CDK5 (cyclin-dependent kinase 5)

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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret
Donations are also welcome

CDK5 (cyclin-dependent kinase 5)

Identity

Other names	PSSALRE
HGNC (Hugo)	CDK5
LocusID (NCBI)	1020
Location	7q36.1
Location_base_pair	Starts at 150750902 and ends at 150755052 bp from pter ( according to hg19-Feb_2009)
Note	Non-annotated gene. Preliminary data : if you are an author who wish to write a full paper/card on this gene, go to How to contribute

DNA/RNA

Other Leukemias implicated (Data extracted from papers in the Atlas)

Leukemias

11q23ChildAMLID1615

External links

	Nomenclature
HGNC (Hugo)	CDK5 1774
	Cards
Entrez_Gene (NCBI)	CDK5 1020 cyclin-dependent kinase 5
GeneCards (Weizmann)	CDK5
Ensembl hg19 (Hinxton)	[Gene_View] chr7:150750902-150755052 [Contig_View] CDK5 [Vega]
Ensembl hg38 (Hinxton)	[Gene_View] chr7:150750902-150755052 [Contig_View] CDK5 [Vega]
cBioPortal	CDK5
AceView (NCBI)	CDK5
Genatlas (Paris)	CDK5
WikiGenes	1020
SOURCE (Princeton)	CDK5
	Genomic and cartography
GoldenPath hg19 (UCSC)	CDK5 - chr7:150750902-150755052 - 7q36.1 [Description] (hg19-Feb_2009)
GoldenPath hg38 (UCSC)	CDK5 - 7q36.1 [Description] (hg38-Dec_2013)
Ensembl	CDK5 - 7q36.1 [CytoView hg19] CDK5 - 7q36.1 [CytoView hg38]
Mapping of homologs : NCBI	CDK5 [Mapview hg19] CDK5 [Mapview hg38]
OMIM	123831
	Gene and transcription
Genbank (Entrez)	AK026533 AY049778 AY927560 BC005115 BP309068
RefSeq transcript (Entrez)	NM_001164410 NM_004935
RefSeq genomic (Entrez)	AC_000139 NC_000007 NC_018918 NT_007933 NW_001839088 NW_004929333
Consensus coding sequences : CCDS (NCBI)	CDK5
Cluster EST : Unigene	Hs.647078 [ NCBI ]
CGAP (NCI)	Hs.647078
Alternative Splicing : Fast-db (Paris)	GSHG0028714
Gene Expression	CDK5 [ NCBI-GEO ] CDK5 [ SEEK ] CDK5 [ MEM ]
SOURCE (Princeton)	Expression in : [Normal Tissue Atlas] [carcinoma Classsification] [NCI60]
	Protein : pattern, domain, 3D structure
UniProt/SwissProt	Q00535 (Uniprot)
NextProt	Q00535 [Medical]
With graphics : InterPro	Q00535
Splice isoforms : SwissVar	Q00535 (Swissvar)
Catalytic activity : Enzyme	2.7.11.22 [ Enzyme-Expasy ] 2.7.11.22 2.7.11.22 [ IntEnz-EBI ] 2.7.11.22 [ BRENDA ] 2.7.11.22 [ KEGG ]
Domaine pattern : Prosite (Expaxy)	PROTEIN_KINASE_ATP (PS00107) PROTEIN_KINASE_DOM (PS50011) PROTEIN_KINASE_ST (PS00108)
Domains : Interpro (EBI)	Kinase-like_dom Prot_kinase_dom Protein_kinase_ATP_BS Ser/Thr_dual-sp_kinase_dom Ser/Thr_kinase_AS
Related proteins : CluSTr	Q00535
Domain families : Pfam (Sanger)	Pkinase (PF00069)
Domain families : Pfam (NCBI)	pfam00069
Domain families : Smart (EMBL)	S_TKc (SM00220)
DMDM Disease mutations	1020
Blocks (Seattle)	Q00535
PDB (SRS)	1H4L 1LFR 1UNG 1UNH 1UNL 3O0G 4AU8
PDB (PDBSum)	1H4L 1LFR 1UNG 1UNH 1UNL 3O0G 4AU8
PDB (IMB)	1H4L 1LFR 1UNG 1UNH 1UNL 3O0G 4AU8
PDB (RSDB)	1H4L 1LFR 1UNG 1UNH 1UNL 3O0G 4AU8
Peptide Atlas	Q00535
HPRD	00449
IPI	IPI00023530 IPI00827700
	Protein Interaction databases
DIP (DOE-UCLA)	Q00535
IntAct (EBI)	Q00535
BioGRID	CDK5
IntegromeDB	CDK5
STRING (EMBL)	CDK5
	Ontologies - Pathways
QuickGO	Q00535
Ontology : AmiGO	neuron migration synaptic transmission, dopaminergic p53 binding protein kinase activity protein serine/threonine kinase activity protein serine/threonine kinase activity protein serine/threonine kinase activity cyclin-dependent protein serine/threonine kinase activity ErbB-2 class receptor binding protein binding ATP binding nucleus cytoplasm cytosol intracellular protein transport nucleocytoplasmic transport cell cycle cell-matrix adhesion synaptic transmission axon guidance synapse assembly skeletal muscle tissue development blood coagulation motor neuron axon guidance cell proliferation visual learning