Human Gene CDK5RAP1 (ENST00000339269.5) from GENCODE V44
  Description: Homo sapiens CDK5 regulatory subunit associated protein 1 (CDK5RAP1), transcript variant 4, mRNA; nuclear gene for mitochondrial product. (from RefSeq NM_001278168)
RefSeq Summary (NM_001278168): 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].
Gencode Transcript: ENST00000339269.5
Gencode Gene: ENSG00000101391.21
Transcript (Including UTRs)
   Position: hg38 chr20:33,358,839-33,401,561 Size: 42,723 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg38 chr20:33,359,043-33,397,064 Size: 38,022 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:33,358,839-33,401,561)mRNA (may differ from genome)Protein (510 aa)
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-  Comments and Description Text from UniProtKB
  ID: CK5P1_HUMAN
DESCRIPTION: RecName: Full=CDK5 regulatory subunit-associated protein 1; AltName: Full=CDK5 activator-binding protein C42;
FUNCTION: Specifically inhibits CDK5 activation by CDK5R1.
COFACTOR: Binds 2 4Fe-4S clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine (By similarity).
SUBUNIT: Interacts with CDK5R1 (p35 form). CDK5RAP1, CDK5RAP2 and CDK5RAP3 show competitive binding to CDK5R1. Forms a complex with CDK5R1 and CDK5.
INTERACTION: Q9NQT5:EXOSC3; NbExp=1; IntAct=EBI-372956, EBI-371866; Q9NQT4:EXOSC5; NbExp=1; IntAct=EBI-372956, EBI-371876;
TISSUE SPECIFICITY: Widely expressed. Expressed in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas.
SIMILARITY: Belongs to the methylthiotransferase family. MiaB subfamily.
SIMILARITY: Contains 1 MTTase N-terminal domain.
SIMILARITY: Contains 1 TRAM domain.
SEQUENCE CAUTION: Sequence=AAD34147.1; Type=Frameshift; Positions=3, 32, 128, 133, 569; Sequence=AAF29131.1; Type=Frameshift; Positions=213, 244, 267, 282; Sequence=BAB55120.1; Type=Erroneous termination; Positions=500; Note=Translated as Glu;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 15.40 RPKM in Spleen
Total median expression: 511.03 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -62.40154-0.405 Picture PostScript Text
3' UTR -58.00204-0.284 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006638 - Elp3/MiaB/NifB
IPR005839 - Methylthiotransferase
IPR020612 - Methylthiotransferase_CS
IPR013848 - Methylthiotransferase_N
IPR006463 - MiaB_methiolase
IPR007197 - rSAM
IPR023404 - rSAM_horseshoe
IPR002792 - TRAM_dom

Pfam Domains:
PF04055 - Radical SAM superfamily
PF01938 - TRAM domain
PF00919 - Uncharacterized protein family UPF0004

ModBase Predicted Comparative 3D Structure on Q96SZ6
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
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Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0016740 transferase activity
GO:0019901 protein kinase binding
GO:0035597 N6-isopentenyladenosine methylthiotransferase activity
GO:0044877 macromolecular complex binding
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process:
GO:0000079 regulation of cyclin-dependent protein serine/threonine kinase activity
GO:0006400 tRNA modification
GO:0007420 brain development
GO:0035600 tRNA methylthiolation
GO:0045664 regulation of neuron differentiation
GO:0045736 negative regulation of cyclin-dependent protein serine/threonine kinase activity
GO:0045903 positive regulation of translational fidelity
GO:0070131 positive regulation of mitochondrial translation
GO:0070900 mitochondrial tRNA modification

Cellular Component:
GO:0005575 cellular_component
GO:0005737 cytoplasm
GO:0005739 mitochondrion


