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CDK5RAP2 CDK5 regulatory subunit associated protein 2 [ Homo sapiens (human) ]

Gene ID: 55755, updated on 14-Jul-2019

Summary

Official Symbol
CDK5RAP2provided by HGNC
Official Full Name
CDK5 regulatory subunit associated protein 2provided by HGNC
Primary source
HGNC:HGNC:18672
See related
Ensembl:ENSG00000136861 MIM:608201
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
C48; MCPH3; Cep215
Summary
This gene encodes a regulator of CDK5 (cyclin-dependent kinase 5) activity. The protein encoded by this gene is localized to the centrosome and Golgi complex, interacts with CDK5R1 and pericentrin (PCNT), plays a role in centriole engagement and microtubule nucleation, and has been linked to primary microcephaly and Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]
Expression
Ubiquitous expression in testis (RPKM 15.8), bone marrow (RPKM 9.3) and 25 other tissues See more
Orthologs

Genomic context

See CDK5RAP2 in Genome Data Viewer
Location:
9q33.2
Exon count:
39
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (120388869..120580170, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (123151147..123342448, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene microRNA 147a Neighboring gene uncharacterized LOC105376253 Neighboring gene multiple EGF like domains 9 Neighboring gene NFE2L2 motif-containing MPRA enhancer 171 Neighboring gene adenosylhomocysteinase pseudogene 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association of lipid-lowering response to statins in combined study populations.
NHGRI GWA Catalog
Novel risk loci for rheumatoid arthritis in Han Chinese and congruence with risk variants in Europeans.
NHGRI GWA Catalog

Pathways from BioSystems

  • AURKA Activation by TPX2, organism-specific biosystem (from REACTOME)
    AURKA Activation by TPX2, organism-specific biosystemTPX2 binds to aurora kinase A (AURKA) at centrosomes and promotes its activation by facilitating AURKA active conformation and autophosphorylation of the AURKA threonine residue T288 (Bayliss et al. ...
  • Anchoring of the basal body to the plasma membrane, organism-specific biosystem (from REACTOME)
    Anchoring of the basal body to the plasma membrane, organism-specific biosystemCilium biogenesis is initiated by the docking of basal bodies, a centriole-derived organelle, to the plasma membrane (reviewed in Reiter et al, 2012). The centriole consists of a multiprotein core su...
  • Cell Cycle, organism-specific biosystem (from REACTOME)
    Cell Cycle, organism-specific biosystem
    Cell Cycle
  • Cell Cycle, Mitotic, organism-specific biosystem (from REACTOME)
    Cell Cycle, Mitotic, organism-specific biosystemThe replication of the genome and the subsequent segregation of chromosomes into daughter cells are controlled by a series of events collectively known as the cell cycle. DNA replication is carried o...
  • Centrosome maturation, organism-specific biosystem (from REACTOME)
    Centrosome maturation, organism-specific biosystemThe centrosome is the primary microtubule organizing center (MTOC) in vertebrate cells and plays an important role in orchestrating the formation of the mitotic spindle. Centrosome maturation is an ...
  • Cilium Assembly, organism-specific biosystem (from REACTOME)
    Cilium Assembly, organism-specific biosystemCilia are membrane covered organelles that extend from the surface of eukaryotic cells. Cilia may be motile, such as respiratory cilia) or non-motile (such as the primary cilium) and are distinguishe...
  • G2/M Transition, organism-specific biosystem (from REACTOME)
    G2/M Transition, organism-specific biosystemCyclin A can also form complexes with Cdc2 (Cdk1). Together with three B-type cyclins, Cdc2 (Cdk1) regulates the transition from G2 into mitosis. These complexes are activated by dephosphorylation of...
  • Loss of Nlp from mitotic centrosomes, organism-specific biosystem (from REACTOME)
    Loss of Nlp from mitotic centrosomes, organism-specific biosystemDuring interphase, Nlp interacts with gamma-tubulin ring complexes (gamma-TuRC), and is thought to contribute to the organization of interphase microtubules (Casenghi et al.,2003). Plk1 is activated...
  • Loss of proteins required for interphase microtubule organization from the centrosome, organism-specific biosystem (from REACTOME)
    Loss of proteins required for interphase microtubule organization from the centrosome, organism-specific biosystemIn addition to recruiting proteins and complexes necessary for increased microtubule nucleation, centrosomal maturation involves the loss of proteins involved in interphase microtubule organization ...
  • Mitotic G2-G2/M phases, organism-specific biosystem (from REACTOME)
    Mitotic G2-G2/M phases, organism-specific biosystem
    Mitotic G2-G2/M phases
  • Organelle biogenesis and maintenance, organism-specific biosystem (from REACTOME)
    Organelle biogenesis and maintenance, organism-specific biosystemThis module describes the biogenesis of organelles. Organelles are subcellular structures of distinctive morphology and function. The organelles of human cells include: mitochondria, endoplasmic reti...
  • Recruitment of mitotic centrosome proteins and complexes, organism-specific biosystem (from REACTOME)
    Recruitment of mitotic centrosome proteins and complexes, organism-specific biosystemThe mitotic spindle becomes established once centrosomes have migrated to opposite poles and the nuclear envelope has broken down. During this stage, interphase centrosomes mature into mitotic centro...
  • Regulation of PLK1 Activity at G2/M Transition, organism-specific biosystem (from REACTOME)
    Regulation of PLK1 Activity at G2/M Transition, organism-specific biosystemThe kinase activity of PLK1 is required for cell cycle progression as PLK1 phosphorylates and regulates a number of cellular proteins during mitosis. Centrosomic AURKA (Aurora A kinase), catalyticall...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1633, DKFZp686B1070, DKFZp686D1070

