Human Gene CDK5 (uc003wis.2)
  Description: Homo sapiens cyclin-dependent kinase 5 (CDK5), transcript variant 1, mRNA.
RefSeq Summary (NM_001164410): This gene encodes a proline-directed serine/threonine kinase that is a member of the cyclin-dependent kinase family of proteins. Unlike other members of the family, the protein encoded by this gene does not directly control cell cycle regulation. Instead the protein, which is predominantly expressed at high levels in mammalian postmitotic central nervous system neurons, functions in diverse processes such as synaptic plasticity and neuronal migration through phosphorylation of proteins required for cytoskeletal organization, endocytosis and exocytosis, and apoptosis. In humans, an allelic variant of the gene that results in undetectable levels of the protein has been associated with lethal autosomal recessive lissencephaly-7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2015].
Transcript (Including UTRs)
   Position: hg19 chr7:150,750,899-150,755,052 Size: 4,154 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr7:150,751,096-150,754,935 Size: 3,840 Coding Exon Count: 11 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:150,750,899-150,755,052)mRNA (may differ from genome)Protein (260 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMalacardsMGIOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CDK5
CDC HuGE Published Literature: CDK5
Positive Disease Associations: Alzheimer's disease
Related Studies:
  1. Alzheimer's disease
    Alejandro Arias-Vasquez , et al. Journal of neurology 2008 255(5):655-62, Cyclin-dependent kinase 5 is associated with risk for Alzheimer's disease in a Dutch population-based study., Journal of neurology 2008 255(5):655-62. [PubMed 18350355]

-  MalaCards Disease Associations
  MalaCards Gene Search: CDK5
Diseases sorted by gene-association score: lissencephaly 7 with cerebellar hypoplasia* (969), lissencephaly (24), ischemia (10), aneurysmal bone cysts (9), lissencephaly with cerebellar hypoplasia (7), pachygyria (7), non-syndromic intellectual disability (6), alzheimer disease (6), lateral sclerosis (3), neuroblastoma (3), amyotrophic lateral sclerosis 1 (2), parkinson disease, late-onset (2), syndromic intellectual disability (2), charcot-marie-tooth disease, type 2e (1), dementia, lewy body (1), nervous system disease (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 50.81 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 726.08 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -64.90117-0.555 Picture PostScript Text
3' UTR -86.50197-0.439 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF00069 - Protein kinase domain
PF07714 - Protein tyrosine kinase

SCOP Domains:
56112 - Protein kinase-like (PK-like)

ModBase Predicted Comparative 3D Structure on Q00535-2
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  L04658 - Homo sapiens gene sequence.
BC005115 - Homo sapiens cyclin-dependent kinase 5, mRNA (cDNA clone MGC:1469 IMAGE:3537202), complete cds.
GQ900934 - Homo sapiens clone HEL-T-46 epididymis secretory sperm binding protein mRNA, complete cds.
AK026533 - Homo sapiens cDNA: FLJ22880 fis, clone KAT03552, highly similar to HSSTHPKE Homo sapiens mRNA PSSALRE for serine/threonine protein kinase.
AY927560 - Homo sapiens mRNA sequence.
X66364 - H.sapiens mRNA PSSALRE for serine/threonine protein kinase.
AY049778 - Homo sapiens cyclin-dependent kinase 5 (CDK5) mRNA, complete cds.
BT006680 - Homo sapiens cyclin-dependent kinase 5 mRNA, complete cds.
DQ411039 - Homo sapiens protein kinase CDK5 splicing variant mRNA, complete cds, alternatively spliced.
KJ905165 - Synthetic construct Homo sapiens clone ccsbBroadEn_14575 CDK5 gene, encodes complete protein.
KJ890884 - Synthetic construct Homo sapiens clone ccsbBroadEn_00278 CDK5 gene, encodes complete protein.
CU674995 - Synthetic construct Homo sapiens gateway clone IMAGE:100016981 5' read CDK5 mRNA.
KU177968 - Homo sapiens cyclin-dependent kinase 5 isoform 1 (CDK5) mRNA, partial cds.
KU177969 - Homo sapiens cyclin-dependent kinase 5 isoform 2 (CDK5) mRNA, partial cds.
AB463550 - Synthetic construct DNA, clone: pF1KB8207, Homo sapiens CDK5 gene for cyclin-dependent kinase 5, without stop codon, in Flexi system.
CR457041 - Homo sapiens full open reading frame cDNA clone RZPDo834B0318D for gene CDK5, cyclin-dependent kinase 5; complete cds, incl. stopcodon.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04360 - Axon guidance
hsa05010 - Alzheimer's disease

