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Aliases for CDC40 Gene

Aliases for CDC40 Gene

  • Cell Division Cycle 40 2 3 5
  • Cell Division Cycle 40 Homolog 3 4
  • EH-Binding Protein 3 3 4
  • PRP17 Homolog 3 4
  • PRPF17 3 4
  • HPRP17 3 4
  • PRP17 3 4
  • EHB3 3 4
  • Cell Division Cycle 40 Homolog (S. Cerevisiae) 2
  • Cell Division Cycle 40 Homolog (Yeast) 2
  • Pre-MRNA-Processing Factor 17 3
  • Pre-MRNA Splicing Factor 17 3

External Ids for CDC40 Gene

Previous GeneCards Identifiers for CDC40 Gene

  • GC06P110501
  • GC06P110547
  • GC06P110608
  • GC06P108068

Summaries for CDC40 Gene

Entrez Gene Summary for CDC40 Gene

  • Pre-mRNA splicing occurs in two sequential transesterification steps. The protein encoded by this gene is found to be essential for the catalytic step II in pre-mRNA splicing process. It is found in the spliceosome, and contains seven WD repeats, which function in protein-protein interactions. This protein has a sequence similarity to yeast Prp17 protein, which functions in two different cellular processes: pre-mRNA splicing and cell cycle progression. It suggests that this protein may play a role in cell cycle progression. [provided by RefSeq, Jul 2008]

GeneCards Summary for CDC40 Gene

CDC40 (Cell Division Cycle 40) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Major Pathway and RNA Polymerase II Transcription Termination. An important paralog of this gene is WDR25.

UniProtKB/Swiss-Prot for CDC40 Gene

  • Associates with the spliceosome late in the splicing pathway and may function in the second step of pre-mRNA splicing.

Gene Wiki entry for CDC40 Gene

Additional gene information for CDC40 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDC40 Gene

Genomics for CDC40 Gene

GeneHancer (GH) Regulatory Elements for CDC40 Gene

Promoters and enhancers for CDC40 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
GH06I110178 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 555 +0.4 351 4.2 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 WASF1 CDC40 ZBTB24 CD164 SMPD2 CNN2P9 FIG4
GH06I110981 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 12.5 +802.2 802188 2.7 PKNOX1 CLOCK SMAD1 MLX ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 RPF2 CDC40 GTF3C6 RNU6-957P GC06M111009
GH06I110873 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.9 +696.4 696414 6.6 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 ZNF143 SP3 NFYC NBN AMD1 MFSD4B ENSG00000220506 BRD7P4 RPF2 CDK19 CNN2P9 FCF1P5 GTF3C6 RNU6-957P
GH06I109379 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 9.9 -797.8 -797787 6.3 CLOCK MLX FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 SSRP1 ENSG00000260273 CD164 ZBTB24 SMPD2 MICAL1 AK9 PPIL6 PTCHD3P3 ENSG00000233908 CCDC162P
GH06I110813 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 9.9 +635.2 635166 4.1 CLOCK ZFP64 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 ZNF263 SP3 CDK19 AMD1 MFSD4B ENSG00000220506 FCF1P5 RPF2 CNN2P9 BRD7P4 CDC40
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CDC40 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CDC40 gene promoter:

Genomic Locations for CDC40 Gene

Genomic Locations for CDC40 Gene
chr6:110,180,141-110,254,275
(GRCh38/hg38)
Size:
74,135 bases
Orientation:
Plus strand
chr6:110,501,344-110,575,478
(GRCh37/hg19)

Genomic View for CDC40 Gene

Genes around CDC40 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDC40 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDC40 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDC40 Gene

Proteins for CDC40 Gene

  • Protein details for CDC40 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60508-PRP17_HUMAN
    Recommended name:
    Pre-mRNA-processing factor 17
    Protein Accession:
    O60508
    Secondary Accessions:
    • B2RBC5
    • O75471
    • Q5SRN0
    • Q9UPG1

    Protein attributes for CDC40 Gene

    Size:
    579 amino acids
    Molecular mass:
    65521 Da
    Quaternary structure:
    • Identified in the spliceosome C complex.
    SequenceCaution:
    • Sequence=AAC25166.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CDC40 Gene

neXtProt entry for CDC40 Gene

Post-translational modifications for CDC40 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CDC40 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CDC40 Gene

Domains & Families for CDC40 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CDC40: view

No data available for UniProtKB/Swiss-Prot for CDC40 Gene

Function for CDC40 Gene

Molecular function for CDC40 Gene

UniProtKB/Swiss-Prot Function:
Associates with the spliceosome late in the splicing pathway and may function in the second step of pre-mRNA splicing.

