RPA1
replication protein A1 | HSSB, REPA1, RF-A, RP-A, RPA70

This gene encodes the largest subunit of the heterotrimeric Replication Protein A (RPA) complex, which binds to single-stranded DNA (ssDNA), forming a nucleoprotein complex that plays an important role in DNA metabolism, being involved in DNA replication, repair, recombination, telomere maintenance, and co-ordinating the cellular response to DNA damage through activation of the ataxia telangiectasia and Rad3-related protein (ATR) kinase. The nucleoprotein complex protects the single-stranded DNA from nucleases, prevents formation of secondary structures that would interfere with repair, and co-ordinates the recruitment and departure of different genome maintenance factors. This subunit contains four oligonucleotide/oligosaccharide-binding (OB) domains, though the majority of ssDNA binding occurs in two of these domains. The heterotrimeric complex has two different modes of ssDNA binding, a low-affinity and high-affinity mode, determined by which ssDNA binding domains are utilized. The different binding modes differ in the length of DNA bound and in the proteins with which it interacts, thereby playing a role in regulating different genomic maintenance pathways. [provided by RefSeq, Sep 2017]

Member of: DE-6
Biological processes 57 terms
DNA binding (GO:0003677)DNA damage response (GO:0006974)DNA recombination (GO:0006310)DNA recombination (GO:0006310)DNA repair (GO:0006281)DNA repair (GO:0006281)DNA repair (GO:0006281)DNA replication (GO:0006260)DNA replication (GO:0006260)DNA replication (GO:0006260)DNA replication (GO:0006260)DNA replication factor A complex (GO:0005662)DNA replication factor A complex (GO:0005662)DNA replication factor A complex (GO:0005662)DNA-templated DNA replication (GO:0006261)G-rich strand telomeric DNA binding (GO:0098505)G-rich strand telomeric DNA binding (GO:0098505)PML body (GO:0016605)PML body (GO:0016605)PML body (GO:0016605)base-excision repair (GO:0006284)chromatin binding (GO:0003682)chromatin organization (GO:0006325)chromatin-protein adaptor activity (GO:0140463)chromosome, telomeric region (GO:0000781)condensed chromosome (GO:0000793)condensed nuclear chromosome (GO:0000794)damaged DNA binding (GO:0003684)damaged DNA binding (GO:0003684)double-strand break repair via homologous recombination (GO:0000724)double-strand break repair via homologous recombination (GO:0000724)double-strand break repair via homologous recombination (GO:0000724)lateral element (GO:0000800)male germ cell nucleus (GO:0001673)meiotic cell cycle (GO:0051321)mismatch repair (GO:0006298)nuclear chromosome (GO:0000228)nucleic acid binding (GO:0003676)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleotide-excision repair (GO:0006289)nucleotide-excision repair (GO:0006289)nucleotide-excision repair (GO:0006289)nucleus (GO:0005634)nucleus (GO:0005634)protein binding (GO:0005515)protein localization to chromosome (GO:0034502)protein localization to site of double-strand break (GO:1990166)single-stranded DNA binding (GO:0003697)single-stranded DNA binding (GO:0003697)single-stranded telomeric DNA binding (GO:0043047)site of DNA damage (GO:0090734)site of double-strand break (GO:0035861)telomere maintenance (GO:0000723)telomere maintenance (GO:0000723)telomere maintenance (GO:0000723)telomere maintenance via telomerase (GO:0007004)
Expression (TPM)
RPA1 — as a Regulated Gene

TFs regulating RPA1 0 TFs

Transcription factors with Perturb-seq knockdown data for RPA1. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = RPA1 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to RPA1

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of RPA1, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Accessibility Element Dist. to TSS Link type TFs
chr17:1,562,314–1,563,047 267.1 kb Distal (>10kb) Multiome 685
chr17:1,589,843–1,590,457 239.9 kb Distal (>10kb) Multiome 538
chr17:1,627,811–1,629,617 201.2 kb Distal (>10kb) Multiome 753
chr17:1,642,697–1,644,482 186.7 kb Distal (>10kb) Multiome 467
chr17:1,648,163–1,650,244 180.8 kb Distal (>10kb) Multiome 932
chr17:1,684,343–1,685,342 145.1 kb Distal (>10kb) Multiome 728
chr17:1,710,017–1,710,765 119.5 kb Distal (>10kb) Multiome 500
chr17:1,713,886–1,717,908 112.5 kb Distal (>10kb) Multiome 1042
chr17:1,724,373–1,725,206 105.2 kb Distal (>10kb) Multiome 720
chr17:1,829,368–1,830,287 42 bp At TSS Multiome 660
chr17:1,908,573–1,908,999 78.7 kb Distal (>10kb) Multiome 239
chr17:1,931,964–1,932,566 102.3 kb Distal (>10kb) Multiome 198
chr17:1,960,870–1,961,658 131.4 kb Distal (>10kb) Multiome 192
chr17:1,997,556–1,998,757 168.1 kb Distal (>10kb) Multiome 543
chr17:2,023,483–2,024,229 193.8 kb Distal (>10kb) Multiome 281
chr17:2,024,769–2,026,284 195.5 kb Distal (>10kb) Multiome 459
chr17:2,029,741–2,030,885 200.9 kb Distal (>10kb) Multiome 871
chr17:2,041,423–2,042,366 211.9 kb Distal (>10kb) Multiome 834
chr17:2,048,764–2,051,218 219.1 kb Distal (>10kb) Multiome 658
chr17:2,053,643–2,054,179 223.8 kb Distal (>10kb) Multiome 473
chr17:2,054,616–2,055,766 225.1 kb Distal (>10kb) Multiome 544
chr17:2,058,401–2,059,503 228.8 kb Distal (>10kb) Multiome 366

Genome Browser

Genomic view of the RPA1 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.

chr17:1,552,314 – 2,069,503
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq