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CDK5RAP3 CDK5 regulatory subunit associated protein 3 [ Homo sapiens (human) ]

Gene ID: 80279, updated on 17-Jun-2019

Summary

Official Symbol
CDK5RAP3provided by HGNC
Official Full Name
CDK5 regulatory subunit associated protein 3provided by HGNC
Primary source
HGNC:HGNC:18673
See related
Ensembl:ENSG00000108465 MIM:608202
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
C53; IC53; LZAP; HSF-27; MST016; PP1553; OK/SW-cl.114
Summary
This gene encodes a protein that has been reported to function in signaling pathways governing transcriptional regulation and cell cycle progression. It may play a role in tumorigenesis and metastasis. A pseudogene of this gene is located on the long arm of chromosome 20. Alternative splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, May 2013]
Expression
Ubiquitous expression in spleen (RPKM 44.2), lymph node (RPKM 40.3) and 25 other tissues See more
Orthologs

Genomic context

See CDK5RAP3 in Genome Data Viewer
Location:
17q21.32
Exon count:
16
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (47967904..47981786)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (46047894..46059152)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene pyridoxamine 5'-phosphate oxidase Neighboring gene proline rich 15 like Neighboring gene coatomer protein complex subunit zeta 2 Neighboring gene microRNA 10226 Neighboring gene microRNA 152

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 analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32
NHGRI GWA Catalog
Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
MDM2/MDM4 family protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
NF-kappaB binding IPI
Inferred from Physical Interaction
more info
PubMed 
cyclin binding IPI
Inferred from Physical Interaction
more info
PubMed 
mitogen-activated protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase binding NAS
Non-traceable Author Statement
more info
PubMed 
ubiquitin-like protein ligase binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
apoptotic nuclear changes IMP
Inferred from Mutant Phenotype
more info
PubMed 
brain development NAS
Non-traceable Author Statement
more info
PubMed 
cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum unfolded protein response IMP
Inferred from Mutant Phenotype
more info
PubMed 
mitotic G2 DNA damage checkpoint IMP
Inferred from Mutant Phenotype
more info
PubMed 
mitotic G2/M transition checkpoint IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of MAP kinase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of NF-kappaB transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cellular protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of protein kinase activity by regulation of protein phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of protein phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of protein serine/threonine kinase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein localization to nucleus IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of protein ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of signal transduction by p53 class mediator IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
NOT positive regulation of ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
protein ufmylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of cyclin-dependent protein serine/threonine kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of cyclin-dependent protein serine/threonine kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of mitotic cell cycle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of neuron differentiation NAS
Non-traceable Author Statement
more info
PubMed 
regulation of phosphatase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
membrane HDA PubMed 
colocalizes_with microtubule IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
 
NOT nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
CDK5 regulatory subunit-associated protein 3
Names
CDK5 regulatory subunit associated protein IC53-2
LXXLL/leucine-zipper-containing ARF-binding protein
LXXLL/leucine-zipper-containing ARFbinding protein
ischemic heart CDK5 activator-binding protein C53

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.

mRNA and Protein(s)

  1. NM_001278197.1NP_001265126.1  CDK5 regulatory subunit-associated protein 3 isoform c

    See identical proteins and their annotated locations for NP_001265126.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and has multiple coding region differences compared to variant 1. These differences cause translation initiation at an alternate AUG and result in an isoform (c) with a longer N-terminus, compared to isoform e.
    Source sequence(s)
    AA427702, AK300643, DA410409, DA410477, DB515989
    Consensus CDS
    CCDS62232.1
    UniProtKB/Swiss-Prot
    Q96JB5
    Related
    ENSP00000438886.2, ENST00000536708.6
    Conserved Domains (1) summary
    pfam05600
    Location:30528
    DUF773; Protein of unknown function (DUF773)
  2. NM_001278198.2NP_001265127.1  CDK5 regulatory subunit-associated protein 3 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) includes an alternate penultimate exon, compared to variant 1, resulting in a novel 3' coding region and shorter 3' UTR. It encodes isoform d which has a distinct C-terminus, compared to isoform e.
    Source sequence(s)
    AA427702, AF217982, AK225274
    UniProtKB/Swiss-Prot
    Q96JB5
    Related
    ENSP00000464286.1, ENST00000583697.1
    Conserved Domains (1) summary
    pfam05600
    Location:1287
    DUF773; Protein of unknown function (DUF773)
  3. NM_001278216.1NP_001265145.1  CDK5 regulatory subunit-associated protein 3 isoform e

    See identical proteins and their annotated locations for NP_001265145.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform e.
    Source sequence(s)
    AA427702, AF217982, DB075547, DB515989
    UniProtKB/Swiss-Prot
    Q96JB5
    Conserved Domains (1) summary
    pfam05600
    Location:1278
    DUF773; Protein of unknown function (DUF773)
  4. NM_001278217.1NP_001265146.1  CDK5 regulatory subunit-associated protein 3 isoform f

    See identical proteins and their annotated locations for NP_001265146.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and has multiple coding region differences compared to variant 1. These differences cause translation initiation at an alternate AUG and result in an isoform (f) with a longer N-terminus, compared to isoform e.
    Source sequence(s)
    AA427702, AF110322, AF217982, DB075547, DB515989
    UniProtKB/Swiss-Prot
    Q96JB5
    Conserved Domains (1) summary
    pfam05600
    Location:26416
    DUF773; Protein of unknown function (DUF773)
  5. NM_176096.3NP_788276.1  CDK5 regulatory subunit-associated protein 3 isoform b

    See identical proteins and their annotated locations for NP_788276.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and has multiple coding region differences compared to variant 1. These differences cause translation initiation at an alternate AUG and result in an isoform (b) with a longer N-terminus, compared to isoform e.
    Source sequence(s)
    AA427702, AK023722
    Consensus CDS
    CCDS42356.1
    UniProtKB/Swiss-Prot
    Q96JB5
    Related
    ENSP00000344683.4, ENST00000338399.9
    Conserved Domains (1) summary
    pfam05600
    Location:5503
    DUF773; Protein of unknown function (DUF773)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

    Range
    47967904..47981786
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011525297.1XP_011523599.1  CDK5 regulatory subunit-associated protein 3 isoform X1

    See identical proteins and their annotated locations for XP_011523599.1

    UniProtKB/Swiss-Prot
    Q96JB5
    Conserved Domains (1) summary
    pfam05600
    Location:30528
    DUF773; Protein of unknown function (DUF773)
  2. XM_017025166.2XP_016880655.1  CDK5 regulatory subunit-associated protein 3 isoform X3

    Conserved Domains (1) summary
    pfam05600
    Location:1410
    DUF773; Protein of unknown function (DUF773)
  3. XM_017025164.2XP_016880653.1  CDK5 regulatory subunit-associated protein 3 isoform X2

    UniProtKB/Swiss-Prot
    Q96JB5
    Conserved Domains (1) summary
    pfam05600
    Location:26416
    DUF773; Protein of unknown function (DUF773)
  4. XM_017025165.2XP_016880654.1  CDK5 regulatory subunit-associated protein 3 isoform X2

    UniProtKB/Swiss-Prot
    Q96JB5
    Conserved Domains (1) summary
    pfam05600
    Location:26416
    DUF773; Protein of unknown function (DUF773)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_025197.2: Suppressed sequence

    Description
    NM_025197.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
  2. NM_176095.1: Suppressed sequence

    Description
    NM_176095.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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