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Aliases for CDK5RAP1 Gene

Aliases for CDK5RAP1 Gene

  • CDK5 Regulatory Subunit Associated Protein 1 2 3 5
  • CDK5 Activator-Binding Protein C42 3 4
  • C20orf34 3 4
  • CDK5 Regulatory Subunit-Associated Protein 1 3
  • Chromosome 20 Open Reading Frame 34 2
  • HSPC167 3
  • CGI-05 3
  • C42 3

External Ids for CDK5RAP1 Gene

Previous HGNC Symbols for CDK5RAP1 Gene

  • C20orf34

Previous GeneCards Identifiers for CDK5RAP1 Gene

  • GC20M031705
  • GC20M032615
  • GC20M032662
  • GC20M031410
  • GC20M031946
  • GC20M028734

Summaries for CDK5RAP1 Gene

Entrez Gene Summary for CDK5RAP1 Gene

  • This gene encodes a regulator of cyclin-dependent kinase 5 activity. This protein has also been reported to modify RNA by adding a methylthio-group and may thus have a dual function as an RNA methylthiotransferase and as an inhibitor of cyclin-dependent kinase 5 activity. Alternative splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, May 2013]

GeneCards Summary for CDK5RAP1 Gene

CDK5RAP1 (CDK5 Regulatory Subunit Associated Protein 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include protein kinase binding and transferase activity. An important paralog of this gene is CDKAL1.

UniProtKB/Swiss-Prot for CDK5RAP1 Gene

  • Specifically inhibits CDK5 activation by CDK5R1.

Gene Wiki entry for CDK5RAP1 Gene

Additional gene information for CDK5RAP1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDK5RAP1 Gene

Genomics for CDK5RAP1 Gene

GeneHancer (GH) Regulatory Elements for CDK5RAP1 Gene

Promoters and enhancers for CDK5RAP1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20I033400 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 575.2 +0.5 540 2.1 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 CDK5RAP1 ZNF341-AS1 ENSG00000272945 ASIP GC20P033389
GH20I033810 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 21.8 -411.0 -411006 4.6 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 CHMP4B ZNF341-AS1 CDK5RAP1 TPM3P2
GH20I033665 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 16 -265.2 -265228 3.1 HDGF PKNOX1 ATF1 SMAD1 SIN3A ZNF2 IRF4 ZNF48 YY1 ZNF143 ACTL10 CDK5RAP1 CBFA2T2 DNMT3B ZNF341-AS1 ENSG00000272945 E2F1 CHMP4B C20orf144 NECAB3
GH20I033991 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 12.2 -592.1 -592145 4.5 HDGF PKNOX1 CLOCK SMAD1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 RALY RALY-AS1 CDK5RAP1 ENSG00000272945 PIGU MAP1LC3A AHCY ENSG00000275784
GH20I032631 Enhancer 0.9 dbSUPER 19.8 +768.7 768730 3.8 TCF12 POLR2B ZNF766 ZNF143 ATF7 NCOA1 GTF2B ZNF592 MEF2D ATF4 TM9SF4 ASXL1 POFUT1 CDK5RAP1 NOL4L ENSG00000233293 PLAGL2 C20orf203 COMMD7 DNMT3B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CDK5RAP1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CDK5RAP1 gene promoter:

Genomic Locations for CDK5RAP1 Gene

Genomic Locations for CDK5RAP1 Gene
43,064 bases
Minus strand

Genomic View for CDK5RAP1 Gene

Genes around CDK5RAP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDK5RAP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDK5RAP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDK5RAP1 Gene

Proteins for CDK5RAP1 Gene

  • Protein details for CDK5RAP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    CDK5 regulatory subunit-associated protein 1
    Protein Accession:
    Secondary Accessions:
    • A8K7R0
    • Q5QP46
    • Q5QP47
    • Q5QP48
    • Q675N4
    • Q675N5
    • Q9BVG6
    • Q9BWZ5
    • Q9H859
    • Q9NZZ9
    • Q9Y3F0

    Protein attributes for CDK5RAP1 Gene

    601 amino acids
    Molecular mass:
    67689 Da
    Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
    Quaternary structure:
    • Interacts with CDK5R1 (p35 form). CDK5RAP1, CDK5RAP2 and CDK5RAP3 show competitive binding to CDK5R1. Forms a complex with CDK5R1 and CDK5.
    • Sequence=AAD34147.1; Type=Frameshift; Positions=3, 32, 128, 133, 569; Evidence={ECO:0000305}; Sequence=AAF29131.1; Type=Frameshift; Positions=213, 244, 267, 282; Evidence={ECO:0000305}; Sequence=BAB55120.1; Type=Erroneous termination; Positions=500; Note=Translated as Glu.; Evidence={ECO:0000305};

