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    ATRIP ATR interacting protein [ Homo sapiens (human) ]

    Gene ID: 84126, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ATRIPprovided by HGNC
    Official Full Name
    ATR interacting proteinprovided by HGNC
    Primary source
    HGNC:HGNC:33499
    See related
    Ensembl:ENSG00000164053 MIM:606605; AllianceGenome:HGNC:33499
    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
    Summary
    This gene encodes an essential component of the DNA damage checkpoint. The encoded protein binds to single-stranded DNA coated with replication protein A. The protein also interacts with the ataxia telangiectasia and Rad3 related protein kinase, resulting in its accumulation at intranuclear foci induced by DNA damage. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2012]
    Annotation information
    Note: GeneID 11277 was annotated as a single gene with two non-overlapping coding regions. GeneID 11277 now represents only the downstream coding region encoding three prime repair exonuclease 1. The upstream coding region is represented by geneID 84126. [29 May 2007]
    Expression
    Broad expression in testis (RPKM 11.6), thyroid (RPKM 3.8) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ATRIP in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (48446737..48467645)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (48474745..48495650)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (48488141..48509044)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene plexin B1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14326 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14327 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48471449-48472442 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:48473797-48474996 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48476193-48477035 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14328 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19828 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14330 Neighboring gene coiled-coil domain containing 51 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14331 Neighboring gene ATRIP-TREX1 readthrough Neighboring gene translation machinery associated 7 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19829 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48507557-48508438 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48508439-48509318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48509460-48510226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19831 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48513959-48514818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19833 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48515680-48516539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19834 Neighboring gene shisa family member 5 Neighboring gene three prime repair exonuclease 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14332 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14333 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48542139-48542692 Neighboring gene MPRA-validated peak4641 silencer Neighboring gene 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 Neighboring gene microRNA 6823

    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 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. Dimerization of the ATRIP protein through the coiled-coil motif and its implication to the maintenance of stalled replication forks. Itakura E, et al. Mol Biol Cell, 2005 Dec. PMID 16176973, Free PMC Article
    2. Variants in ATRIP are associated with breast cancer susceptibility in the Polish population and UK Biobank. Cybulski C, et al. Am J Hum Genet, 2023 Apr 6. PMID 36977412, Free PMC Article
    3. ATR signalling: more than meeting at the fork. Nam EA, et al. Biochem J, 2011 Jun 15. PMID 21615334, Free PMC Article
    4. Quaternary structure of ATR and effects of ATRIP and replication protein A on its DNA binding and kinase activities. Unsal-Kaçmaz K, et al. Mol Cell Biol, 2004 Feb. PMID 14729973, Free PMC Article
    5. ATR-dependent phosphorylation of ATRIP in response to genotoxic stress. Itakura E, et al. Biochem Biophys Res Commun, 2004 Oct 29. PMID 15451423

    See all (104) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Variants in ATRIP are associated with breast cancer susceptibility in the Polish population and UK Biobank.
      Title: Variants in ATRIP are associated with breast cancer susceptibility in the Polish population and UK Biobank.
    2. ATRIP protects progenitor cells against DNA damage in vivo.
      Title: ATRIP protects progenitor cells against DNA damage in vivo.
    3. ATRIP deacetylation by SIRT2 promotes ATR-ATRIP binding to replication protein A-single-stranded DNA to drive ATR activation and thus facilitate recovery from replication stress.
      Title: ATRIP Deacetylation by SIRT2 Drives ATR Checkpoint Activation by Promoting Binding to RPA-ssDNA.
    4. ATRIP SUMOylation promotes ATR activation by providing a unique type of protein glue that boosts multiple protein interactions along the ATR pathway
      Title: SUMOylation of ATRIP potentiates DNA damage signaling by boosting multiple protein interactions in the ATR pathway.
    5. Data on crystal structure of BRCA1 binding with phosphopeptides suggest that C-terminal domain of BRCA1 interacts with ATRIP and BAAT1 with preferences for specific side chains; in ATRIP, phospho-Ser239 and Phe242 are the main interacting residues.
      Title: Structural basis for the BRCA1 BRCT interaction with the proteins ATRIP and BAAT1.
    6. Data indicate that ATRIP is a direct target gene of HIF-1, and the increased ATRIP then activates the ATR signaling pathway under hypoxia.
      Title: HIF1-regulated ATRIP expression is required for hypoxia induced ATR activation.
    7. our analysis exposes an overlapping clinical manifestation between the disorders but allows an expanded spectrum of clinical features for ATR-ATRIP Seckel Syndrome to be defined
      Title: Identification of the first ATRIP-deficient patient and novel mutations in ATR define a clinical spectrum for ATR-ATRIP Seckel Syndrome.
    8. as an ATR-associated kinase, Nek1 enhances the stability and activity of ATR-ATRIP before DNA damage, priming ATR-ATRIP for a robust DNA damage response
      Title: Nek1 kinase associates with ATR-ATRIP and primes ATR for efficient DNA damage signaling.
    9. ATRIP may function outside the context of the canonical ATR damage signaling pathway during HSV-1 infection to participate in the viral life cycle.
      Title: ATR and ATRIP are recruited to herpes simplex virus type 1 replication compartments even though ATR signaling is disabled.
    10. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    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

