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RNPS1 RNA binding protein with serine rich domain 1 [ Homo sapiens (human) ]

Gene ID: 10921, updated on 2-Nov-2024

Summary

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Official Symbol
RNPS1provided by HGNC
Official Full Name
RNA binding protein with serine rich domain 1provided by HGNC
Primary source
HGNC:HGNC:10080
See related
Ensembl:ENSG00000205937 MIM:606447; AllianceGenome:HGNC:10080
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
E5.1
Summary
This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. This protein contains many serine residues. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]
Expression
Ubiquitous expression in bone marrow (RPKM 25.4), testis (RPKM 24.3) and 25 other tissues See more
Orthologs
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Genomic context

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See RNPS1 in Genome Data Viewer
Location:
16p13.3
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (2253116..2268126, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (2275563..2290572, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (2303117..2318127, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene deoxyribonuclease 1 like 2 Neighboring gene ECI1 antisense RNA 1 Neighboring gene enoyl-CoA delta isomerase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10261 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7039 Neighboring gene uncharacterized LOC107984839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2303743-2304516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10263 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7040 Neighboring gene MIR3677 and MIR940 host gene Neighboring gene microRNA 3677 Neighboring gene microRNA 940

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. Identification and characterisation of a novel human RNA-binding protein. Badolato J, et al. Gene, 1995 Dec 12. PMID 8543184
  2. Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing. Mayeda A, et al. EMBO J, 1999 Aug 16. PMID 10449421, Free PMC Article
  3. Splicing enhances translation in mammalian cells: an additional function of the exon junction complex. Nott A, et al. Genes Dev, 2004 Jan 15. PMID 14752011, Free PMC Article
  4. RNPS1 functions as an oncogenic splicing factor in cervical cancer cells. Deka B, et al. IUBMB Life, 2023 Jun. PMID 36300671
  5. RNA-binding protein with serine-rich domain 1 regulates microsatellite instability of uterine corpus endometrial adenocarcinoma. Liu X, et al. Clinics (Sao Paulo), 2021. PMID 34817046, Free PMC Article

See all (148) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RNPS1 stabilizes NAT10 protein to facilitate translation in cancer via tRNA ac[4]C modification.
    Title: RNPS1 stabilizes NAT10 protein to facilitate translation in cancer via tRNA ac(4)C modification.
  2. RNPS1 functions as an oncogenic splicing factor in cervical cancer cells.
    Title: RNPS1 functions as an oncogenic splicing factor in cervical cancer cells.
  3. RNA-binding protein with serine-rich domain 1 regulates microsatellite instability of uterine corpus endometrial adenocarcinoma.
    Title: RNA-binding protein with serine-rich domain 1 regulates microsatellite instability of uterine corpus endometrial adenocarcinoma.
  4. ubiquitin-specific protease 4 (USP4) is a binding partner of RNPS1.
    Title: RNPS1 is modulated by ubiquitin-specific protease 4.
  5. SRBD1 gene polymorphism is associated with the development of HTG as well as NTG, including late-onset NTG.
    Title: Association between SRBD1 and ELOVL5 gene polymorphisms and primary open-angle glaucoma.
  6. RNPS1 is able to function together with ASF/SF2 to form ribonucleoprotein complexes on nascent transcripts, and thereby prevent formation of transcriptional R-loops.
    Title: The RNA binding protein RNPS1 alleviates ASF/SF2 depletion-induced genomic instability.
  7. The phosphorylation of RNPS1 at Ser-53 influences the efficiencies of both splicing and translation.
    Title: Activation of pre-mRNA splicing by human RNPS1 is regulated by CK2 phosphorylation.
  8. has a role in mRNA surveillance (detecting mRNAs with truncated open reading frames and subjecting them to nonsense-mediated mRNA decay (NMD))
    Title: Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1.
  9. binds to Upf complexes which bind upstream of mRNA exon-exon junctions
    Title: Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex.
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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of RNA binding protein S1, serine-rich domain (RNPS1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC117332

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
NOT enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables mRNA 3'-UTR binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA-templated transcription TAS
Traceable Author Statement
more info
 PubMed 
involved_in RNA splicing TAS
Traceable Author Statement
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of apoptotic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of alternative mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of ASAP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of ASAP complex IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
part_of exon-exon junction complex TAS
Traceable Author Statement
more info
 PubMed 
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
RNA-binding protein with serine-rich domain 1
Names
RNA binding protein with serine-rich domain
RNA-binding protein S1, serine-rich domain
SR protein
SR-related protein LDC2

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_001286625.1 → NP_001273554.1  RNA-binding protein with serine-rich domain 1 isoform a

    See identical proteins and their annotated locations for NP_001273554.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant (2). Variants 1, 2, and 3 all encode the same isoform (a).
    Source sequence(s)
    BC108316, DA062271, L37368
    Consensus CDS
    CCDS10465.1
    UniProtKB/Swiss-Prot
    A8K1P0, B4DDU8, B4DZU7, B7ZA17, O75308, Q15287, Q32P25, Q8WY42, Q9NYG3
    UniProtKB/TrEMBL
    D3DU92, H3BTC0
    Related
    ENSP00000457723.1, ENST00000565678.5
    Conserved Domains (1) summary
    cd12365
    Location:163 → 236
    RRM_RNPS1; RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