-  Descriptions from all associated GenBank mRNAs
  AF152097 - Homo sapiens CGI-05 protein mRNA, complete cds.
AF161516 - Homo sapiens HSPC167 mRNA, complete cds.
AK222745 - Homo sapiens mRNA for CDK5 regulatory subunit associated protein 1 isoform a variant, clone: DMC05378.
AK095644 - Homo sapiens cDNA FLJ38325 fis, clone FCBBF3024793, highly similar to Rattus norvegicus clone C42 CDK5 activator-binding protein mRNA.
AK027449 - Homo sapiens cDNA FLJ14543 fis, clone NT2RM2001524.
AK023992 - Homo sapiens cDNA FLJ13930 fis, clone Y79AA1000748, moderately similar to Rattus norvegicus clone C42 CDK5 activator-binding protein mRNA.
AK292075 - Homo sapiens cDNA FLJ75109 complete cds, highly similar to Homo sapiens CDK5 regulatory subunit associated protein 1 (CDK5RAP1), transcript variant 2, mRNA.
AK295342 - Homo sapiens cDNA FLJ53994 complete cds, highly similar to CDK5 regulatory subunit-associated protein 1.
BC001215 - Homo sapiens CDK5 regulatory subunit associated protein 1, mRNA (cDNA clone MGC:727 IMAGE:3535564), complete cds.
BC050706 - Homo sapiens CDK5 regulatory subunit associated protein 1, mRNA (cDNA clone MGC:60311 IMAGE:4418659), complete cds.
JD144865 - Sequence 125889 from Patent EP1572962.
JD156872 - Sequence 137896 from Patent EP1572962.
AK314532 - Homo sapiens cDNA, FLJ95354.
JF432520 - Synthetic construct Homo sapiens clone IMAGE:100073742 CDK5 regulatory subunit associated protein 1 (CDK5RAP1) gene, encodes complete protein.
KJ898940 - Synthetic construct Homo sapiens clone ccsbBroadEn_08334 CDK5RAP1 gene, encodes complete protein.
KJ902610 - Synthetic construct Homo sapiens clone ccsbBroadEn_12004 CDK5RAP1 gene, encodes complete protein.
KU178644 - Homo sapiens CDK5 regulatory subunit associated protein 1 isoform 1 (CDK5RAP1) mRNA, partial cds, alternatively spliced.
KU178645 - Homo sapiens CDK5 regulatory subunit associated protein 1 isoform 2 (CDK5RAP1) mRNA, partial cds.
AB463477 - Synthetic construct DNA, clone: pF1KB6129, Homo sapiens CDK5RAP1 gene for CDK5 regulatory subunit associated protein 1, without stop codon, in Flexi system.
AY462283 - Homo sapiens CDK5 regulatory subunit associated protein 1 transcript variant 3 mRNA, complete cds, alternatively spliced.
AY462284 - Homo sapiens CDK5 regulatory subunit associated protein 1 transcript variant 4 mRNA, complete cds, alternatively spliced.
AK309906 - Homo sapiens cDNA, FLJ99947.
CU690774 - Synthetic construct Homo sapiens gateway clone IMAGE:100021500 5' read CDK5RAP1 mRNA.
JD493308 - Sequence 474332 from Patent EP1572962.
JD206114 - Sequence 187138 from Patent EP1572962.
JD481947 - Sequence 462971 from Patent EP1572962.
JD228826 - Sequence 209850 from Patent EP1572962.
JD061374 - Sequence 42398 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K7R0, C20orf34, CGI-05, CK5P1_HUMAN, ENST00000339269.1, ENST00000339269.2, ENST00000339269.3, ENST00000339269.4, HSPC167, NM_001278168, Q5QP46, Q5QP47, Q5QP48, Q96SZ6, Q9BVG6, Q9BWZ5, Q9H859, Q9NZZ9, Q9Y3F0, uc010gem.1, uc010gem.2, uc010gem.3, uc010gem.4, uc010gem.5
UCSC ID: ENST00000339269.5
RefSeq Accession: NM_001278168
Protein: Q96SZ6 (aka CK5P1_HUMAN or C5P1_HUMAN)
CCDS: CCDS63255.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.