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

Gene ID: 80279, updated on 2-Nov-2024

Summary

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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; AllianceGenome:HGNC:18673
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
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Genomic context

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See CDK5RAP3 in Genome Data Viewer
Location:
17q21.32
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (47967904..47981781)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (48829702..48843580)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (46047894..46059147)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 5948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12320 Neighboring gene pyridoxamine 5'-phosphate oxidase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:46033917-46034862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:46034863-46035808 Neighboring gene proline rich 15 like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8645 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46048841-46049468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:46052765-46053265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:46072377-46072975 Neighboring gene Sharpr-MPRA regulatory region 8372 Neighboring gene uncharacterized LOC124904017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:46092391-46092892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:46092893-46093392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8647 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46103594-46104152 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46104153-46104709 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:46105093-46105359 Neighboring gene COPI coat complex subunit zeta 2 Neighboring gene microRNA 10226

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Overexpression of IC53d promotes the proliferation of gastric cancer cells by activating the AKT/GSK3β/cyclin D1 signaling pathway. Lin JX, et al. Oncol Rep, 2019 May. PMID 30864700, Free PMC Article
  2. CDK5RAP3 acts as a putative tumor inhibitor in papillary thyroid carcinoma via modulation of Akt/GSK-3β/Wnt/β-catenin signaling. Feng X, et al. Toxicol Appl Pharmacol, 2022 Apr 1. PMID 35219640
  3. A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress. Stephani M, et al. Elife, 2020 Aug 27. PMID 32851973, Free PMC Article
  4. CDK5RAP3 as tumour suppressor negatively regulates self-renewal and invasion and is regulated by ERK1/2 signalling in human gastric cancer. Lin JX, et al. Br J Cancer, 2020 Sep. PMID 32606358, Free PMC Article
  5. CDK5RAP3 acts as a tumour suppressor in gastric cancer through the infiltration and polarization of tumour-associated macrophages. Wang JB, et al. Cancer Gene Ther, 2023 Jan. PMID 35999359, Free PMC Article

See all (121) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CDK5RAP3 is a novel super-enhancer-driven gene activated by master TFs and regulates ER-Phagy in neuroblastoma.
    Title: CDK5RAP3 is a novel super-enhancer-driven gene activated by master TFs and regulates ER-Phagy in neuroblastoma.
  2. TSPAN6 reinforces the malignant progression of glioblastoma via interacting with CDK5RAP3 and regulating STAT3 signaling pathway.
    Title: TSPAN6 reinforces the malignant progression of glioblastoma via interacting with CDK5RAP3 and regulating STAT3 signaling pathway.
  3. CDK5RAP3 acts as a tumour suppressor in gastric cancer through the infiltration and polarization of tumour-associated macrophages.
    Title: CDK5RAP3 acts as a tumour suppressor in gastric cancer through the infiltration and polarization of tumour-associated macrophages.
  4. CDK5RAP3 acts as a putative tumor inhibitor in papillary thyroid carcinoma via modulation of Akt/GSK-3beta/Wnt/beta-catenin signaling.
    Title: CDK5RAP3 acts as a putative tumor inhibitor in papillary thyroid carcinoma via modulation of Akt/GSK-3β/Wnt/β-catenin signaling.
  5. CDK5RAP3 as tumour suppressor negatively regulates self-renewal and invasion and is regulated by ERK1/2 signalling in human gastric cancer.
    Title: CDK5RAP3 as tumour suppressor negatively regulates self-renewal and invasion and is regulated by ERK1/2 signalling in human gastric cancer.
  6. The current findings advance innovation in drug discovery and highlight C53 as a novel pGC-B activator with sustained in vivo activity and anti-fibrotic actions in vitro.
    Title: C53: A novel particulate guanylyl cyclase B receptor activator that has sustained activity in vivo with anti-fibrotic actions in human cardiac and renal fibroblasts.
  7. CDK5RAP3 is associated with autophagy and down-regulated in renal cancer.
    Title: CDK5RAP3 Participates in Autophagy Regulation and Is Downregulated in Renal Cancer.
  8. Study demonstrated that CDK5RAP3/C53 isoform d (IC53d) was upregulated in gastric cancer tissues and was associated with tumor Tstage. Furthermore, overexpression of IC53d promoted the proliferation, colony formation and G1/S phase transition of gastric cancer cells, leading to enhancement of tumorigenesis in vitro and in vivo.
    Title: Overexpression of IC53d promotes the proliferation of gastric cancer cells by activating the AKT/GSK3β/cyclin D1 signaling pathway.
  9. Our results demonstrated that CDK5RAP3 negatively regulates the Wnt/beta-catenin signaling pathway by repressing AKT phosphorylation, which leads to better survival of patients with gastric cancer.
    Title: CDK5RAP3 suppresses Wnt/β-catenin signaling by inhibiting AKT phosphorylation in gastric cancer.
  10. Prognostic analysis showed that the co-expression of CDK5RAP3 and DDRGK1 was an independent prognostic factor correlating with the overall survival of gastric cancer patients.
    Title: Low expression of CDK5RAP3 and DDRGK1 indicates a poor prognosis in patients with gastric cancer.
Submit: New GeneRIF Correction See all GeneRIFs (27)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See Variation Viewer (GRCh37.p13)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

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

General protein information

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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)

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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_001278197.2 → NP_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
    Consensus CDS
    CCDS62232.1
    UniProtKB/Swiss-Prot
    Q96JB5
    Related
    ENSP00000438886.2, ENST00000536708.6
    Conserved Domains (1) summary
    pfam05600
    Location:30 → 528
    DUF773; Protein of unknown function (DUF773)

  2. NM_001278198.2 → NP_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/TrEMBL
    J3QRM1
    Related
    ENST00000580287.5
    Conserved Domains (1) summary
    pfam05600
    Location:1 → 287
    DUF773; Protein of unknown function (DUF773)

  3. NM_001278216.2 → NP_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
    UniProtKB/TrEMBL
    J3QRM1
    Related
    ENST00000584063.5
    Conserved Domains (1) summary
    pfam05600
    Location:1 → 278
    DUF773; Protein of unknown function (DUF773)

  4. NM_001278217.2 → NP_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
    UniProtKB/Swiss-Prot
    Q96JB5
    Related
    ENST00000585163.5
    Conserved Domains (1) summary
    pfam05600
    Location:26 → 416
    DUF773; Protein of unknown function (DUF773)

  5. NM_176096.3 → NP_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
    B7Z6N4, D3DTU1, D3DTU2, F5H3I5, Q53FA2, Q96JB5, Q9H3F8, Q9H8G0, Q9HBR9
    Related
    ENSP00000344683.4, ENST00000338399.9
    Conserved Domains (1) summary
    pfam05600
    Location:5 → 503
    DUF773; Protein of unknown function (DUF773)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    47967904..47981781
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011525297.1 → XP_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:30 → 528
    DUF773; Protein of unknown function (DUF773)

  2. XM_017025166.3 → XP_016880655.1  CDK5 regulatory subunit-associated protein 3 isoform X2

    Conserved Domains (1) summary
    pfam05600
    Location:1 → 410
    DUF773; Protein of unknown function (DUF773)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    48829702..48843580
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054317408.1 → XP_054173383.1  CDK5 regulatory subunit-associated protein 3 isoform X1

  2. XM_054317409.1 → XP_054173384.1  CDK5 regulatory subunit-associated protein 3 isoform X2

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.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96JB5.2 GenPept UniProtKB/Swiss-Prot:Q96JB5

Gene LinkOut

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Chemical Information
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