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CDK5RAP1 CDK5 regulatory subunit associated protein 1 [ Homo sapiens (human) ]

Gene ID: 51654, updated on 11-Apr-2024

Summary

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Official Symbol
CDK5RAP1provided by HGNC
Official Full Name
CDK5 regulatory subunit associated protein 1provided by HGNC
Primary source
HGNC:HGNC:15880
See related
Ensembl:ENSG00000101391 MIM:608200; AllianceGenome:HGNC:15880
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
C42; CGI-05; HSPC167; C20orf34
Summary
This gene encodes a regulator of cyclin-dependent kinase 5 activity. This protein has also been reported to modify RNA by adding a methylthio-group and may thus have a dual function as an RNA methylthiotransferase and as an inhibitor of cyclin-dependent kinase 5 activity. Alternative splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, May 2013]
Expression
Ubiquitous expression in thyroid (RPKM 5.1), bone marrow (RPKM 5.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
20q11.21
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (33358839..33401569, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (35086043..35128797, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (31946645..31989375, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31909477-31909976 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31911786-31912403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17728 Neighboring gene BPI fold containing family B member 5, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31934530-31935364 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31937032-31937864 Neighboring gene BPI fold containing family B member 9, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17730 Neighboring gene uncharacterized LOC124904889 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32006871-32007371 Neighboring gene VISTA enhancer hs2173 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17731 Neighboring gene syntrophin alpha 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:32027926-32028104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12811 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12812 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32032043-32032543 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32064897-32065812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12813 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32077069-32077617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12814 Neighboring gene CBFA2/RUNX1 partner transcriptional co-repressor 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32104950-32105714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32115920-32116420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32116421-32116921 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32118677-32119177 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32121705-32122204 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32124101-32124819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17735 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32144891-32145546 Neighboring gene Sharpr-MPRA regulatory region 10659 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32156001-32156927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32169053-32169552 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32169790-32170374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32170375-32170958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32175233-32175732 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12815

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. Cdk5rap1-mediated 2-methylthio-N6-isopentenyladenosine modification is absent from nuclear-derived RNA species. Fakruddin M, et al. Nucleic Acids Res, 2017 Nov 16. PMID 28981754, Free PMC Article
  2. CDK5RAP1 deficiency induces cell cycle arrest and apoptosis in human breast cancer cell line by the ROS/JNK signaling pathway. Wang H, et al. Oncol Rep, 2015 Mar. PMID 25607831
  3. Association between CDK5RAP1 polymorphisms and susceptibility to vitiligo in the Korean population. Shin MK, et al. Eur J Dermatol, 2012 Jul-Aug. PMID 22534366
  4. The CDK5 repressor CDK5RAP1 is a methylthiotransferase acting on nuclear and mitochondrial RNA. Reiter V, et al. Nucleic Acids Res, 2012 Jul. PMID 22422838, Free PMC Article
  5. Cloning, characterization and expression of CDK5RAP1_v3 and CDK5RAP1_v4, two novel splice variants of human CDK5RAP1. Zou X, et al. Genes Genet Syst, 2004 Jun. PMID 15329498

See all (50) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The mitochondrial localization of ms2i6A modification was diminished in HeLa cells when transfected with siRNA against Cdk5 regulatory subunit-associated protein 1 (Cdk5rap1), suggesting that the modification occurs in tRNAs in mitochondria.
    Title: Cdk5rap1-mediated 2-methylthio-N6-isopentenyladenosine modification is absent from nuclear-derived RNA species.
  2. Which resulted in respiratory defects in Cdk5rap1 knockout (KO) mice.
    Title: Cdk5rap1-mediated 2-methylthio modification of mitochondrial tRNAs governs protein translation and contributes to myopathy in mice and humans.
  3. data indicated that CDK5RAP1 deficiency induced cell cycle arrest and apoptosis in human breast cancer
    Title: CDK5RAP1 deficiency induces cell cycle arrest and apoptosis in human breast cancer cell line by the ROS/JNK signaling pathway.
  4. CDK5RAP1 may be a risk factor of vitiligo in the Korean population
    Title: Association between CDK5RAP1 polymorphisms and susceptibility to vitiligo in the Korean population.
  5. CDK5RAP1 is a radical SAM enzyme, which postsynthetically converts the RNA modification N6-isopentenyladenosine into 2-methylthio-N6-isopentenyladenosine.
    Title: The CDK5 repressor CDK5RAP1 is a methylthiotransferase acting on nuclear and mitochondrial RNA.
  6. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: An approach based on a genome-wide association study reveals candidate loci for narcolepsy.
Submit: New GeneRIF Correction

