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CDKN2AIP CDKN2A interacting protein [ Homo sapiens (human) ]

Gene ID: 55602, updated on 7-Apr-2024

Summary

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Official Symbol
CDKN2AIPprovided by HGNC
Official Full Name
CDKN2A interacting proteinprovided by HGNC
Primary source
HGNC:HGNC:24325
See related
Ensembl:ENSG00000168564 MIM:615914; AllianceGenome:HGNC:24325
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
CARF
Summary
The protein encoded by this gene regulates the DNA damage response through several different signaling pathways. One such pathway is the p53-HDM2-p21(WAF1) pathway, which is critical to the DNA damage response. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]
Expression
Ubiquitous expression in testis (RPKM 11.6), bone marrow (RPKM 11.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
4q35.1
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (183444636..183449064)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (186787446..186791876)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (184365789..184370217)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene chimerin 1 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:184319106-184319897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22183 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:184328963-184329801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:184340331-184340831 Neighboring gene FBL pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:184351159-184351908 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:184351909-184352659 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:184359150-184360349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22184 Neighboring gene uncharacterized LOC124900823 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:184403604-184404104 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:184404105-184404605 Neighboring gene vesicle transport through interaction with t-SNAREs 1B pseudogene 2

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. Fatty Acid Excess Dysregulates CARF to Initiate the Development of Hepatic Steatosis. Hasan KM, et al. Cells, 2023 Apr 1. PMID 37048142, Free PMC Article
  2. Stress-induced changes in CARF expression determine cell fate to death, survival, or malignant transformation. Kalra RS, et al. Cell Stress Chaperones, 2020 May. PMID 32221864, Free PMC Article
  3. CARF is a multi-module regulator of cell proliferation and a molecular bridge between cellular senescence and carcinogenesis. Wadhwa R, et al. Mech Ageing Dev, 2017 Sep. PMID 28754531
  4. Molecular characterization of collaborator of ARF (CARF) as a DNA damage response and cell cycle checkpoint regulatory protein. Singh R, et al. Exp Cell Res, 2014 Apr 1. PMID 24485912
  5. Molecular characterization of apoptosis induced by CARF silencing in human cancer cells. Cheung CT, et al. Cell Death Differ, 2011 Apr. PMID 21052095, Free PMC Article

See all (78) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Fatty Acid Excess Dysregulates CARF to Initiate the Development of Hepatic Steatosis.
    Title: Fatty Acid Excess Dysregulates CARF to Initiate the Development of Hepatic Steatosis.
  2. CDKN2AIP-induced cell senescence and apoptosis of testicular seminoma are associated with CARM1 and eIF4beta.
    Title: CDKN2AIP-induced cell senescence and apoptosis of testicular seminoma are associated with CARM1 and eIF4β.
  3. Stress-induced changes in CARF expression determine cell fate to death, survival, or malignant transformation.
    Title: Stress-induced changes in CARF expression determine cell fate to death, survival, or malignant transformation.
  4. a comprehensive current understanding into the molecular mechanisms of CARF functions in regulation of DNA damage response, cell cycle checkpoints, cell survival and death signaling pathways.
    Title: CARF is a multi-module regulator of cell proliferation and a molecular bridge between cellular senescence and carcinogenesis.
  5. report that CARF (Collaborator of ARF) is a new target of miR-335 that regulates its growth suppressor function by complex crosstalk with other proteins including p16(INK4A), pRB, HDM2 and p21(WAF1)
    Title: Loss-of-function screening to identify miRNAs involved in senescence: tumor suppressor activity of miRNA-335 and its new target CARF.
  6. Oncogenic functions of CARF in hepatocellular carcinoma tumorigenesis is a result of activation of beta-catenin/TCF signaling.
    Title: CARF activates beta-catenin/TCF signaling in the hepatocellular carcinoma.
  7. CARF promotes carcinogenesis in p53-deficient cells by repressing p21WAF1 and promoting cell cycle progression.
    Title: CARF (Collaborator of ARF) overexpression in p53-deficient cells promotes carcinogenesis.
  8. The results suggest that CARF regulates early steps of pre-rRNA processing during ribosome biogenesis by controlling spatial distribution of XRN2 between the nucleoplasm and nucleolus.
    Title: Collaborator of alternative reading frame protein (CARF) regulates early processing of pre-ribosomal RNA by retaining XRN2 (5'-3' exoribonuclease) in the nucleoplasm.
  9. CARF regulates proliferative fate of human cells by dose-dependent regulation of DNA damage signaling.
    Title: Collaborator of ARF (CARF) regulates proliferative fate of human cells by dose-dependent regulation of DNA damage signaling.
  10. Analysis of indel variations in the human disease-associated genes CDKN2AIP, WDR66, USP20 and OR7C2 in a Korean population.
    Title: Analysis of indel variations in the human disease-associated genes CDKN2AIP, WDR66, USP20 and OR7C2 in a Korean population.
Submit: New GeneRIF Correction See all GeneRIFs (16)

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

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

Clone Names

  • FLJ20036

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables p53 binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of signal transduction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of protein stability IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in granular component IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
CDKN2A-interacting protein
Names
collaborates/cooperates with ARF (alternate reading frame) protein
collaborator of ARF

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.

Genomic

  1. NG_050671.1 RefSeqGene

    Range
    5002..9430
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001317343.2 → NP_001304272.1  CDKN2A-interacting protein isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice junction at the 3' end of an exon compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AA622329, AC112698, AF246705, AK000043, AK096180, CN427056
    Consensus CDS
    CCDS82979.1
    UniProtKB/TrEMBL
    D6RGD2, J3KNE1
    Related
    ENSP00000303788.4, ENST00000302350.4
    Conserved Domains (1) summary
    pfam11952
    Location:19 → 124
    XTBD; XRN-Two Binding Domain, XTBD

  2. NM_017632.4 → NP_060102.1  CDKN2A-interacting protein isoform 1

    See identical proteins and their annotated locations for NP_060102.1

    Status: REVIEWED

    Source sequence(s)
    AA622329, AC112698, AF246705, AK000043
    Consensus CDS
    CCDS34110.1
    UniProtKB/Swiss-Prot
    Q8TBM5, Q9NXV6, Q9NYH0
    Related
    ENSP00000427108.1, ENST00000504169.2
    Conserved Domains (1) summary
    pfam11952
    Location:19 → 124
    XTBD; XRN-Two Binding Domain, XTBD

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    183444636..183449064
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    186787446..186791876
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NXV6.3 GenPept UniProtKB/Swiss-Prot:Q9NXV6

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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