RPAIN RPA interacting protein [Homo sapiens (human)] - Gene

Summary

Official Symbol: RPAINprovided by HGNC
Official Full Name: RPA interacting proteinprovided by HGNC
Primary source: HGNC:HGNC:28641
See related: Ensembl:ENSG00000129197 MIM:617299; AllianceGenome:HGNC:28641
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RIP; HRIP
Summary: Predicted to enable metal ion binding activity. Acts upstream of or within protein import into nucleus and response to UV. Located in PML body; cytoplasm; and fibrillar center. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in lymph node (RPKM 8.1), testis (RPKM 8.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17p13.2

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (5420182..5432877)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (5313918..5326613)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (5323502..5336197)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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?

Suggest that increased RPAIN levels may contribute to the development of preeclampsia through regulating trophoblast invasion and apoptosis via C1q.
Title: Long non-coding RNA RPAIN regulates the invasion and apoptosis of trophoblast cell lines via complement protein C1q.
hRIPalpha is involved in cell proliferation through regulation of RPA transport
Title: Elevated level of human RPA interacting protein α (hRIPα) in cervical tumor cells is involved in cell proliferation through regulating RPA transport.
The results show that DDX3, eIF5A, and hRIP enhance HIV-1 internal ribosomal entry site-mediated translation.
Title: Translational regulation of HIV-1 replication by HIV-1 Rev cellular cofactors Sam68, eIF5A, hRIP, and DDX3.
Observational study of gene-disease association. (HuGE Navigator)
Title: New genetic associations detected in a host response study to hepatitis B vaccine.
hRIPbeta localises to the PML nuclear body and transports replication protein A (PML) into the PML nuclear body and releases RPA upon UV irradiation.
Title: Sumoylation of the novel protein hRIP{beta} is involved in replication protein A deposition in PML nuclear bodies.

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D17S2014 (e-PCR)
- UniSTS:69376

PMC156606P4 (e-PCR)
- UniSTS:271411

D8S2279 (e-PCR)
- UniSTS:473907

D1S1361 (e-PCR)
- UniSTS:149557

L17796 (e-PCR)
- UniSTS:12896

D10S16 (e-PCR)
- UniSTS:155756

D16S325 (e-PCR)
- UniSTS:147089

D13S1568 (e-PCR)
- UniSTS:473497

WI-18770 (e-PCR)
- UniSTS:19911

RH93604 (e-PCR)
- UniSTS:86742

STS-T86983 (e-PCR)
- UniSTS:2803

C1QBP_3122 (e-PCR)
- UniSTS:462068

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in protein import into nucleus	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within protein import into nucleus	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within response to UV	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in PML body	IDA Inferred from Direct Assay more info	PubMed
located_in PML body	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in fibrillar center	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: RPA-interacting protein

Names: RAP interaction protein; nuclear transporter

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)

NM_001033002.4 → NP_001028174.2 RPA-interacting protein isoform b

See identical proteins and their annotated locations for NP_001028174.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. It encodes isoform b, which has a shorter and distinct C-terminus compared to isoform a.

Source sequence(s)

AY775314, BC013831, BI091755

Consensus CDS

CCDS32536.1

UniProtKB/Swiss-Prot

A0A0B4J1T3, B4DI36, B4DTX7, E9PDG9, E9PES3, J3KNH8, Q4G2Y0, Q4G2Y5, Q4G2Y8, Q6B4V9, Q6B4W0, Q6B4W1, Q6B4W4, Q86UA6, Q86X49, Q9BT00

Related

ENSP00000370606.3, ENST00000381209.8

Conserved Domains (3) summary

pfam14766
Location:8 → 46

RPA_interact_N; Replication protein A interacting N-terminal

pfam14767
Location:60 → 124

RPA_interact_M; Replication protein A interacting middle

pfam14768
Location:137 → 217

RPA_interact_C; Replication protein A interacting C-terminal
NM_001160243.2 → NP_001153715.1 RPA-interacting protein isoform a

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AK096001, AK295394, AY775314, BC013831

