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    RPAIN RPA interacting protein [ Homo sapiens (human) ]

    Gene ID: 84268, updated on 2-Nov-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 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

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    See RPAIN in Genome Data Viewer
    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_000017.11Genomic 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 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 (26) 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 
    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 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)

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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