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

Gene ID: 9410, updated on 10-Oct-2019

Summary

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
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

Genomic context

See SNRNP40 in Genome Data Viewer
Location:
1p35.2
Exon count:
10
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (31259568..31296788, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (31732415..31769644, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984935 Neighboring gene sodium/potassium transporting ATPase interacting 1 Neighboring gene zinc finger CCHC-type containing 17 Neighboring gene fatty acid binding protein 3 Neighboring gene uncharacterized LOC105378623

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

NHGRI 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.
NHGRI GWA Catalog

HIV-1 interactions

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 BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, 35S U5-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, 35S U5-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, 35S U5-snRNP, conserved biosystem (from KEGG)
    Spliceosome, 35S U5-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystem (from KEGG)
    Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mRNA Splicing - Minor Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Minor Pathway, organism-specific biosystemThe splicing of a subset of pre-mRNA introns occurs by a second pathway, designated the AT-AC or U12-dependent splicing pathway. AT-AC introns have highly conserved, non-canonical splice sites that ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC1910, FLJ41108

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA processing TAS
Traceable Author Statement
more info
PubMed 
RNA splicing TAS
Traceable Author Statement
more info
PubMed 
RNA splicing, via transesterification reactions TAS
Traceable Author Statement
more info
PubMed 
mRNA splicing, via spliceosome IC
Inferred by Curator
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
U2-type catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
U5 snRNP TAS
Traceable Author Statement
more info
PubMed 
catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
nuclear speck IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
small nucleolar ribonucleoprotein complex NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

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 (hPrp8-binding)
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)

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_004814.3NP_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
    Q96DI7
    UniProtKB/TrEMBL
    A0MNP2
    Related
    ENSP00000263694.4, ENST00000263694.9
    Conserved Domains (2) summary
    cd00200
    Location:62351
    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:70107
    7WD40; WD40 repeat [structural motif]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

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