embryo development Schwann cell development postsynaptic density membrane synaptic vesicle exocytosis kinase activity phosphorylation cyclin-dependent protein kinase 5 holoenzyme complex peptidyl-serine phosphorylation peptidyl-threonine phosphorylation sensory perception of pain cerebellar cortex formation hippocampus development layer formation in cerebral cortex central nervous system neuron development corpus callosum development lamellipodium cell junction filopodium neuron differentiation neuron differentiation regulation of cell migration axon dendrite growth cone negative regulation of axon extension acetylcholine receptor activator activity cortical actin cytoskeleton organization neuron projection development negative regulation of protein ubiquitination neuromuscular junction negative regulation of synaptic plasticity positive regulation of protein binding receptor catabolic process serine phosphorylation of STAT3 protein synaptic transmission, glutamatergic protein localization to synapse regulation of apoptotic process neuronal cell body receptor clustering ErbB-3 class receptor binding perikaryon positive regulation of neuron apoptotic process regulated secretory pathway postsynaptic membrane negative regulation of cell cycle positive regulation of protein kinase activity negative regulation of proteolysis negative regulation of transcription, DNA-templated positive regulation of calcium ion-dependent exocytosis protein autophosphorylation negative regulation of protein export from nucleus ephrin receptor binding behavioral response to cocaine regulation of synaptic plasticity regulation of synaptic plasticity synaptic vesicle endocytosis rhythmic process axon extension oligodendrocyte differentiation dendrite morphogenesis tau-protein kinase activity cell division neuron apoptotic process regulation of excitatory postsynaptic membrane potential regulation of dendritic spine morphogenesis calcium ion import regulation of cell cycle arrest positive regulation of protein targeting to membrane negative regulation of neuron death positive regulation of actin cytoskeleton reorganization positive regulation of receptor activity positive regulation of receptor activity
Ontology : EGO-EBI	neuron migration synaptic transmission, dopaminergic p53 binding protein kinase activity protein serine/threonine kinase activity protein serine/threonine kinase activity protein serine/threonine kinase activity cyclin-dependent protein serine/threonine kinase activity ErbB-2 class receptor binding protein binding ATP binding nucleus cytoplasm cytosol intracellular protein transport nucleocytoplasmic transport cell cycle cell-matrix adhesion synaptic transmission axon guidance synapse assembly skeletal muscle tissue development blood coagulation motor neuron axon guidance cell proliferation visual learning embryo development Schwann cell development postsynaptic density membrane synaptic vesicle exocytosis kinase activity phosphorylation cyclin-dependent protein kinase 5 holoenzyme complex peptidyl-serine phosphorylation peptidyl-threonine phosphorylation sensory perception of pain cerebellar cortex formation hippocampus development layer formation in cerebral cortex central nervous system neuron development corpus callosum development lamellipodium cell junction filopodium neuron differentiation neuron differentiation regulation of cell migration axon dendrite growth cone negative regulation of axon extension acetylcholine receptor activator activity cortical actin cytoskeleton organization neuron projection development negative regulation of protein ubiquitination neuromuscular junction negative regulation of synaptic plasticity positive regulation of protein binding