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Aliases for SNRNP40 Gene

Aliases for SNRNP40 Gene

  • Small Nuclear Ribonucleoprotein U5 Subunit 40 2 3 5
  • Small Nuclear Ribonucleoprotein, U5 40kDa Subunit 2 3
  • Small Nuclear Ribonucleoprotein 40kDa (U5) 2 3
  • WD Repeat Domain 57 (U5 SnRNP Specific) 2 3
  • WD Repeat-Containing Protein 57 3 4
  • U5 SnRNP 40 KDa Protein 3 4
  • 38 KDa-Splicing Factor 3 4
  • Prp8-Binding Protein 3 4
  • HPRP8BP 3 4
  • PRP8BP 3 4
  • U5-40K 3 4
  • WDR57 3 4
  • U5 Small Nuclear Ribonucleoprotein 40 KDa Protein 3
  • U5 SnRNP-Specific 40 KDa Protein (HPrp8-Binding) 3
  • U5 SnRNP-Specific 40 KDa Protein 4
  • U5-40kD Protein 3
  • PRPF8BP 3
  • SPF38 3
  • SFP38 4
  • 40K 3

External Ids for SNRNP40 Gene

Previous HGNC Symbols for SNRNP40 Gene

  • WDR57

Previous GeneCards Identifiers for SNRNP40 Gene

  • GC01M031506
  • GC01M031732
  • GC01M029838

Summaries for SNRNP40 Gene

Entrez Gene Summary for SNRNP40 Gene

  • 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]

GeneCards Summary for SNRNP40 Gene

SNRNP40 (Small Nuclear Ribonucleoprotein U5 Subunit 40) is a Protein Coding gene. Diseases associated with SNRNP40 include Intermediate Charcot-Marie-Tooth Neuropathy. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. GO annotations related to this gene include poly(A) RNA binding. An important paralog of this gene is WDR5B.

UniProtKB/Swiss-Prot for SNRNP40 Gene

  • Component of the U5 small nuclear ribonucleoprotein (snRNP) complex. The U5 snRNP is part of the spliceosome, a multiprotein complex that catalyzes the removal of introns from pre-messenger RNAs.

Gene Wiki entry for SNRNP40 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SNRNP40 Gene

Genomics for SNRNP40 Gene

Regulatory Elements for SNRNP40 Gene

Enhancers for SNRNP40 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
- Elite enhancer/Elite enhancer-gene association

Enhancers around SNRNP40 on UCSC Golden Path with GeneCards custom track

Promoters for SNRNP40 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for SNRNP40 Gene

Chromosome:
1
Start:
31,259,568 bp from pter
End:
31,296,797 bp from pter
Size:
37,230 bases
Orientation:
Minus strand

Genomic View for SNRNP40 Gene

Genes around SNRNP40 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SNRNP40 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SNRNP40 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SNRNP40 Gene

Proteins for SNRNP40 Gene

  • Protein details for SNRNP40 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96DI7-SNR40_HUMAN
    Recommended name:
    U5 small nuclear ribonucleoprotein 40 kDa protein
    Protein Accession:
    Q96DI7
    Secondary Accessions:
    • B4DQJ1
    • O75938
    • O95320

    Protein attributes for SNRNP40 Gene

    Size:
    357 amino acids
    Molecular mass:
    39311 Da
    Quaternary structure:
    • Identified in the spliceosome C complex. Part of the U5 snRNP complex. Interacts with PRPF8. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39.
    SequenceCaution:
    • Sequence=AAC64084.1; Type=Frameshift; Positions=319; Note=An insertion/deletion of a short nucleotide stretch in its cDNA resulting in a frameshift.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SNRNP40 Gene

    Alternative splice isoforms for SNRNP40 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SNRNP40 Gene

Post-translational modifications for SNRNP40 Gene

  • Ubiquitination at Lys 270 and Lys 286
  • Modification sites at PhosphoSitePlus