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calmodulin binding IDA
Inferred from Direct Assay
more info
PubMed 
gamma-tubulin binding IDA
Inferred from Direct Assay
more info
PubMed 
microtubule binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
tubulin binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
G2/M transition of mitotic cell cycle TAS
Traceable Author Statement
more info
 
brain development ISS
Inferred from Sequence or Structural Similarity
more info
 
brain development NAS
Non-traceable Author Statement
more info
PubMed 
centriole replication IMP
Inferred from Mutant Phenotype
more info
PubMed 
centrosome cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
chromosome segregation IMP
Inferred from Mutant Phenotype
more info
PubMed 
ciliary basal body-plasma membrane docking TAS
Traceable Author Statement
more info
 
establishment of mitotic spindle orientation ISS
Inferred from Sequence or Structural Similarity
more info
 
microtubule bundle formation IDA
Inferred from Direct Assay
more info
PubMed 
microtubule cytoskeleton organization IDA
Inferred from Direct Assay
more info
PubMed 
microtubule organizing center organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of centriole replication ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
neurogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of microtubule polymerization IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of G2/M transition of mitotic cell cycle TAS
Traceable Author Statement
more info
 
regulation of mitotic cell cycle spindle assembly checkpoint IDA
Inferred from Direct Assay
more info
PubMed 
regulation of neuron differentiation NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
cell junction IDA
Inferred from Direct Assay
more info
 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoskeleton NAS
Non-traceable Author Statement
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
colocalizes_with gamma-tubulin ring complex IDA
Inferred from Direct Assay
more info
PubMed 
microtubule IDA
Inferred from Direct Assay
more info
PubMed 
microtubule plus-end IDA
Inferred from Direct Assay
more info
PubMed 
mitotic spindle pole IEA
Inferred from Electronic Annotation
more info
 
pericentriolar material IDA
Inferred from Direct Assay
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
spindle pole IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
CDK5 regulatory subunit-associated protein 2
Names
CDK5 activator-binding protein C48
centrosomal protein 215 kDa
centrosomin

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008999.1 RefSeqGene

    Range
    4990..196291
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001011649.3NP_001011649.1  CDK5 regulatory subunit-associated protein 2 isoform b

