 Ensembl 16.8 +23.3 23293 2.8 RPA4 NDUFB5P2 DIAPH2 ERVFC1
GH0XJ096908 Enhancer 0.2 Ensembl 16.2 +25.6 25593 1.4 RPA4 NDUFB5P2 DIAPH2 ERVFC1
GH0XJ096983 Enhancer 0.2 Ensembl 12.1 +98.8 98793 0.2 RPA4 piR-52294-155 NDUFB5P2 DIAPH2 ERVFC1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RPA4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RPA4

Top Transcription factor binding sites by QIAGEN in the RPA4 gene promoter:
  • aMEF-2
  • FOXI1
  • FOXL1
  • HFH-3
  • MEF-2
  • MEF-2A
  • POU2F1
  • POU2F1a
  • Sox9
  • TBP

Genomic Locations for RPA4 Gene

Latest Assembly
chrX:96,883,908-96,885,467
(GRCh38/hg38)
Size:
1,560 bases
Orientation:
Plus strand

Previous Assembly
chrX:96,138,907-96,140,466
(GRCh37/hg19 by Entrez Gene)
Size:
1,560 bases
Orientation:
Plus strand

chrX:96,138,907-96,140,446
(GRCh37/hg19 by Ensembl)
Size:
1,540 bases
Orientation:
Plus strand

Genomic View for RPA4 Gene

Genes around RPA4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPA4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPA4 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RPA4 Gene

Proteins for RPA4 Gene

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  • Protein details for RPA4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13156-RFA4_HUMAN
    Recommended name:
    Replication protein A 30 kDa subunit
    Protein Accession:
    Q13156
    Secondary Accessions:
    • Q3SY03

    Protein attributes for RPA4 Gene

    Size:
    261 amino acids
    Molecular mass:
    28868 Da
    Quaternary structure:
    • Component of the aRPA, the alternative replication protein A complex, a trimeric complex similar to the replication protein A complex/RPA but where RPA1 and RPA3 are associated with RPA4 instead of RPA2. Interacts with RPA1 and RPA3.

neXtProt entry for RPA4 Gene

Protein Expression for RPA4 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for RPA4 Gene

No Post-translational modifications

Other Protein References for RPA4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RPA4 Gene

Domains & Families for RPA4 Gene

Gene Families for RPA4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RPA4 Gene

InterPro:
Blocks:
  • OB-fold nucleic acid binding domain

Suggested Antigen Peptide Sequences for RPA4 Gene

GenScript: Design optimal peptide antigens:
  • Replication factor A protein 4 (RFA4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q13156

UniProtKB/Swiss-Prot:

RFA4_HUMAN :
  • Belongs to the replication factor A protein 2 family.
Family:
  • Belongs to the replication factor A protein 2 family.
genes like me logo Genes that share domains with RPA4: view

Function for RPA4 Gene

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  6. Cell Lines for research

Molecular function for RPA4 Gene

UniProtKB/Swiss-Prot Function:
As part of the alternative replication protein A complex, aRPA, binds single-stranded DNA and probably plays a role in DNA repair. Compared to the RPA2-containing, canonical RPA complex, may not support chromosomal DNA replication and cell cycle progression through S-phase. The aRPA may not promote efficient priming by DNA polymerase alpha but could support 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) - Molecular Function for RPA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003697 single-stranded DNA binding TAS,IBA 21873635
GO:0005515 protein binding IPI 32296183
genes like me logo Genes that share ontologies with RPA4: view
genes like me logo Genes that share phenotypes with RPA4: view

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPA4

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RPA4 Gene

Localization for RPA4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RPA4 Gene

Nucleus. Note=Localizes to DNA repair foci after DNA damage.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RPA4 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RPA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000781 chromosome, telomeric region IBA 21873635
GO:0005634 nucleus IBA,IDA 19942684
GO:0005654 nucleoplasm TAS --
GO:0005662 DNA replication factor A complex TAS,IDA 19116208
GO:0035861 site of double-strand break IBA 21873635
genes like me logo Genes that share ontologies with RPA4: view

Pathways & Interactions for RPA4 Gene

genes like me logo Genes that share pathways with RPA4: view

Gene Ontology (GO) - Biological Process for RPA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000077 DNA damage checkpoint IDA 19942684
GO:0000082 G1/S transition of mitotic cell cycle TAS --
GO:0000724 double-strand break repair via homologous recombination IBA 21873635
GO:0006260 DNA replication IBA 21873635
GO:0006270 DNA replication initiation TAS 7760808
genes like me logo Genes that share ontologies with RPA4: view

