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

Gene ID: 9410, updated on 7-Apr-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
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Genomic context

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Location:
1p35.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (31259568..31296788, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (31111784..31149010, complement)
105.20220307 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. NKAIN1-SERINC2 is a functional, replicable and genome-wide significant risk gene region specific for alcohol dependence in subjects of European descent. Zuo L, et al. Drug Alcohol Depend, 2013 May 1. PMID 23455491, Free PMC Article

See all (105) 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)

Genotypes

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_2023_10

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.

Chemical Information
Molecular Biology Databases
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Tools
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