Format

Send to:

Choose Destination

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

Gene ID: 51654, updated on 4-Oct-2020

Summary

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
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

Genomic context

See CDK5RAP1 in Genome Data Viewer
Location:
20q11.21
Exon count:
16
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (33358839..33403030, complement)
105 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 BPI fold containing family B member 5, pseudogene Neighboring gene BPI fold containing family B member 9, pseudogene Neighboring gene VISTA enhancer hs2173 Neighboring gene syntrophin alpha 1 Neighboring gene CBFA2/RUNX1 partner transcriptional co-repressor 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 Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Web-based, participant-driven studies yield novel genetic associations for common traits.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
4 iron, 4 sulfur cluster binding IEA
Inferred from Electronic Annotation
more info
 
N6-isopentenyladenosine methylthiotransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein kinase binding NAS
Non-traceable Author Statement
more info
PubMed 
protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cellular_component ND
No biological Data available
more info
 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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_011527160.1
XP_011527161.1
XP_011527162.1
XP_016883365.1
XP_016883366.1
XP_024307660.1
XP_024307661.1
XP_024307662.1
XP_024307663.1
XP_024307664.1
XP_024307665.1

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_001278167.2NP_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
    Q53H36
    Conserved Domains (3) summary
    PRK14329
    Location:88573
    PRK14329; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
    pfam00919
    Location:101204
    UPF0004; Uncharacterized protein family UPF0004
    pfam01938
    Location:500574
    TRAM; TRAM domain
  2. NM_001278168.2NP_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/Swiss-Prot
    Q96SZ6
    UniProtKB/TrEMBL
    A0A0S2Z592
    Related
    ENSP00000341840.5, ENST00000339269.5
    Conserved Domains (3) summary
    PRK14329
    Location:88497
    PRK14329; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
    pfam00919
    Location:101204
    UPF0004; Uncharacterized protein family UPF0004
    pfam01938
    Location:424498
    TRAM; TRAM domain
  3. NM_001278169.1NP_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/Swiss-Prot
    Q96SZ6
    Conserved Domains (3) summary
    PRK14329
    Location:61547
    PRK14329; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
    pfam00919
    Location:74177
    UPF0004; Uncharacterized protein family UPF0004
    pfam01938
    Location:474548
    TRAM; TRAM domain
  4. NM_001365728.1NP_001352657.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform f

    Status: REVIEWED

    Source sequence(s)
    AL355392
    Related
    ENSP00000350558.4, ENST00000357886.8
    Conserved Domains (1) summary
    cl27627
    Location:88588
    UPF0004; Uncharacterized protein family UPF0004
  5. NM_016082.4NP_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/Swiss-Prot
    Q96SZ6
    Conserved Domains (3) summary
    PRK14329
    Location:89575
    PRK14329; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
    pfam00919
    Location:102205
    UPF0004; Uncharacterized protein family UPF0004
    pfam01938
    Location:502576
    TRAM; TRAM domain
  6. NM_016408.4NP_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/Swiss-Prot
    Q96SZ6
    UniProtKB/TrEMBL
    A0A0S2Z5J9
    Related
    ENSP00000217372.2, ENST00000346416.7
    Conserved Domains (1) summary
    cl27627
    Location:88574
    UPF0004; Uncharacterized protein family UPF0004

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    33358839..33403030 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011528856.3XP_011527158.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X1

    Conserved Domains (3) summary
    PRK14335
    Location:35472
    PRK14335; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
    pfam00919
    Location:41100
    UPF0004; Uncharacterized protein family UPF0004
    pfam01938
    Location:397471
    TRAM; TRAM domain
  2. XM_024451893.1XP_024307661.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X4

    Conserved Domains (1) summary
    cl27627
    Location:1391
    UPF0004; Uncharacterized protein family UPF0004
  3. XM_017027876.2XP_016883365.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X5

    Conserved Domains (1) summary
    cl27627
    Location:1320
    UPF0004; Uncharacterized protein family UPF0004
  4. XM_011528858.1XP_011527160.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X3

    See identical proteins and their annotated locations for XP_011527160.1

    Conserved Domains (3) summary
    PRK14328
    Location:5448
    PRK14328; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
    pfam00919
    Location:877
    UPF0004; Uncharacterized protein family UPF0004
    pfam01938
    Location:374448
    TRAM; TRAM domain
  5. XM_024451897.1XP_024307665.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X5

    Conserved Domains (1) summary
    cl27627
    Location:1320
    UPF0004; Uncharacterized protein family UPF0004
  6. XM_011528860.1XP_011527162.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X5

    Conserved Domains (1) summary
    cl27627
    Location:1320
    UPF0004; Uncharacterized protein family UPF0004
  7. XM_024451895.1XP_024307663.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X4

    Conserved Domains (1) summary
    cl27627
    Location:1391
    UPF0004; Uncharacterized protein family UPF0004
  8. XM_024451896.1XP_024307664.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X5

    Conserved Domains (1) summary
    cl27627
    Location:1320
    UPF0004; Uncharacterized protein family UPF0004
  9. XM_011528859.2XP_011527161.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X3

    See identical proteins and their annotated locations for XP_011527161.1

    Conserved Domains (3) summary
    PRK14328
    Location:5448
    PRK14328; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
    pfam00919
    Location:877
    UPF0004; Uncharacterized protein family UPF0004
    pfam01938
    Location:374448
    TRAM; TRAM domain
  10. XM_011528857.2XP_011527159.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X2

    Conserved Domains (3) summary
    PRK14329
    Location:1464
    PRK14329; (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
    pfam00919
    Location:194
    UPF0004; Uncharacterized protein family UPF0004
    pfam01938
    Location:391465
    TRAM; TRAM domain
  11. XM_024451894.1XP_024307662.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X4

    Conserved Domains (1) summary
    cl27627
    Location:1391
    UPF0004; Uncharacterized protein family UPF0004
  12. XM_024451892.1XP_024307660.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X4

    Conserved Domains (1) summary
    cl27627
    Location:1391
    UPF0004; Uncharacterized protein family UPF0004
  13. XM_017027877.1XP_016883366.1  mitochondrial tRNA methylthiotransferase CDK5RAP1 isoform X6

RNA

  1. XR_001754289.2 RNA Sequence

  2. XR_001754290.2 RNA Sequence

Support Center