Human Gene CDKN2AIP (ENST00000504169.2_10) from GENCODE V47lift37
  Description: CDKN2A interacting protein, transcript variant 1 (from RefSeq NM_017632.4)
Gencode Transcript: ENST00000504169.2_10
Gencode Gene: ENSG00000168564.6_12
Transcript (Including UTRs)
   Position: hg19 chr4:184,365,789-184,370,217 Size: 4,429 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr4:184,365,951-184,368,580 Size: 2,630 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:184,365,789-184,370,217)mRNA (may differ from genome)Protein (580 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CARF_HUMAN
DESCRIPTION: RecName: Full=CDKN2A-interacting protein; AltName: Full=Collaborator of ARF;
FUNCTION: Activates p53/TP53 by CDKN2A-dependent and CDKN2A- independent pathways.
SUBUNIT: Interacts with CDKN2A/p14ARF, p53/TP53 and MDM2.
SUBCELLULAR LOCATION: Nucleus, nucleoplasm.
TISSUE SPECIFICITY: Ubiquitously expressed.
PTM: May be ubiquitinated.
SIMILARITY: Belongs to the CARF family.
SIMILARITY: Contains 1 DRBM (double-stranded RNA-binding) domain.
SEQUENCE CAUTION: Sequence=AAF68967.1; Type=Frameshift; Positions=4;

-  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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.42 RPKM in Testis
Total median expression: 364.83 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 -76.50162-0.472 Picture PostScript Text
3' UTR -350.701637-0.214 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
IPR001159 - Ds-RNA-bd
IPR021859 - DUF3469

Pfam Domains:
PF11952 - XRN-Two Binding Domain, XTBD

SCOP Domains:
54768 - dsRNA-binding domain-like

ModBase Predicted Comparative 3D Structure on Q9NXV6
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0002039 p53 binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0006974 cellular response to DNA damage stimulus
GO:0009967 positive regulation of signal transduction
GO:0030307 positive regulation of cell growth
GO:0030308 negative regulation of cell growth
GO:0031647 regulation of protein stability

Cellular Component:
GO:0001652 granular component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  KJ902837 - Synthetic construct Homo sapiens clone ccsbBroadEn_12231 CDKN2AIP gene, encodes complete protein.
LF208105 - JP 2014500723-A/15608: Polycomb-Associated Non-Coding RNAs.
AK000043 - Homo sapiens cDNA FLJ20036 fis, clone COL00219.
JD142705 - Sequence 123729 from Patent EP1572962.
AF246705 - Homo sapiens putative serine-rich protein mRNA, partial cds.
JD024439 - Sequence 5463 from Patent EP1572962.
JD034437 - Sequence 15461 from Patent EP1572962.
JD551137 - Sequence 532161 from Patent EP1572962.
LF213944 - JP 2014500723-A/21447: Polycomb-Associated Non-Coding RNAs.
JD476188 - Sequence 457212 from Patent EP1572962.
AK096180 - Homo sapiens cDNA FLJ38861 fis, clone MESAN2011984, highly similar to Homo sapiens collaborates/cooperates with ARF (alternate reading frame) protein (CARF), mRNA.
JD146462 - Sequence 127486 from Patent EP1572962.
BC022270 - Homo sapiens CDKN2A interacting protein, mRNA (cDNA clone MGC:22346 IMAGE:4697255), complete cds.
AK225848 - Homo sapiens mRNA for collaborates/cooperates with ARF (alternate reading frame) protein variant, clone: FCC125H11.
EU446516 - Synthetic construct Homo sapiens clone IMAGE:100070051; IMAGE:100011725; FLH258283.01L CDKN2A interacting protein (CDKN2AIP) gene, encodes complete protein.
CU692522 - Synthetic construct Homo sapiens gateway clone IMAGE:100022269 5' read CDKN2AIP mRNA.
BX538162 - Homo sapiens mRNA; cDNA DKFZp686M0665 (from clone DKFZp686M0665).
DQ599722 - Homo sapiens piRNA piR-37788, complete sequence.
LF372423 - JP 2014500723-A/179926: Polycomb-Associated Non-Coding RNAs.
LF372422 - JP 2014500723-A/179925: Polycomb-Associated Non-Coding RNAs.
LF372421 - JP 2014500723-A/179924: Polycomb-Associated Non-Coding RNAs.
JD323943 - Sequence 304967 from Patent EP1572962.
JD243004 - Sequence 224028 from Patent EP1572962.
JD053190 - Sequence 34214 from Patent EP1572962.
LF372420 - JP 2014500723-A/179923: Polycomb-Associated Non-Coding RNAs.
MA449521 - JP 2018138019-A/21447: Polycomb-Associated Non-Coding RNAs.
MA608000 - JP 2018138019-A/179926: Polycomb-Associated Non-Coding RNAs.
MA607999 - JP 2018138019-A/179925: Polycomb-Associated Non-Coding RNAs.
MA607998 - JP 2018138019-A/179924: Polycomb-Associated Non-Coding RNAs.
MA607997 - JP 2018138019-A/179923: Polycomb-Associated Non-Coding RNAs.
MA443682 - JP 2018138019-A/15608: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: CARF, CARF_HUMAN, ENST00000504169.1, NM_017632, Q8TBM5, Q9NXV6, Q9NYH0, uc322ydo.1, uc322ydo.2
UCSC ID: ENST00000504169.2_10
RefSeq Accession: NM_017632.4
Protein: Q9NXV6 (aka CARF_HUMAN)

-  Gene Model Information
  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.