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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
    mouse all
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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

    Gene LinkOut

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