receptor catabolic process serine phosphorylation of STAT3 protein synaptic transmission, glutamatergic protein localization to synapse regulation of apoptotic process neuronal cell body receptor clustering ErbB-3 class receptor binding perikaryon positive regulation of neuron apoptotic process regulated secretory pathway postsynaptic membrane negative regulation of cell cycle positive regulation of protein kinase activity negative regulation of proteolysis negative regulation of transcription, DNA-templated positive regulation of calcium ion-dependent exocytosis protein autophosphorylation negative regulation of protein export from nucleus ephrin receptor binding behavioral response to cocaine regulation of synaptic plasticity regulation of synaptic plasticity synaptic vesicle endocytosis rhythmic process axon extension oligodendrocyte differentiation dendrite morphogenesis tau-protein kinase activity cell division neuron apoptotic process regulation of excitatory postsynaptic membrane potential regulation of dendritic spine morphogenesis calcium ion import regulation of cell cycle arrest positive regulation of protein targeting to membrane negative regulation of neuron death positive regulation of actin cytoskeleton reorganization positive regulation of receptor activity positive regulation of receptor activity
Pathways : BIOCARTA	FOSB gene expression and drug abuse [Genes] Deregulation of CDK5 in Alzheimers Disease [Genes] Phosphorylation of MEK1 by cdk5/p35 down regulates the MAP kinase pathway [Genes] Rac 1 cell motility signaling pathway [Genes] Bioactive Peptide Induced Signaling Pathway [Genes] Estrogen-responsive protein Efp controls cell cycle and breast tumors growth [Genes] Reelin Signaling Pathway [Genes] Lissencephaly gene (LIS1) in neuronal migration and development [Genes] Regulation of ck1/cdk5 by type 1 glutamate receptors [Genes]
Pathways : KEGG	Axon guidance Alzheimer's disease Cocaine addiction
Protein Interaction Database	CDK5
DoCM (Curated mutations)	CDK5
Wikipedia pathways	CDK5
	Gene fusion - rearrangements
	Polymorphisms : SNP, variants
NCBI Variation Viewer	CDK5 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)	CDK5
dbVar	CDK5
ClinVar	CDK5
1000_Genomes	CDK5
Exome Variant Server	CDK5
SNP (GeneSNP Utah)	CDK5
SNP : HGBase	CDK5
Genetic variants : HAPMAP	CDK5
Genomic Variants (DGV)	CDK5 [DGVbeta]
	Mutations
Somatic Mutations in Cancer : COSMIC	CDK5
CONAN: Copy Number Analysis	CDK5
LOVD (Leiden Open Variation Database)	Whole genome datasets
LOVD (Leiden Open Variation Database)	LOVD 3.0 shared installation
Impact of mutations	[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor]
	Diseases
DECIPHER (Syndromes)	7:150750902-150755052
Mutations and Diseases : HGMD	CDK5
OMIM	123831
Medgen	CDK5
NextProt	Q00535 [Medical]
GENETests	CDK5
Disease Genetic Association	CDK5
Huge Navigator	CDK5 [HugePedia] CDK5 [HugeCancerGEM]
snp3D : Map Gene to Disease	1020
DGIdb (Drug Gene Interaction db)	CDK5
	General knowledge
Homologs : HomoloGene	CDK5
Homology/Alignments : Family Browser (UCSC)	CDK5
Phylogenetic Trees/Animal Genes : TreeFam	CDK5
Chemical/Protein Interactions : CTD	1020
Chemical/Pharm GKB Gene	PA26310
Clinical trial	CDK5
	Other databases
	Probes
	Litterature
PubMed	247 Pubmed reference(s) in Entrez
CoreMine	CDK5
GoPubMed	CDK5
iHOP	CDK5

Genes in title	automatic search in PubMed
REVIEW articles	automatic search in PubMed
Last year publications	automatic search in PubMed

Search in all EBI NCBI

Contributor(s)

Written	09-2002	Dessen P, Le Minor S

Updated	12-2014	Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology

indexed on : Sat Feb 14 15:07:49 CET 2015

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jlhuret@AtlasGeneticsOncology.org.