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    SNRNP40 small nuclear ribonucleoprotein U5 subunit 40 [ Homo sapiens (human) ]

    Gene ID: 9410, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SNRNP40provided by HGNC
    Official Full Name
    small nuclear ribonucleoprotein U5 subunit 40provided by HGNC
    Primary source
    HGNC:HGNC:30857
    See related
    Ensembl:ENSG00000060688 MIM:607797; AllianceGenome:HGNC:30857
    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
    40K; SPF38; WDR57; PRP8BP; HPRP8BP; PRPF8BP
    Summary
    This gene encodes a component of the U5 small nuclear ribonucleoprotein (snRNP) particle. The U5 snRNP is part of the spliceosome, a multiprotein complex that catalyzes the removal of introns from pre-messenger RNAs. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in lymph node (RPKM 17.2), testis (RPKM 14.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SNRNP40 in Genome Data Viewer
    Location:
    1p35.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (31259568..31296788, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (31111784..31149010, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (31732415..31769635, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 565 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:31628398-31629033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31636659-31637158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31639725-31640224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 566 Neighboring gene Sharpr-MPRA regulatory region 5533 Neighboring gene sodium/potassium transporting ATPase interacting 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31671341-31671841 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:31688981-31689480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31695101-31695601 Neighboring gene MPRA-validated peak156 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 641 Neighboring gene zinc finger CCHC-type containing 17 Neighboring gene Sharpr-MPRA regulatory region 7682 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:31827736-31827903 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:31839312-31839494 Neighboring gene Sharpr-MPRA regulatory region 13821 Neighboring gene uncharacterized LOC124903892 Neighboring gene Sharpr-MPRA regulatory region 3310 Neighboring gene fatty acid binding protein 3

    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. Highly variable cancer subpopulations that exhibit enhanced transcriptome variability and metastatic fitness. Nguyen A, et al. Nat Commun, 2016 May 3. PMID 27138336, Free PMC Article
    2. Roles of the U5 snRNP in spliceosome dynamics and catalysis. Turner IA, et al. Biochem Soc Trans, 2004 Dec. PMID 15506927
    3. Novel genetic variants linked to prelabor rupture of membranes among Chinese pregnant women. Kan H, et al. Placenta, 2023 Jun. PMID 37054626
    4. The mammalian analogue of the yeast PRP8 splicing protein is present in the U4/5/6 small nuclear ribonucleoprotein particle and the spliceosome. Pinto AL, et al. Proc Natl Acad Sci U S A, 1989 Nov. PMID 2479028, Free PMC Article
    5. The human U5-220kD protein (hPrp8) forms a stable RNA-free complex with several U5-specific proteins, including an RNA unwindase, a homologue of ribosomal elongation factor EF-2, and a novel WD-40 protein. Achsel T, et al. Mol Cell Biol, 1998 Nov. PMID 9774689, Free PMC Article

    See all (124) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel genetic variants linked to prelabor rupture of membranes among Chinese pregnant women.
      Title: Novel genetic variants linked to prelabor rupture of membranes among Chinese pregnant women.
    2. Clinically, low SNRNP40 expression is associated with metastatic relapse.
      Title: Highly variable cancer subpopulations that exhibit enhanced transcriptome variability and metastatic fitness.
    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

    EBI GWAS Catalog

    Description
    NKAIN1-SERINC2 is a functional, replicable and genome-wide significant risk gene region specific for alcohol dependence in subjects of European descent.
    EBI GWAS Catalog

    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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    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, small nuclear ribonucleoprotein 40kDa (SNRNP40), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells 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

    • MGC1910, FLJ41108

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA processing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in RNA splicing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in RNA splicing, via transesterification reactions TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of U2-type catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U4/U6 x U5 tri-snRNP complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of U5 snRNP TAS
    Traceable Author Statement
    more info
    		 PubMed 
    part_of catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of sno(s)RNA-containing ribonucleoprotein complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    U5 small nuclear ribonucleoprotein 40 kDa protein
    Names
    38 kDa-splicing factor
    Prp8-binding protein
    U5 snRNP 40 kDa protein
    U5 snRNP-specific 40 kDa protein
    U5-40K
    U5-40kD protein
    WD repeat domain 57 (U5 snRNP specific)
    WD repeat-containing protein 57
    small nuclear ribonucleoprotein 40kDa (U5)
    small nuclear ribonucleoprotein, U5 40kDa subunit

    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_004814.3 → NP_004805.2  U5 small nuclear ribonucleoprotein 40 kDa protein

      See identical proteins and their annotated locations for NP_004805.2

      Status: REVIEWED

      Source sequence(s)
      AC114495, BC001494, BM150898, CR736901
      Consensus CDS
      CCDS340.1
      UniProtKB/Swiss-Prot
      B4DQJ1, O75938, O95320, Q96DI7
      UniProtKB/TrEMBL
      A0MNP2, B2R9I9
      Related
      ENSP00000263694.4, ENST00000263694.9
      Conserved Domains (2) summary
      cd00200
      Location:62 → 351
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      sd00039
      Location:70 → 107
      7WD40; WD40 repeat [structural motif]

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      31259568..31296788 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      31111784..31149010 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96DI7.1 GenPept UniProtKB/Swiss-Prot:Q96DI7

    Gene LinkOut

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

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