  2. NM_001286626.2 → NP_001273555.1  RNA-binding protein with serine-rich domain 1 isoform b

    See identical proteins and their annotated locations for NP_001273555.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate exon compared to variant 2. The resulting isoform (b) has a shorter and distinct N-terminus compared to isoform a.
    Source sequence(s)
    AK316132, BC108316
    Consensus CDS
    CCDS66907.1
    UniProtKB/Swiss-Prot
    Q15287
    Related
    ENSP00000456352.1, ENST00000566458.5
    Conserved Domains (1) summary
    cd12365
    Location:140 → 213
    RRM_RNPS1; RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

  3. NM_001286627.2 → NP_001273556.1  RNA-binding protein with serine-rich domain 1 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two alternate exons compared to variant 2. The resulting isoform (c) has shorter and distinct N- and C-termini compared to isoform a.
    Source sequence(s)
    BC108316, BI819738, DA818573
    Consensus CDS
    CCDS73811.1
    UniProtKB/TrEMBL
    H3BMS0
    Related
    ENSP00000454513.1, ENST00000567147.5
    Conserved Domains (1) summary
    cd12365
    Location:140 → 203
    RRM_RNPS1; RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

  4. NM_006711.5 → NP_006702.1  RNA-binding protein with serine-rich domain 1 isoform a

    See identical proteins and their annotated locations for NP_006702.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR compared to variant (2). Variants 1, 2, and 3 all encode the same isoform (a).
    Source sequence(s)
    BC108316, HY012482
    Consensus CDS
    CCDS10465.1
    UniProtKB/Swiss-Prot
    A8K1P0, B4DDU8, B4DZU7, B7ZA17, O75308, Q15287, Q32P25, Q8WY42, Q9NYG3
    UniProtKB/TrEMBL
    D3DU92, H3BTC0
    Related
    ENSP00000380275.2, ENST00000397086.6
    Conserved Domains (1) summary
    cd12365
    Location:163 → 236
    RRM_RNPS1; RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

  5. NM_080594.4 → NP_542161.1  RNA-binding protein with serine-rich domain 1 isoform a

    See identical proteins and their annotated locations for NP_542161.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the predominant transcript and encodes the longest isoform (a). Variants 1, 2, and 3 all encode the same isoform (a).
    Source sequence(s)
    BC108316, BQ059026, DA818573
    Consensus CDS
    CCDS10465.1
    UniProtKB/Swiss-Prot
    A8K1P0, B4DDU8, B4DZU7, B7ZA17, O75308, Q15287, Q32P25, Q8WY42, Q9NYG3
    UniProtKB/TrEMBL
    D3DU92, H3BTC0
    Related
    ENSP00000315859.5, ENST00000320225.10
    Conserved Domains (1) summary
    cd12365
    Location:163 → 236
    RRM_RNPS1; RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

RNA

  1. NR_104485.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) has an alternate 5' end and lacks an alternate internal exon compared to variant 2. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, compared to variant 2.
    Source sequence(s)
    AC009065, AF274003, AL559988, BC108316, DA818573
    Related
    ENST00000561718.5

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    2253116..2268126 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005255048.3 → XP_005255105.1  RNA-binding protein with serine-rich domain 1 isoform X1

    See identical proteins and their annotated locations for XP_005255105.1

    UniProtKB/Swiss-Prot
    A8K1P0, B4DDU8, B4DZU7, B7ZA17, O75308, Q15287, Q32P25, Q8WY42, Q9NYG3
    UniProtKB/TrEMBL
    D3DU92, H3BTC0
    Related
    ENSP00000454461.1, ENST00000561518.5
    Conserved Domains (1) summary
    cd12365
    Location:163 → 236
    RRM_RNPS1; RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

  2. XM_047433516.1 → XP_047289472.1  RNA-binding protein with serine-rich domain 1 isoform X1

    UniProtKB/Swiss-Prot
    A8K1P0, B4DDU8, B4DZU7, B7ZA17, O75308, Q15287, Q32P25, Q8WY42, Q9NYG3
    UniProtKB/TrEMBL
    D3DU92
    Related
    ENSP00000457820.1, ENST00000568631.5

  3. XM_005255049.5 → XP_005255106.1  RNA-binding protein with serine-rich domain 1 isoform X1

    See identical proteins and their annotated locations for XP_005255106.1

    UniProtKB/Swiss-Prot
    A8K1P0, B4DDU8, B4DZU7, B7ZA17, O75308, Q15287, Q32P25, Q8WY42, Q9NYG3
    UniProtKB/TrEMBL
    D3DU92, H3BTC0
    Conserved Domains (1) summary
    cd12365
    Location:163 → 236
    RRM_RNPS1; RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    2275563..2290572 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054379411.1 → XP_054235386.1  RNA-binding protein with serine-rich domain 1 isoform X1

    UniProtKB/Swiss-Prot
    A8K1P0, B4DDU8, B4DZU7, B7ZA17, O75308, Q15287, Q32P25, Q8WY42, Q9NYG3
    UniProtKB/TrEMBL
    D3DU92

  2. XM_054379412.1 → XP_054235387.1  RNA-binding protein with serine-rich domain 1 isoform X1

    UniProtKB/Swiss-Prot
    A8K1P0, B4DDU8, B4DZU7, B7ZA17, O75308, Q15287, Q32P25, Q8WY42, Q9NYG3
    UniProtKB/TrEMBL
    D3DU92

  3. XM_054379413.1 → XP_054235388.1  RNA-binding protein with serine-rich domain 1 isoform X1

    UniProtKB/Swiss-Prot
    A8K1P0, B4DDU8, B4DZU7, B7ZA17, O75308, Q15287, Q32P25, Q8WY42, Q9NYG3
    UniProtKB/TrEMBL
    D3DU92
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15287.1 GenPept UniProtKB/Swiss-Prot:Q15287

Gene LinkOut

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