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
Web-based, participant-driven studies yield novel genetic associations for common traits.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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 4 iron, 4 sulfur cluster binding IEA
Inferred from Electronic Annotation
more info
  
enables N6-isopentenyladenosine methylthiotransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein kinase binding NAS
Non-traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in brain development NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in mitochondrial tRNA modification IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of cyclin-dependent protein serine/threonine kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of cyclin-dependent protein serine/threonine kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of cyclin-dependent protein serine/threonine kinase activity TAS
Traceable Author Statement
more info
 PubMed 
involved_in positive regulation of mitochondrial translation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of translational fidelity IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of neuron differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
  
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
mitochondrial tRNA methylthiotransferase CDK5RAP1
Names
CDK5 activator-binding protein C42
mt-tRNA-2-methylthio-N6-dimethylallyladenosine synthase
mt-tRNA-N6-(dimethylallyl)adenosine(37) methylthiotransferase
NP_001265096.1
NP_001265097.1
NP_001265098.1
NP_001352657.1
NP_057166.4
NP_057492.2
XP_011527158.1
XP_011527159.1
XP_011527161.1
XP_024307661.1
XP_024307663.1
XP_047296150.1
XP_047296151.1
XP_047296152.1
XP_047296153.1
XP_054179466.1
XP_054179467.1
XP_054179468.1
XP_054179469.1
XP_054179470.1
XP_054179471.1
XP_054179472.1
XP_054179473.1

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_001278167.2 → NP_001265096.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform c

    See identical proteins and their annotated locations for NP_001265096.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the coding region compared to variant 1. It encodes isoform c which is shorter compared to isoform a.
    Source sequence(s)
    AK222745, DA028522
    UniProtKB/TrEMBL
    B4DI01, Q53H36
    Conserved Domains (3) summary
    PRK14329
    Location:88 → 573
    PRK14329; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
    pfam00919
    Location:101 → 204
    UPF0004; Uncharacterized protein family UPF0004
    pfam01938
    Location:500 → 574
    TRAM; TRAM domain

  2. NM_001278168.2 → NP_001265097.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform d

    See identical proteins and their annotated locations for NP_001265097.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon in the coding region compared to variant 1. It encodes isoform d which is shorter compared to isoform a.
    Source sequence(s)
    AA721451, BC001215, BM834342, DC427896
    Consensus CDS
    CCDS63255.1
    UniProtKB/TrEMBL
    A0A0S2Z592, B4DI01
    Related
    ENSP00000341840.5, ENST00000339269.5
    Conserved Domains (3) summary
    PRK14329
    Location:88 → 497
    PRK14329; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
    pfam00919
    Location:101 → 204
    UPF0004; Uncharacterized protein family UPF0004
    pfam01938
    Location:424 → 498
    TRAM; TRAM domain

  3. NM_001278169.1 → NP_001265098.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) 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 (e) with a distinct and shorter N-terminus compared to isoform a.
    Source sequence(s)
    AA721451, AK292075, DC427896
    UniProtKB/TrEMBL
    B4DI01
    Conserved Domains (3) summary
    PRK14329
    Location:61 → 547
    PRK14329; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
    pfam00919
    Location:74 → 177
    UPF0004; Uncharacterized protein family UPF0004
    pfam01938
    Location:474 → 548
    TRAM; TRAM domain