No data available for SIGNOR curated interactions for RPA4 Gene

Drugs & Compounds for RPA4 Gene

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  1. Drug products for research

(1) Additional Compounds for RPA4 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with RPA4: view

Transcripts for RPA4 Gene

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mRNA/cDNA for RPA4 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPA4

Alternative Splicing Database (ASD) splice patterns (SP) for RPA4 Gene

No ASD Table

Relevant External Links for RPA4 Gene

GeneLoc Exon Structure for
RPA4

Expression for RPA4 Gene

Products:

  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RPA4 Gene

mRNA expression in normal human tissues for RPA4 Gene
mRNA expression by GTEx for RPA4 GenemRNA expression by BioGPS for RPA4 Gene

mRNA differential expression in normal tissues according to GTEx for RPA4 Gene

This gene is overexpressed in Testis (x8.9).

Protein differential expression in normal tissues from HIPED for RPA4 Gene

This gene is overexpressed in Testis (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for RPA4 Gene



Protein tissue co-expression partners for RPA4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RPA4

SOURCE GeneReport for Unigene cluster for RPA4 Gene:

Hs.659349

mRNA Expression by UniProt/SwissProt for RPA4 Gene:

Q13156-RFA4_HUMAN
Tissue specificity: Preferentially expressed in placental and colon mucosa. Widely expressed at intermediate or lower levels.
genes like me logo Genes that share expression patterns with RPA4: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for RPA4 Gene

Orthologs for RPA4 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for RPA4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia RPA4 29
  • 99.49 (n)
Dog
(Canis familiaris)
 Mammalia RPA4 30
  • 49 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia -- 30
  • 42 (a)
 ManyToMany
-- 30
  • 42 (a)
 ManyToMany
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 30
  • 34 (a)
 OneToMany
Chicken
(Gallus gallus)
 Aves RPA2 30
  • 38 (a)
 OneToMany
Lizard
(Anolis carolinensis)
 Reptilia -- 30
  • 37 (a)
 OneToMany
Zebrafish
(Danio rerio)
 Actinopterygii rpa2 30
  • 35 (a)
 OneToMany
Fruit Fly
(Drosophila melanogaster)
 Insecta RPA2 30
  • 21 (a)
 OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes RFA2 30
  • 19 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.6662 30
  • 25 (a)
 OneToMany
Species where no ortholog for RPA4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • Cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Mouse (Mus musculus)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for RPA4 Gene

ENSEMBL:
Gene Tree for RPA4 (if available)
TreeFam:
Gene Tree for RPA4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RPA4: view image
Alliance of Genome Resources:
Additional Orthologs for RPA4

Paralogs for RPA4 Gene

Paralogs for RPA4 Gene

(1) SIMAP similar genes for RPA4 Gene using alignment to 1 proteins:

  • RFA4_HUMAN
genes like me logo Genes that share paralogs with RPA4: view

Variants for RPA4 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RPA4 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
rs2642219 -- p.Ala33Thr

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RPA4 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for RPA4 Gene

Variant ID Type Subtype PubMed ID
dgv520n21 CNV gain 19592680

Variation tolerance for RPA4 Gene

Residual Variation Intolerance Score: 29.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.38; 63.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RPA4 Gene

Human Gene Mutation Database (HGMD)
RPA4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RPA4
Leiden Open Variation Database (LOVD)
RPA4

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RPA4 Gene

Disorders for RPA4 Gene

MalaCards: The human disease database

(3) MalaCards diseases for RPA4 Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards
Search RPA4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RPA4

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with RPA4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RPA4 Gene

Publications for RPA4 Gene

  1. Rpa4, a homolog of the 34-kilodalton subunit of the replication protein A complex. (PMID: 7760808) Keshav KF … Dutta A (Molecular and cellular biology 1995) 2 3 4 22
  2. An alternative form of replication protein a expressed in normal human tissues supports DNA repair. (PMID: 19996105) Kemp MG … Wold MS (The Journal of biological chemistry 2010) 3 4 22
  3. A naturally occurring human RPA subunit homolog does not support DNA replication or cell-cycle progression. (PMID: 19942684) Haring SJ … Wold MS (Nucleic acids research 2010) 3 4 22
  4. An alternative form of replication protein a prevents viral replication in vitro. (PMID: 19116208) Mason AC … Wold MS (The Journal of biological chemistry 2009) 3 4 22
  5. Genetic susceptibility to distinct bladder cancer subphenotypes. (PMID: 19692168) Guey LT … EPICURO/Spanish Bladder Cancer Study investigators (European urology 2010) 3 40

ExternalLinks

View latest publications for RPA4 gene in Mastermind

Products for RPA4 Gene

Sources for RPA4 Gene