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RPAIN RPA interacting protein [ Homo sapiens (human) ]

Gene ID: 84268, updated on 3-Apr-2024

Summary

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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 several processes, including DNA metabolic process; protein import into nucleus; and response to UV. Located in PML body; cytoplasm; and fibrillar center. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in lymph node (RPKM 8.1), testis (RPKM 8.0) and 25 other tissues See more
Orthologs
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Genomic context

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See RPAIN in Genome Data Viewer
Location:
17p13.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (5420182..5432877)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (5313918..5326613)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (5323502..5336197)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene rabaptin, RAB GTPase binding effector protein 1 Neighboring gene uncharacterized LOC105371505 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:5265177-5265872 Neighboring gene nucleoporin 88 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:5316624-5317823 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:5322619-5323156 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:5323157-5323694 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8070 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:5342450-5342632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11573 Neighboring gene complement C1q binding protein Neighboring gene DEAH-box helicase 33 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:5371354-5371936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11575 Neighboring gene DHX33 divergent transcript

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. Long non-coding RNA RPAIN regulates the invasion and apoptosis of trophoblast cell lines via complement protein C1q. Song X, et al. Oncotarget, 2017 Jan 31. PMID 28032589, Free PMC Article
  2. Elevated level of human RPA interacting protein α (hRIPα) in cervical tumor cells is involved in cell proliferation through regulating RPA transport. Namkoong S, et al. FEBS Lett, 2012 Oct 19. PMID 23010595
  3. Identification, expression pattern, and subcellular location of human RIP isoforms. Chen JZ, et al. DNA Cell Biol, 2005 Jul. PMID 16008515
  4. Translational regulation of HIV-1 replication by HIV-1 Rev cellular cofactors Sam68, eIF5A, hRIP, and DDX3. Liu J, et al. J Neuroimmune Pharmacol, 2011 Jun. PMID 21360055
  5. Sumoylation of the novel protein hRIP{beta} is involved in replication protein A deposition in PML nuclear bodies. Park J, et al. Mol Cell Biol, 2005 Sep. PMID 16135809, Free PMC Article

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: New genetic associations detected in a host response study to hepatitis B vaccine.
  5. 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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC4189, FLJ25625, FLJ30490, FLJ42429

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 
Component Evidence Code Pubs
is_active_in PML body IBA
Inferred from Biological aspect of Ancestor
more info
  
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)

  1. 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

  2. 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

  3. 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

  4. 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)

  5. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    5420182..5432877
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Related
    ENSP00000446453.2, ENST00000539417.6

  2. XM_047436928.1 → XP_047292884.1  RPA-interacting protein isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    5313918..5326613
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054317544.1 → XP_054173519.1  RPA-interacting protein isoform X1

  2. XM_054317545.1 → XP_054173520.1  RPA-interacting protein isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. 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.

  2. NM_032308.1: Suppressed sequence

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

  3. NR_027678.1: Suppressed sequence

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

  4. NR_027680.1: Suppressed sequence

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

  5. NR_027681.1: Suppressed sequence

    Description
    NR_027681.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86UA6.2 GenPept UniProtKB/Swiss-Prot:Q86UA6

Gene LinkOut

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