  4. NM_001365728.1 → NP_001352657.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform f

    Status: REVIEWED

    Source sequence(s)
    AL355392
    Consensus CDS
    CCDS93031.1
    UniProtKB/Swiss-Prot
    A8K7R0, Q5QP46, Q5QP47, Q5QP48, Q675N4, Q675N5, Q96SZ6, Q9BVG6, Q9BWZ5, Q9H859, Q9NZZ9, Q9Y3F0
    UniProtKB/TrEMBL
    B4DI01
    Related
    ENSP00000350558.4, ENST00000357886.8
    Conserved Domains (1) summary
    cl27627
    Location:88 → 588
    UPF0004; Uncharacterized protein family UPF0004

  5. NM_016082.4 → NP_057166.4  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform b

    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 (b) with a distinct and longer N-terminus, compared to isoform a.
    Source sequence(s)
    AA721451, AK027449, BM792566, CX785345, DA565688, DC427896, DR156307
    UniProtKB/TrEMBL
    B4DI01
    Conserved Domains (3) summary
    PRK14329
    Location:89 → 575
    PRK14329; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
    pfam00919
    Location:102 → 205
    UPF0004; Uncharacterized protein family UPF0004
    pfam01938
    Location:502 → 576
    TRAM; TRAM domain

  6. NM_016408.4 → NP_057492.2  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform a

    See identical proteins and their annotated locations for NP_057492.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform (a).
    Source sequence(s)
    AA721451, AK314532, DA028522
    Consensus CDS
    CCDS13219.1
    UniProtKB/TrEMBL
    A0A0S2Z5J9, B4DI01
    Related
    ENSP00000217372.2, ENST00000346416.7
    Conserved Domains (1) summary
    cl27627
    Location:88 → 574
    UPF0004; Uncharacterized protein family UPF0004

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    33358839..33401569 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011528856.4 → XP_011527158.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X1

    UniProtKB/TrEMBL
    B4DI01
    Conserved Domains (1) summary
    PRK14329
    Location:41 → 470
    PRK14329; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional

  2. XM_024451893.2 → XP_024307661.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X5

    Conserved Domains (1) summary
    cl27627
    Location:1 → 391
    UPF0004; Uncharacterized protein family UPF0004

  3. XM_011528857.3 → XP_011527159.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X2

    UniProtKB/TrEMBL
    B4DI01
    Conserved Domains (3) summary
    PRK14329
    Location:1 → 464
    PRK14329; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
    pfam00919
    Location:1 → 94
    UPF0004; Uncharacterized protein family UPF0004
    pfam01938
    Location:391 → 465
    TRAM; TRAM domain

  4. XM_011528859.3 → XP_011527161.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X3

    See identical proteins and their annotated locations for XP_011527161.1

    UniProtKB/TrEMBL
    B4DI01
    Conserved Domains (3) summary
    PRK14328
    Location:5 → 448
    PRK14328; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
    pfam00919
    Location:8 → 77
    UPF0004; Uncharacterized protein family UPF0004
    pfam01938
    Location:374 → 448
    TRAM; TRAM domain

  5. XM_047440194.1 → XP_047296150.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X3

  6. XM_047440196.1 → XP_047296152.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X6

  7. XM_024451895.2 → XP_024307663.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X5

    Conserved Domains (1) summary
    cl27627
    Location:1 → 391
    UPF0004; Uncharacterized protein family UPF0004

  8. XM_047440195.1 → XP_047296151.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X4

  9. XM_047440197.1 → XP_047296153.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    35086043..35128797 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054323491.1 → XP_054179466.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X1

  2. XM_054323495.1 → XP_054179470.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X5

  3. XM_054323492.1 → XP_054179467.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X2

  4. XM_054323493.1 → XP_054179468.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X3

  5. XM_054323497.1 → XP_054179472.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X6

  6. XM_054323496.1 → XP_054179471.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X5

  7. XM_054323494.1 → XP_054179469.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X4

  8. XM_054323498.1 → XP_054179473.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96SZ6.2 GenPept UniProtKB/Swiss-Prot:Q96SZ6

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