    Alternative splice isoforms for CDK5RAP1 Gene

neXtProt entry for CDK5RAP1 Gene

Post-translational modifications for CDK5RAP1 Gene

  • Ubiquitination at posLast=7070 and Lys378
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CDK5RAP1 Gene

Domains & Families for CDK5RAP1 Gene

Gene Families for CDK5RAP1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for CDK5RAP1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the methylthiotransferase family. MiaB subfamily.
  • Belongs to the methylthiotransferase family. MiaB subfamily.
genes like me logo Genes that share domains with CDK5RAP1: view

Function for CDK5RAP1 Gene

Molecular function for CDK5RAP1 Gene

UniProtKB/Swiss-Prot Function:
Specifically inhibits CDK5 activation by CDK5R1.

Phenotypes From GWAS Catalog for CDK5RAP1 Gene

Gene Ontology (GO) - Molecular Function for CDK5RAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0016740 transferase activity IEA --
GO:0019901 protein kinase binding NAS 10721722
GO:0032403 protein complex binding IEA --
GO:0035597 N6-isopentenyladenosine methylthiotransferase activity IEA --
genes like me logo Genes that share ontologies with CDK5RAP1: view
genes like me logo Genes that share phenotypes with CDK5RAP1: view

Animal Models for CDK5RAP1 Gene

MGI Knock Outs for CDK5RAP1:

Animal Model Products

miRNA for CDK5RAP1 Gene

miRTarBase miRNAs that target CDK5RAP1

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CDK5RAP1 Gene

Localization for CDK5RAP1 Gene

Subcellular locations from

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 CDK5RAP1 gene
Compartment Confidence
mitochondrion 3
nucleus 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CDK5RAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IEA --
genes like me logo Genes that share ontologies with CDK5RAP1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for CDK5RAP1 Gene

Pathways & Interactions for CDK5RAP1 Gene

SuperPathways for CDK5RAP1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CDK5RAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006400 tRNA modification IEA --
GO:0007420 brain development NAS 10915792
GO:0035600 tRNA methylthiolation IEA --
GO:0045664 regulation of neuron differentiation NAS 10721722
GO:0045736 negative regulation of cyclin-dependent protein serine/threonine kinase activity TAS 17491008
genes like me logo Genes that share ontologies with CDK5RAP1: view

No data available for Pathways by source and SIGNOR curated interactions for CDK5RAP1 Gene

Drugs & Compounds for CDK5RAP1 Gene

(1) Additional Compounds for CDK5RAP1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine
  • 2-S-Adenosyl-L-methionine
  • 5'-Deoxyadenosine-5'-L-methionine disulfate ditosylate
  • 5'-Deoxyadenosine-5'-L-methionine disulphate ditosylate
  • Active methionine
genes like me logo Genes that share compounds with CDK5RAP1: view

Transcripts for CDK5RAP1 Gene

Unigene Clusters for CDK5RAP1 Gene

CDK5 regulatory subunit associated protein 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CDK5RAP1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c · 10d · 10e · 10f ^ 11a · 11b ^ 12a ·
SP1: - - - - -
SP2: - - - - -
SP3: - - - - - -
SP4: - - - - -
SP5: - - - - - - - - - - -
SP6: - - - - -
SP7: - - - - - -
SP8: - - - - -
SP9: - - - - - - - - - - - - - -
SP10: - - - -
SP11: - - - - -
SP12: -
SP13: - - - - - - - - -
SP14: - - - - - - - - - - -
SP15: -
SP16: - - - - - -
SP17: - - - - - - - - - - - -
SP19: - - -
SP20: - - - -

ExUns: 12b ^ 13 ^ 14 ^ 15a · 15b · 15c · 15d ^ 16
SP1: - -
SP2: - -
SP3: - -
SP5: - -
SP6: -

Relevant External Links for CDK5RAP1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CDK5RAP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CDK5RAP1 Gene

Protein differential expression in normal tissues from HIPED for CDK5RAP1 Gene

This gene is overexpressed in Cerebrospinal fluid (54.9) and Plasma (14.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CDK5RAP1 Gene

Protein tissue co-expression partners for CDK5RAP1 Gene

NURSA nuclear receptor signaling pathways regulating expression of CDK5RAP1 Gene:


SOURCE GeneReport for Unigene cluster for CDK5RAP1 Gene:


mRNA Expression by UniProt/SwissProt for CDK5RAP1 Gene:

Tissue specificity: Widely expressed. Expressed in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas.

