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

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

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; 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

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

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

Bibliography

Phenotypes

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

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 PubChem

Interactions

General gene information

Clone Names

  • MGC1910, FLJ41108

Gene Ontology Provided by GOA

Component Evidence Code Pubs
part_of U2-type catalytic step 2 spliceosome PubMed 
part_of U4/U6 x U5 tri-snRNP complex PubMed 
part_of U5 snRNP PubMed 
part_of catalytic step 2 spliceosome  
part_of catalytic step 2 spliceosome PubMed 
located_in cytosol  
located_in nuclear speck  
located_in nucleoplasm  
located_in nucleus PubMed 
part_of sno(s)RNA-containing ribonucleoprotein complex 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
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_004814.3NP_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
    B4DQJ1, O75938, O95320, Q96DI7
    UniProtKB/TrEMBL
    A0MNP2, B2R9I9
    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: 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)
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