Other Protein References for SNRNP40 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for SNRNP40 Gene

Domains & Families for SNRNP40 Gene

Gene Families for SNRNP40 Gene

Graphical View of Domain Structure for InterPro Entry

Q96DI7

UniProtKB/Swiss-Prot:

SNR40_HUMAN :
  • Contains 7 WD repeats.
Similarity:
  • Contains 7 WD repeats.
genes like me logo Genes that share domains with SNRNP40: view

Function for SNRNP40 Gene

Molecular function for SNRNP40 Gene

UniProtKB/Swiss-Prot Function:
Component of the U5 small nuclear ribonucleoprotein (snRNP) complex. The U5 snRNP is part of the spliceosome, a multiprotein complex that catalyzes the removal of introns from pre-messenger RNAs.

Gene Ontology (GO) - Molecular Function for SNRNP40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 9774689
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with SNRNP40: view
genes like me logo Genes that share phenotypes with SNRNP40: view

Animal Model Products

CRISPR Products

miRNA for SNRNP40 Gene

miRTarBase miRNAs that target SNRNP40

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SNRNP40 Gene

Localization for SNRNP40 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SNRNP40 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SNRNP40 Gene COMPARTMENTS Subcellular localization image for SNRNP40 gene
Compartment Confidence
nucleus 5
cytosol 4
extracellular 2
chloroplast 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for SNRNP40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0005682 U5 snRNP TAS 9774689
GO:0005732 small nucleolar ribonucleoprotein complex NAS 9774689
GO:0005737 cytoplasm IDA --
GO:0071011 precatalytic spliceosome IBA --
genes like me logo Genes that share ontologies with SNRNP40: view

Pathways & Interactions for SNRNP40 Gene

genes like me logo Genes that share pathways with SNRNP40: view

Pathways by source for SNRNP40 Gene

1 KEGG pathway for SNRNP40 Gene

Gene Ontology (GO) - Biological Process for SNRNP40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000375 RNA splicing, via transesterification reactions TAS 9774689
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006396 RNA processing TAS 9774689
GO:0008380 RNA splicing TAS 9774689
genes like me logo Genes that share ontologies with SNRNP40: view

No data available for SIGNOR curated interactions for SNRNP40 Gene

Drugs & Compounds for SNRNP40 Gene

No Compound Related Data Available

Transcripts for SNRNP40 Gene

Unigene Clusters for SNRNP40 Gene

Small nuclear ribonucleoprotein 40kDa (U5):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SNRNP40 Gene

No ASD Table

Relevant External Links for SNRNP40 Gene

GeneLoc Exon Structure for
SNRNP40
ECgene alternative splicing isoforms for
SNRNP40

Expression for SNRNP40 Gene

mRNA expression in normal human tissues for SNRNP40 Gene

Protein differential expression in normal tissues from HIPED for SNRNP40 Gene

This gene is overexpressed in CD8 Tcells (8.1), Monocytes (7.7), and Peripheral blood mononuclear cells (7.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SNRNP40 Gene



Protein tissue co-expression partners for SNRNP40 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SNRNP40 Gene:

SNRNP40

SOURCE GeneReport for Unigene cluster for SNRNP40 Gene:

Hs.33962
genes like me logo Genes that share expression patterns with SNRNP40: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for SNRNP40 Gene

