Human Gene CDK5RAP1 (uc002wyy.4) Description and Page Index
  Description: Homo sapiens CDK5 regulatory subunit associated protein 1 (CDK5RAP1), transcript variant 2, mRNA.
RefSeq Summary (NM_016082): 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].
Transcript (Including UTRs)
   Position: hg19 chr20:31,946,645-31,989,375 Size: 42,731 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr20:31,946,849-31,984,600 Size: 37,752 Coding Exon Count: 13 

Page IndexSequence and LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:31,946,645-31,989,375)mRNA (may differ from genome)Protein (588 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHuman Cortex Gene ExpressionLynxMGI
OMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CDK5RAP1
CDC HuGE Published Literature: CDK5RAP1
Positive Disease Associations: Hair Color , Iron
Related Studies:
  1. Hair Color
    Nicholas Eriksson et al. PLoS genetics 2010, Web-based, participant-driven studies yield novel genetic associations for common traits., PLoS genetics. [PubMed 20585627]
  2. Iron
    , , . [PubMed 0]

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

+  Common Gene Haplotype Alleles
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-  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
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -102.90284-0.362 Picture PostScript Text
3' UTR -59.70204-0.293 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
  Pfam Domains:
PF00919 - Uncharacterized protein family UPF0004
PF01938 - TRAM domain
PF04055 - Radical SAM superfamily

SCOP Domains:
102114 - Radical SAM enzymes

ModBase Predicted Comparative 3D Structure on Q96SZ6-3
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
No orthologNo orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  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.
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.
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.
AK095644 - Homo sapiens cDNA FLJ38325 fis, clone FCBBF3024793, highly similar to Rattus norvegicus clone C42 CDK5 activator-binding protein mRNA.
JD144865 - Sequence 125889 from Patent EP1572962.
JD156872 - Sequence 137896 from Patent EP1572962.
JD493308 - Sequence 474332 from Patent EP1572962.
JD206114 - Sequence 187138 from Patent EP1572962.
JD481947 - Sequence 462971 from Patent EP1572962.
JD061374 - Sequence 42398 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: C20orf34, CGI-05, HSPC167, NM_016082, NP_057166, Q96SZ6-3, uc002wyy.3
UCSC ID: uc002wyy.4
RefSeq Accession: NM_016082
Protein: Q96SZ6-3

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_016082.4
exon count: 14CDS single in 3' UTR: no RNA size: 1995
ORF size: 1494CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3678.00frame shift in genome: no % Coverage: 99.35
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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