BioCarta from NCI Cancer Genome Anatomy Project
h_fosbPathway - FOSB gene expression and drug abuse
h_p35alzheimersPathway - Deregulation of CDK5 in Alzheimers Disease
h_cdk5Pathway - Phosphorylation of MEK1 by cdk5/p35 down regulates the MAP kinase pathway
h_rac1Pathway - Rac 1 cell motility signaling pathway
h_biopeptidesPathway - Bioactive Peptide Induced Signaling Pathway
h_EfpPathway - Estrogen-responsive protein Efp controls cell cycle and breast tumors growth
h_reelinPathway - Reelin Signaling Pathway
h_Lis1Pathway - Lissencephaly gene (LIS1) in neuronal migration and development
h_ck1Pathway - Regulation of ck1/cdk5 by type 1 glutamate receptors

Reactome (by CSHL, EBI, and GO)

Protein Q00535 (Reactome details) participates in the following event(s):

R-HSA-1013833 Cables link CDK5 and ABL1
R-HSA-8863013 CDK5 binds p25
R-NUL-9032945 Ntrk2 phosohorylates CDK5
R-HSA-399946 Recruitment and activation of Cdk5
R-HSA-9032841 Activated NTRK2 binds CDK5
R-HSA-8863587 CDK5:p25 translocates to the nucleus
R-HSA-180047 CDK5 phosphorylates DARPP-32 on Thr75
R-HSA-9032863 CDK5 phosphorylates NTRK2
R-HSA-9032854 NTRK2 phosphorylates CDK5
R-HSA-8863007 p25-bound CDK5 phosphorylates CDC25B
R-HSA-8863011 p25-bound CDK5 phosphorylates CDC25C
R-HSA-8868260 CDK5:p25 phosphorylates GOLGA2
R-HSA-8868567 CDK5:p25 phosphorylates PRDX1
R-HSA-8868573 CDK5:p25 phosphorylates PRDX2
R-HSA-8868666 CDK5:p25 phosphorylates JUN
R-HSA-8870558 CDK5:p25 phosphorylates FOXO3
R-HSA-6805276 CDK5 phosphorylates TP53
R-HSA-8863014 p25-bound CDK5 phosphorylates CDC25A
R-HSA-8868340 CDK5:p25 phosphorylates lamin B1
R-HSA-8868344 CDK5:p25 phosphorylates lamin A
R-HSA-399951 Phosphorylation of CRMPs by GSK3beta
R-HSA-399944 Phosphorylation of CRMPs by Cdk5
R-HSA-983231 Factors involved in megakaryocyte development and platelet production
R-HSA-8862803 Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models
R-HSA-399956 CRMPs in Sema3A signaling
R-HSA-9032845 Activated NTRK2 signals through CDK5
R-HSA-109582 Hemostasis
R-HSA-8863678 Neurodegenerative Diseases
R-HSA-180024 DARPP-32 events
R-HSA-373755 Semaphorin interactions
R-HSA-9006115 Signaling by NTRK2 (TRKB)
R-HSA-1643685 Disease
R-HSA-111885 Opioid Signalling
R-HSA-6804756 Regulation of TP53 Activity through Phosphorylation
R-HSA-422475 Axon guidance
R-HSA-166520 Signaling by NTRKs
R-HSA-418594 G alpha (i) signalling events
R-HSA-5633007 Regulation of TP53 Activity
R-HSA-1266738 Developmental Biology
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-388396 GPCR downstream signalling
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-162582 Signal Transduction
R-HSA-372790 Signaling by GPCR
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: CDKN5, NM_001164410, NP_001157882, Q00535-2
UCSC ID: uc003wis.2
RefSeq Accession: NM_001164410
Protein: Q00535-2, splice isoform of Q00535 CCDS: CCDS55184.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001164410.1
exon count: 11CDS single in 3' UTR: no RNA size: 1111
ORF size: 783CDS single in intron: no Alignment % ID: 99.91
txCdsPredict score: 1766.00frame shift in genome: no % Coverage: 98.47
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 1
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.