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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
    mouse all
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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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    NEW Try the new Transcript table

    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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