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

    Gene ID: 10921, updated on 10-Dec-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
    mouse all
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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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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. 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
    5. RNPS1 functions as an oncogenic splicing factor in cervical cancer cells. Deka B, et al. IUBMB Life, 2023 Jun. PMID 36300671

    See all (149) 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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    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)

    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, H3BTC0
      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, H3BTC0

    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, H3BTC0

    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, H3BTC0
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15287.1 GenPept UniProtKB/Swiss-Prot:Q15287

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