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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. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. 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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for SNRNP40 Gene

Promoters and enhancers for SNRNP40 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I031295 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 589 -0.1 -120 3 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 YY1 POLR2B ZNF207 ZNF143 SNRNP40 ZCCHC17 TXLNA SERINC2 KPNA6 EIF3I KHDRBS1 LOC105378626 ADGRB2
GH01I031924 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 117.7 -639.0 -639036 22.1 CLOCK MLX ZFP64 YBX1 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 GC01P031934 PTP4A2 TXLNA SNRNP40 KHDRBS1 RBBP4 ENSG00000229447 TSSK3 ZBTB8A TMEM39B
GH01I031951 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 110.1 -659.3 -659273 9.1 DMAP1 YBX1 IRF4 YY1 E2F8 ZC3H11A MEF2D GLIS1 RCOR2 NBN SNRNP40 KHDRBS1 TXLNA RBBP4 TSSK3 TMEM39B ENSG00000229447 ZBTB8A IQCC ENSG00000228634
GH01I032289 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 79 -994.5 -994522 3.8 DMAP1 YY1 ZNF213 ZNF416 ZNF143 ZNF548 SP3 NFYC ZFP41 ZNF610 HDAC1 SNRNP40 TSSK3 TXLNA RBBP4 KHDRBS1 TMEM39B ZBTB8A FAM229A ENSG00000235790
GH01I032262 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 81.3 -968.6 -968591 4.8 ZNF493 ZNF529 ZFP64 RARA ZNF213 SCRT2 ZNF654 ZNF680 ZBTB11 CEBPB TXLNA RBBP4 SNRNP40 KHDRBS1 TSSK3 TMEM39B ZBTB8A ZNF362 DCDC2B S100PBP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SNRNP40 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SNRNP40 gene promoter:

Genomic Locations for SNRNP40 Gene

Genomic Locations for SNRNP40 Gene
chr1:31,259,568-31,296,797
(GRCh38/hg38)
Size:
37,230 bases
Orientation:
Minus strand
chr1:31,732,415-31,769,662
(GRCh37/hg19)

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 isoforms=2270 and isoforms=2286

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

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.

Phenotypes From GWAS Catalog for SNRNP40 Gene

Gene Ontology (GO) - Molecular Function for SNRNP40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IBA --
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

miRNA for SNRNP40 Gene

miRTarBase miRNAs that target SNRNP40

Clone 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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
See all subcellular structures

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

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:

Clone 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

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 33
  • 99.35 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SNRNP40 34
  • 95 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 93 (a)
OneToMany
-- 34
  • 81 (a)
OneToMany
dog
(Canis familiaris)
Mammalia SNRNP40 34 33
  • 91.41 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SNRNP40 33 34
  • 90.94 (n)
mouse
(Mus musculus)
Mammalia Snrnp40 16 34 33
  • 89.08 (n)
rat
(Rattus norvegicus)
Mammalia Snrnp40 33
  • 88.8 (n)
chicken
(Gallus gallus)
Aves SNRNP40 34 33
  • 79.62 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SNRNP40 34
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia snrnp40 33
  • 78.24 (n)
Str.6725 33
zebrafish
(Danio rerio)
Actinopterygii snrnp40 33 34
  • 74.88 (n)
zgc56312 33
fruit fly
(Drosophila melanogaster)
Insecta CG3436 34 33
  • 59.55 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009506 33
  • 57.06 (n)
worm
(Caenorhabditis elegans)
Secernentea F08G12.2 33 34
  • 58.07 (n)
C18E3.5 34
  • 53 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G43770 33
  • 60.59 (n)
rice
(Oryza sativa)
Liliopsida Os06g0653800 33
  • 58.31 (n)
Os.4736 33
wheat
(Triticum aestivum)
Liliopsida Ta.7772 33
corn
(Zea mays)
Liliopsida Zm.13837 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes spf38 33
  • 52.67 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU05797 33
  • 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 Variation AA Info Type
rs1000082214 -- 31,288,382(-) C/T intron_variant
rs1000186113 -- 31,281,591(-) T/C intron_variant
rs1000255569 -- 31,264,648(-) C/T intron_variant
rs1000287439 -- 31,293,792(-) G/A intron_variant
rs1000309872 -- 31,277,775(-) A/C 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)

Additional Variant Information 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

Additional Disease Information for SNRNP40

No disorders were found for SNRNP40 Gene.

No data available for MalaCards , 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 (Nature genetics 1998) 2 3 4 58
  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 … Lührmann R (Molecular and cellular biology 1998) 2 3 4 58
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  4. The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP. (PMID: 16723661) Liu S … Lührmann R (RNA (New York, N.Y.) 2006) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for SNRNP40 Gene

Sources for SNRNP40 Gene

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