Orthologs for SNRNP40 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SNRNP40 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia SNRNP40 34
  • 90.94 (n)
  • 97.2 (a)
SNRNP40 35
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SNRNP40 34
  • 91.41 (n)
  • 97.2 (a)
SNRNP40 35
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Snrnp40 34
  • 89.08 (n)
  • 98.32 (a)
Snrnp40 16
Snrnp40 35
  • 98 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SNRNP40 34
  • 99.35 (n)
  • 99.72 (a)
SNRNP40 35
  • 85 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Snrnp40 34
  • 88.8 (n)
  • 98.88 (a)
oppossum
(Monodelphis domestica)
Mammalia SNRNP40 35
  • 95 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 81 (a)
OneToMany
-- 35
  • 93 (a)
OneToMany
chicken
(Gallus gallus)
Aves SNRNP40 34
  • 79.62 (n)
  • 92.96 (a)
SNRNP40 35
  • 85 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SNRNP40 35
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia snrnp40 34
  • 78.24 (n)
  • 91.39 (a)
Str.6725 34
zebrafish
(Danio rerio)
Actinopterygii snrnp40 34
  • 74.88 (n)
  • 85.51 (a)
zgc56312 34
snrnp40 35
  • 85 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009506 34
  • 57.06 (n)
  • 61.47 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG3436 34
  • 59.55 (n)
  • 61.46 (a)
CG3436 35
  • 57 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea F08G12.2 34
  • 58.07 (n)
  • 56.21 (a)
C18E3.5 35
  • 53 (a)
OneToMany
F08G12.2 35
  • 55 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G43770 34
  • 60.59 (n)
  • 59.88 (a)
rice
(Oryza sativa)
Liliopsida Os.4736 34
Os06g0653800 34
  • 58.31 (n)
  • 58.51 (a)
wheat
(Triticum aestivum)
Liliopsida Ta.7772 34
corn
(Zea mays)
Liliopsida Zm.13837 34
bread mold
(Neurospora crassa)
Ascomycetes NCU05797 34
  • 50.73 (n)
  • 47.48 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes spf38 34
  • 52.67 (n)
  • 44.23 (a)
Species where no ortholog for SNRNP40 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for SNRNP40 Gene

ENSEMBL:
Gene Tree for SNRNP40 (if available)
TreeFam:
Gene Tree for SNRNP40 (if available)

Paralogs for SNRNP40 Gene

Paralogs for SNRNP40 Gene

(20) SIMAP similar genes for SNRNP40 Gene using alignment to 2 proteins:

Pseudogenes.org Pseudogenes for SNRNP40 Gene

genes like me logo Genes that share paralogs with SNRNP40: view

Variants for SNRNP40 Gene

Sequence variations from dbSNP and Humsavar for SNRNP40 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1044328 -- 31,289,300(-) CAGGA(A/G)AGGCC reference, missense
rs1001614 -- 31,293,738(+) tagca(A/T)gccat intron-variant
rs1532858 -- 31,289,527(-) GCACA(A/G)CAGGT intron-variant
rs1532859 -- 31,289,142(-) GTCAT(C/T)TCCCA intron-variant
rs1532861 -- 31,293,644(-) tgatc(A/G)cacta intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SNRNP40 Gene

Variant ID Type Subtype PubMed ID
esv2758930 CNV loss 17122850
esv3585645 CNV loss 21293372
nsv10051 CNV gain 18304495
nsv161067 CNV deletion 16902084
nsv471842 CNV novel sequence insertion 20440878

Variation tolerance for SNRNP40 Gene

Residual Variation Intolerance Score: 21.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.67; 14.37% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SNRNP40 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SNRNP40

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SNRNP40 Gene

Disorders for SNRNP40 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SNRNP40 Gene - From: GeneCards

Disorder Aliases PubMed IDs
intermediate charcot-marie-tooth neuropathy
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for SNRNP40

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SNRNP40
genes like me logo Genes that share disorders with SNRNP40: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SNRNP40 Gene

Publications for SNRNP40 Gene

  1. Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. (PMID: 9731529) Neubauer G. … Mann M. (Nat. Genet. 1998) 2 3 4 65
  2. 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. (PMID: 9774689) Achsel T. … Luehrmann R. (Mol. Cell. Biol. 1998) 2 3 4 65
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 65
  4. The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP. (PMID: 16723661) Liu S. … Luehrmann R. (RNA 2006) 3 4 65
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 65

Products for SNRNP40 Gene

Sources for SNRNP40 Gene

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