Phenotypes From GWAS Catalog for CDC40 Gene

Gene Ontology (GO) - Molecular Function for CDC40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA,IDA 22658674
GO:0005515 protein binding IPI 22365833
genes like me logo Genes that share ontologies with CDC40: view
genes like me logo Genes that share phenotypes with CDC40: view

Animal Model Products

CRISPR Products

miRNA for CDC40 Gene

miRTarBase miRNAs that target CDC40

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CDC40 Gene

Localization for CDC40 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDC40 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 CDC40 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CDC40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex TAS 9524131
GO:0071013 catalytic step 2 spliceosome IEA,IDA 11991638
genes like me logo Genes that share ontologies with CDC40: view

Pathways & Interactions for CDC40 Gene

genes like me logo Genes that share pathways with CDC40: view

Pathways by source for CDC40 Gene

1 KEGG pathway for CDC40 Gene

Gene Ontology (GO) - Biological Process for CDC40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006397 mRNA processing IEA --
GO:0006405 RNA export from nucleus TAS --
GO:0006406 mRNA export from nucleus TAS --
genes like me logo Genes that share ontologies with CDC40: view

No data available for SIGNOR curated interactions for CDC40 Gene

Drugs & Compounds for CDC40 Gene

No Compound Related Data Available

Transcripts for CDC40 Gene

Unigene Clusters for CDC40 Gene

Cell division cycle 40:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CDC40 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16
SP1: -
SP2: -
SP3:

Relevant External Links for CDC40 Gene

GeneLoc Exon Structure for
CDC40
ECgene alternative splicing isoforms for
CDC40

Expression for CDC40 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CDC40 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CDC40 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (22.1) and Monocytes (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CDC40 Gene



Protein tissue co-expression partners for CDC40 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CDC40 Gene:

CDC40

SOURCE GeneReport for Unigene cluster for CDC40 Gene:

Hs.428147

Evidence on tissue expression from TISSUES for CDC40 Gene

  • Nervous system(4.6)
  • Intestine(4.2)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with CDC40: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CDC40 Gene

Orthologs for CDC40 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CDC40 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CDC40 33 34
  • 99.88 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CDC40 34
  • 96 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CDC40 33 34
  • 95.22 (n)
oppossum
(Monodelphis domestica)
Mammalia CDC40 34
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CDC40 33 34
  • 94.13 (n)
mouse
(Mus musculus)
Mammalia Cdc40 33 16 34
  • 91.82 (n)
rat
(Rattus norvegicus)
Mammalia Cdc40 33
  • 90.02 (n)
chicken
(Gallus gallus)
Aves CDC40 33 34
  • 81.72 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 99 (a)
OneToMany
-- 34
  • 70 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia cdc40 33
  • 78.94 (n)
Str.2081 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.25695 33
zebrafish
(Danio rerio)
Actinopterygii cdc40 33 34
  • 72.54 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008925 33
  • 59.68 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6015 33 34
  • 59.45 (n)
worm
(Caenorhabditis elegans)
Secernentea prp-17 33 34
  • 57.89 (n)
Y54G2A.12 34
  • 36 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CDC40 34 36
  • 36 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G10580 33
  • 57.9 (n)
rice
(Oryza sativa)
Liliopsida Os03g0397500 33
  • 53.64 (n)
barley
(Hordeum vulgare)
Liliopsida Hv.5314 33
wheat
(Triticum aestivum)
Liliopsida Ta.28744 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 72 (a)
OneToMany
CSA.6770 34
  • 38 (a)
OneToMany
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes prp17 33
  • 52.19 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU06921 33
  • 49.79 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7893 33
Species where no ortholog for CDC40 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • 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 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 CDC40 Gene

ENSEMBL:
Gene Tree for CDC40 (if available)
TreeFam:
Gene Tree for CDC40 (if available)

Paralogs for CDC40 Gene

Paralogs for CDC40 Gene

(3) SIMAP similar genes for CDC40 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with CDC40: view

Variants for CDC40 Gene

Sequence variations from dbSNP and Humsavar for CDC40 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000109896 -- 110,194,105(+) T/C intron_variant
rs1000214946 -- 110,206,908(+) A/G intron_variant
rs1000280317 -- 110,220,520(+) C/A intron_variant
rs1000367041 -- 110,192,527(+) G/A intron_variant
rs1000413684 -- 110,186,322(+) C/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CDC40 Gene

Variant ID Type Subtype PubMed ID
esv2759462 CNV loss 17122850
nsv5439 CNV insertion 18451855

Variation tolerance for CDC40 Gene

Residual Variation Intolerance Score: 22.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.77; 33.49% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDC40 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CDC40

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDC40 Gene

Disorders for CDC40 Gene

Additional Disease Information for CDC40

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for CDC40 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CDC40 Gene

Publications for CDC40 Gene

  1. Identification and functional analysis of hPRP17, the human homologue of the PRP17/CDC40 yeast gene involved in splicing and cell cycle control. (PMID: 9769104) Ben Yehuda S … Kupiec M (RNA (New York, N.Y.) 1998) 2 3 4 22 58
  2. Functional conservation of the human homolog of the yeast pre-mRNA splicing factor Prp17p. (PMID: 9830021) Lindsey LA … Garcia-Blanco MA (The Journal of biological chemistry 1998) 2 3 4 58
  3. Somatic mutations of the CDC4 (FBXW7) gene in hereditary colorectal tumors. (PMID: 19420964) Miyaki M … Mori T (Oncology 2009) 3 44 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 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 CDC40 Gene

Sources for CDC40 Gene

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