Evidence on tissue expression from TISSUES for CDK5RAP1 Gene

  • Lung(4.5)
  • Intestine(4.4)
  • Blood(4.2)
  • Stomach(4.2)
  • Nervous system(3.7)
genes like me logo Genes that share expression patterns with CDK5RAP1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CDK5RAP1 Gene

Orthologs for CDK5RAP1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CDK5RAP1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CDK5RAP1 33 34
  • 98.86 (n)
(Bos Taurus)
Mammalia CDK5RAP1 33 34
  • 89.21 (n)
(Canis familiaris)
Mammalia CDK5RAP1 33 34
  • 89 (n)
(Mus musculus)
Mammalia Cdk5rap1 33 16 34
  • 85.98 (n)
(Rattus norvegicus)
Mammalia Cdk5rap1 33
  • 85.91 (n)
(Monodelphis domestica)
Mammalia CDK5RAP1 34
  • 76 (a)
(Ornithorhynchus anatinus)
Mammalia CDK5RAP1 34
  • 76 (a)
(Gallus gallus)
Aves CDK5RAP1 33 34
  • 76.49 (n)
(Anolis carolinensis)
Reptilia CDK5RAP1 34
  • 66 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cdk5rap1 33
  • 67.99 (n)
Str.13196 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.12738 33
(Danio rerio)
Actinopterygii zgc:162738 33
  • 63.11 (n)
  • 63 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.505 33
fruit fly
(Drosophila melanogaster)
Insecta CG6345 33 34
  • 56.36 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012104 33
  • 55.79 (n)
(Caenorhabditis elegans)
Secernentea F25B5.5 33 34
  • 55.08 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G36390 33
  • 55.42 (n)
(Oryza sativa)
Liliopsida Os11g0592800 33
  • 56.7 (n)
(Hordeum vulgare)
Liliopsida Hv.1217 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 51 (a)
Species where no ortholog for CDK5RAP1 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • 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)
  • 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)
  • wheat (Triticum aestivum)

Evolution for CDK5RAP1 Gene

Gene Tree for CDK5RAP1 (if available)
Gene Tree for CDK5RAP1 (if available)

Paralogs for CDK5RAP1 Gene

Paralogs for CDK5RAP1 Gene

genes like me logo Genes that share paralogs with CDK5RAP1: view

Variants for CDK5RAP1 Gene

Sequence variations from dbSNP and Humsavar for CDK5RAP1 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1000048479 -- 33,391,842(-) T/G genic_upstream_transcript_variant, intron_variant
rs1000101845 -- 33,392,115(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000148161 -- 33,389,316(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000298505 -- 33,367,083(-) G/A intron_variant
rs1000349972 -- 33,398,082(-) T/C genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CDK5RAP1 Gene

Variant ID Type Subtype PubMed ID
nsv1064413 CNV gain 25217958
nsv819750 CNV loss 19587683

Variation tolerance for CDK5RAP1 Gene

Residual Variation Intolerance Score: 74.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.94; 74.54% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDK5RAP1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDK5RAP1 Gene

Disorders for CDK5RAP1 Gene

Additional Disease Information for CDK5RAP1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for CDK5RAP1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CDK5RAP1 Gene

Publications for CDK5RAP1 Gene

  1. Cloning of three novel neuronal Cdk5 activator binding proteins. (PMID: 10721722) Ching YP … Wang JH (Gene 2000) 2 3 4 22 58
  2. Cloning, characterization and expression of CDK5RAP1_v3 and CDK5RAP1_v4, two novel splice variants of human CDK5RAP1. (PMID: 15329498) Zou X … Mao Y (Genes & genetic systems 2004) 2 3 4 58
  3. Identification of a neuronal Cdk5 activator-binding protein as Cdk5 inhibitor. (PMID: 11882646) Ching YP … Wang JH (The Journal of biological chemistry 2002) 2 3 4 58
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  5. An approach based on a genome-wide association study reveals candidate loci for narcolepsy. (PMID: 20677014) Shimada M … Tokunaga K (Human genetics 2010) 3 44 58

Products for CDK5RAP1 Gene

Sources for CDK5RAP1 Gene

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