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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 CIViC summary , 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
GH01G031924 2.1 FANTOM5 Ensembl ENCODE dbSUPER 61.8 -639.0 -639036 22.1 MLX CREB3L1 AGO1 ZFP64 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF416 SNRNP40 ENSG00000229447 TSSK3 LOC105378626 EIF3I MTMR9LP KHDRBS1 HDAC1 ENSG00000224066 ENSG00000203325
GH01G030737 2 FANTOM5 Ensembl ENCODE dbSUPER 57.7 +545.5 545530 28.0 HDGF PKNOX1 CREB3L1 ARNT WRNIP1 ZFP64 SIN3A FEZF1 YY1 ZNF766 SNRNP40 LAPTM5 ENSG00000229447 LOC105378626 MATN1 MATN1-AS1 SDC3 PUM1 LOC105378620 MIR4420
GH01G031795 1.5 FANTOM5 ENCODE dbSUPER 56.4 -501.1 -501126 4.5 ATF1 ZNF493 ZFP64 TCF12 GTF3C2 GLIS2 FOS ZNF263 REST ZNF623 SNRNP40 ENSG00000229447 EIF3I TSSK3 COL16A1 ZBTB8B KPNA6 MTMR9LP PEF1 KHDRBS1
GH01G032262 1.8 FANTOM5 Ensembl ENCODE dbSUPER 43.5 -968.6 -968591 4.8 HDGF ZNF493 ZFP64 ZNF121 GATA2 FOS REST ZNF623 ZNF518A MEF2D SNRNP40 EIF3I MTMR9LP ZBTB8B KPNA6 TSSK3 DCDC2B ENSG00000270115 LCK TXLNA
GH01G031825 1.7 Ensembl ENCODE dbSUPER 39 -530.5 -530465 2.8 CREB3L1 DMAP1 YY1 ZNF143 ZNF416 ZNF548 ZNF263 SP3 NFYC TBX21 SNRNP40 ENSG00000229447 TSSK3 LOC105378626 HDAC1 ENSG00000235790 KPNA6 SPOCD1 ENSG00000203620
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000004168 -103 2201 HDGF PKNOX1 CREB3L1 ARNT ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207

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 Lys270 and Lys286
  • Modification sites at PhosphoSitePlus

Other Protein References for SNRNP40 Gene

ENSEMBL proteins:
REFSEQ proteins:

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

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

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

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:0003723 RNA binding IDA 22658674
GO:0005515 protein binding IPI 9774689
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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SNRNP40 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for SNRNP40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005682 U5 snRNP TAS 9774689
GO:0005732 small nucleolar ribonucleoprotein complex NAS 9774689
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:0006397 mRNA processing IEA --
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

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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

Evidence on tissue expression from TISSUES for SNRNP40 Gene

  • Nervous system(2.4)
  • Kidney(2.2)
  • Pancreas(2.2)
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 , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia SNRNP40 34 35
  • 99.35 (n)
oppossum
(Monodelphis domestica)
Mammalia SNRNP40 35
  • 95 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 93 (a)
OneToMany
-- 35
  • 81 (a)
OneToMany
dog
(Canis familiaris)
Mammalia SNRNP40 34 35
  • 91.41 (n)
cow
(Bos Taurus)
Mammalia SNRNP40 34 35
  • 90.94 (n)
mouse
(Mus musculus)
Mammalia Snrnp40 34 16 35
  • 89.08 (n)
rat
(Rattus norvegicus)
Mammalia Snrnp40 34
  • 88.8 (n)
chicken
(Gallus gallus)
Aves SNRNP40 34 35
  • 79.62 (n)
lizard
(Anolis carolinensis)
Reptilia SNRNP40 35
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia snrnp40 34
  • 78.24 (n)
Str.6725 34
zebrafish
(Danio rerio)
Actinopterygii snrnp40 34 35
  • 74.88 (n)
zgc56312 34
fruit fly
(Drosophila melanogaster)
Insecta CG3436 34 35
  • 59.55 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009506 34
  • 57.06 (n)
worm
(Caenorhabditis elegans)
Secernentea F08G12.2 34 35
  • 58.07 (n)
C18E3.5 35
  • 53 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G43770 34
  • 60.59 (n)
rice
(Oryza sativa)
Liliopsida Os06g0653800 34
  • 58.31 (n)
Os.4736 34
wheat
(Triticum aestivum)
Liliopsida Ta.7772 34
corn
(Zea mays)
Liliopsida Zm.13837 34
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes spf38 34
  • 52.67 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU05797 34
  • 50.73 (n)
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
rs1000082214 -- 31,288,382(+) TAGGC(C/T)TCAGT intron-variant
rs1000186113 -- 31,281,591(+) GGACA(C/T)GAACA intron-variant
rs1000255569 -- 31,264,648(+) GTACA(C/T)TCATC intron-variant
rs1000287439 -- 31,293,792(+) GCCTA(A/G)GCTGG intron-variant
rs1000309872 -- 31,277,775(+) CCACA(A/C)CCCCC 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 64
  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 64
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 64
  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 64
  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 64

Products for SNRNP40 Gene

Sources for SNRNP40 Gene

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