    See identical proteins and their annotated locations for NP_001011649.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (b) is shorter compared to isoform a.
    Source sequence(s)
    AF448860, BC136275, BX495012, BX537759, BX953750
    Consensus CDS
    CCDS43871.1
    UniProtKB/Swiss-Prot
    Q96SN8
    UniProtKB/TrEMBL
    B9EG74
    Related
    ENSP00000353317.4, ENST00000360190.8
    Conserved Domains (3) summary
    cl14654
    Location:289497
    V_Alix_like; Protein-interacting V-domain of mammalian Alix and related domains
    COG0419
    Location:105667
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam07989
    Location:61129
    Cnn_1N; Centrosomin N-terminal motif 1
  2. NM_001272039.1NP_001258968.1  CDK5 regulatory subunit-associated protein 2 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site and lacks three in-frame exons in the coding region, compared to variant 1. The encoded isoform (c) is shorter compared to isoform a.
    Source sequence(s)
    AF448860, BC136275, BX495012, BX537708, BX953708
    Consensus CDS
    CCDS75888.1
    UniProtKB/Swiss-Prot
    Q96SN8
    UniProtKB/TrEMBL
    A0A0A0MRG9, B9EG74, Q7Z3M0
    Related
    ENSP00000354065.4, ENST00000360822.7
    Conserved Domains (2) summary
    cl14654
    Location:289497
    V_Alix_like; Protein-interacting V-domain of mammalian Alix and related domains
    pfam07989
    Location:61129
    Cnn_1N; Centrosomin N-terminal motif 1
  3. NM_018249.6NP_060719.4  CDK5 regulatory subunit-associated protein 2 isoform a

    See identical proteins and their annotated locations for NP_060719.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AF448860, AK122913, BX495012
    Consensus CDS
    CCDS6823.1
    UniProtKB/Swiss-Prot
    Q96SN8
    UniProtKB/TrEMBL
    B3KVI2
    Related
    ENSP00000343818.4, ENST00000349780.9
    Conserved Domains (3) summary
    cl14654
    Location:289497
    V_Alix_like; Protein-interacting V-domain of mammalian Alix and related domains
    COG0419
    Location:105667
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam07989
    Location:61129
    Cnn_1N; Centrosomin N-terminal motif 1

RNA

  1. NR_073554.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses three alternate splice sites in internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF448860, BC019577, BC143732, BX495012
  2. NR_073555.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF448860, BC019577, BC143734, BQ428975, BX495012
  3. NR_073556.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses two alternate splice sites in internal exons and contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF448860, BC143755, BX471011, BX495012
    Related
    ENST00000473282.6
  4. NR_073557.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF448860, BC019577, BC143764, BX495012
  5. NR_073558.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) uses two alternate splice sites in internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF448860, BC143760, BX471011, BX495012
    Related
    ENST00000480112.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    120388869..120580170 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017014921.1XP_016870410.1  CDK5 regulatory subunit-associated protein 2 isoform X3

  2. XM_011518860.1XP_011517162.1  CDK5 regulatory subunit-associated protein 2 isoform X1

    Conserved Domains (2) summary
    cl14654
    Location:289497
    V_Alix_like; Protein-interacting V-domain of mammalian Alix and related domains
    pfam07989
    Location:61129
    Cnn_1N; Centrosomin N-terminal motif 1
  3. XM_017014923.1XP_016870412.1  CDK5 regulatory subunit-associated protein 2 isoform X6

  4. XM_006717185.1XP_006717248.1  CDK5 regulatory subunit-associated protein 2 isoform X4

    Conserved Domains (2) summary
    cl14654
    Location:289497
    V_Alix_like; Protein-interacting V-domain of mammalian Alix and related domains
    pfam07989
    Location:61129
    Cnn_1N; Centrosomin N-terminal motif 1
  5. XM_006717182.1XP_006717245.1  CDK5 regulatory subunit-associated protein 2 isoform X2

    UniProtKB/Swiss-Prot
    Q96SN8
    Conserved Domains (3) summary
    cl14654
    Location:289497
    V_Alix_like; Protein-interacting V-domain of mammalian Alix and related domains
    COG0419
    Location:105667
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam07989
    Location:61129
    Cnn_1N; Centrosomin N-terminal motif 1
  6. XM_017014922.1XP_016870411.1  CDK5 regulatory subunit-associated protein 2 isoform X5

  7. XM_017014924.1XP_016870413.1  CDK5 regulatory subunit-associated protein 2 isoform X7

    Related
    ENSP00000400395.1, ENST00000416449.5

RNA

  1. XR_001746351.1 RNA Sequence

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