Consensus CDS

CCDS54075.1

UniProtKB/Swiss-Prot

Q86UA6

UniProtKB/TrEMBL

A0A0A0MSE7, B3KTT3

Related

ENSP00000385814.4, ENST00000405578.8

Conserved Domains (3) summary

pfam14766
Location:8 → 46

RPA_interact_N; Replication protein A interacting N-terminal

pfam14767
Location:60 → 124

RPA_interact_M; Replication protein A interacting middle

pfam14768
Location:137 → 211

RPA_interact_C; Replication protein A interacting C-terminal
NM_001160244.2 → NP_001153716.1 RPA-interacting protein isoform c

See identical proteins and their annotated locations for NP_001153716.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 3' coding region and 3' UTR, compared to variant 1. It encodes isoform c, which has a shorter and distinct C-terminus compared to isoform a.

Source sequence(s)

AY775316, BC013831, BI091755

Consensus CDS

CCDS54076.1

UniProtKB/Swiss-Prot

Q86UA6

UniProtKB/TrEMBL

E9PDG9

Related

ENSP00000370605.5, ENST00000381208.9

Conserved Domains (3) summary

pfam14766
Location:8 → 46

RPA_interact_N; Replication protein A interacting N-terminal

pfam14767
Location:60 → 124

RPA_interact_M; Replication protein A interacting middle

pfam14768
Location:137 → 165

RPA_interact_C; Replication protein A interacting C-terminal
NM_001160246.2 → NP_001153718.1 RPA-interacting protein isoform d

See identical proteins and their annotated locations for NP_001153718.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 3' UTR and has multiple coding region differences compared to variant 1. This results in a shorter isoform (d) with a distinct C-terminus, compared to isoform a.

Source sequence(s)

AY775321, BI091755, CK005117

Consensus CDS

CCDS54079.1

UniProtKB/TrEMBL

B3KTT3

Related

ENSP00000439939.2, ENST00000536255.6

Conserved Domains (2) summary

pfam14766
Location:8 → 46

RPA_interact_N; Replication protein A interacting N-terminal

cl26943
Location:66 → 106

FbpA; Fibronectin-binding protein A N-terminus (FbpA)
NM_001160266.2 → NP_001153738.1 RPA-interacting protein isoform e

See identical proteins and their annotated locations for NP_001153738.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) differs in the 3' coding region and 3' UTR, compared to variant 1. It encodes isoform e, which has a shorter and distinct C-terminus compared to isoform a.

Source sequence(s)

AA745783, AY775314, N41653

Consensus CDS

CCDS54077.1

UniProtKB/Swiss-Prot

Q86UA6

UniProtKB/TrEMBL

A0A0A0MR35

Related

ENSP00000315069.6, ENST00000327154.10

Conserved Domains (2) summary

pfam14766
Location:8 → 46

RPA_interact_N; Replication protein A interacting N-terminal

pfam14767
Location:60 → 124

RPA_interact_M; Replication protein A interacting middle

RNA

NR_027679.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (8) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK096001, AK295394, AY775323
NR_027682.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (11) has multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AY775315, BC004451, BI091755
NR_027683.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (12) has multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK096001, AY775323, BI091755
NR_027684.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (13) lacks an alternate internal exon and uses an alternate 3' exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AY680658, AY775319, BI091755
NR_027685.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (14) has multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AY775320, BC013831, BI091755

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

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

5420182..5432877

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047436927.1 → XP_047292883.1 RPA-interacting protein isoform X1

Related

ENSP00000446453.2, ENST00000539417.6
XM_047436928.1 → XP_047292884.1 RPA-interacting protein isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

5313918..5326613

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054317544.1 → XP_054173519.1 RPA-interacting protein isoform X1
XM_054317545.1 → XP_054173520.1 RPA-interacting protein isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001160267.1: Suppressed sequence

Description

NM_001160267.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
NM_032308.1: Suppressed sequence

Description

NM_032308.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
NR_027678.1: Suppressed sequence

Description

NR_027678.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
NR_027680.1: Suppressed sequence

Description

NR_027680.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
NR_027681.1: Suppressed sequence

Description

NR_027681.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.