    EBI GWAS Catalog

    Description
    Genome-wide association study in multiple human prion diseases suggests genetic risk factors additional to PRNP.
    EBI GWAS Catalog
    Joint influence of small-effect genetic variants on human longevity.
    EBI GWAS Catalog

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough ATRIP-TREX1

    Readthrough gene: ATRIP-TREX1, Included gene: TREX1

    Homology

    Clone Names

    • FLJ12343, MGC20625, MGC21482, MGC26740, DKFZp762J2115

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables K63-linked polyubiquitin modification-dependent protein 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 checkpoint signaling TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nucleobase-containing compound metabolic process NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of double-strand break repair NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of ATR-ATRIP complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ATR-interacting protein
    Names
    ATM and Rad3-related-interacting protein
    NP_001257951.1
    NP_001257952.1
    NP_115542.2
    NP_569055.1

    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_041782.1 RefSeqGene

      Range
      5028..25936
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001271022.2 → NP_001257951.1  ATR-interacting protein isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks a portion of the 5' coding region, contains an alternate internal exon, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC134772, AK300548, BC030597
      UniProtKB/TrEMBL
      A0A0U1RQJ8
      Related
      ENSP00000489041.2, ENST00000634384.2
      Conserved Domains (1) summary
      pfam03938
      Location:2 → 80
      OmpH; Outer membrane protein (OmpH-like)

    2. NM_001271023.2 → NP_001257952.1  ATR-interacting protein isoform 4

      See identical proteins and their annotated locations for NP_001257952.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC134772, BC030597
      Consensus CDS
      CCDS59449.1
      UniProtKB/TrEMBL
      A0A0U1RQJ8
      Related
      ENSP00000400930.1, ENST00000412052.4
      Conserved Domains (1) summary
      cl09111
      Location:20 → 114
      Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...

    3. NM_032166.4 → NP_115542.2  ATR-interacting protein isoform 2

      See identical proteins and their annotated locations for NP_115542.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC134772, BC014153, DC402185
      Consensus CDS
      CCDS2767.1
      Related
      ENSP00000302338.5, ENST00000346691.9
      Conserved Domains (1) summary
      cl09111
      Location:113 → 207
      Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...

    4. NM_130384.3 → NP_569055.1  ATR-interacting protein isoform 1

      See identical proteins and their annotated locations for NP_569055.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC134772, AF451323, BC030597, CB960784, DC402185
      Consensus CDS
      CCDS2768.1
      UniProtKB/Swiss-Prot
      A8K6A3, A8K714, B2RCE7, B4DU92, B5MEB7, Q69YK9, Q8NHQ2, Q8WUG7, Q8WXE1, Q96CL3, Q9HA30
      Related
      ENSP00000323099.3, ENST00000320211.10
      Conserved Domains (1) summary
      pfam12718
      Location:113 → 212
      Tropomyosin_1; Tropomyosin like

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      48446737..48467645
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      48474745..48495650
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WXE1.1 GenPept UniProtKB/Swiss-Prot:Q8WXE1

    Gene LinkOut

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

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