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    DCLRE1A DNA cross-link repair 1A [ Homo sapiens (human) ]

    Gene ID: 9937, updated on 2-May-2024

    Summary

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    Official Symbol
    DCLRE1Aprovided by HGNC
    Official Full Name
    DNA cross-link repair 1Aprovided by HGNC
    Primary source
    HGNC:HGNC:17660
    See related
    Ensembl:ENSG00000198924 MIM:609682; AllianceGenome:HGNC:17660
    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
    PSO2; SNM1; SNM1A
    Summary
    This gene encodes a conserved protein that is involved in the repair of DNA interstrand cross-links. DNA cross-links suppress transcription, replication, and DNA segregation. The encoded protein is a regulator of the mitotic cell cycle checkpoint. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]
    Expression
    Ubiquitous expression in thyroid (RPKM 3.4), testis (RPKM 3.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    10q25.3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (113834725..113854394, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (114726307..114745963, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (115594484..115614153, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene pleckstrin homology domain containing S1 Neighboring gene microRNA 4483 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:115580091-115580590 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2838 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:115614900-115615604 Neighboring gene uncharacterized LOC124902506 Neighboring gene NHL repeat containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4073 Neighboring gene uncharacterized LOC124902507 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:115718423-115718923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4074

    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. The SNM1A DNA repair nuclease. Baddock HT, et al. DNA Repair (Amst), 2020 Nov. PMID 32866775, Free PMC Article
    2. Structure-specific endonuclease activity of SNM1A enables processing of a DNA interstrand crosslink. Buzon B, et al. Nucleic Acids Res, 2018 Sep 28. PMID 30165656, Free PMC Article
    3. The hSNM1 protein is a DNA 5'-exonuclease. Hejna J, et al. Nucleic Acids Res, 2007. PMID 17804464, Free PMC Article
    4. Translation of hSNM1 is mediated by an internal ribosome entry site that upregulates expression during mitosis. Zhang X, et al. DNA Repair (Amst), 2002 May 30. PMID 12509242
    5. Genomic organization of a potential human DNA-crosslink repair gene, KIAA0086. Demuth I, et al. Mutat Res, 1998 Oct 21. PMID 9806498

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition.
      Title: Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition.
    2. The SNM1A DNA repair nuclease.
      Title: The SNM1A DNA repair nuclease.
    3. Structure-specific endonuclease activity of SNM1A enables processing of a DNA interstrand crosslink.
      Title: Structure-specific endonuclease activity of SNM1A enables processing of a DNA interstrand crosslink.
    4. Strikingly, the addition of the single-stranded DNA (ssDNA)-binding replication protein A (RPA) selectively restores XPF-ERCC1 endonuclease activity on this structure. The 5'-3' exonuclease SNM1A can load from the XPF-ERCC1-RPA-induced incisions and digest past the crosslink to quantitatively complete the unhooking reaction.
      Title: RPA activates the XPF-ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks.
    5. Different charge distributions along the DNA binding groove may account for the drastic difference in processivity and DNA digestion efficiency, including that of damaged substrates, between SNM1A and SNM1B.
      Title: The structures of the SNM1A and SNM1B/Apollo nuclease domains reveal a potential basis for their distinct DNA processing activities.
    6. differences in the substrate selectivities of SNM1A and SNM1B are likely to be relevant to their in vivo roles
      Title: Characterization of the human SNM1A and SNM1B/Apollo DNA repair exonucleases.
    7. collaboration between hSNM1A and XPF-ERCC1 is necessary to initiate interstrand cross-link repair in replicating human cells
      Title: Human SNM1A and XPF-ERCC1 collaborate to initiate DNA interstrand cross-link repair.
    8. RAD18-dependent recruitment of SNM1A to DNA repair complexes by a ubiquitin-binding zinc finger
      Title: RAD18-dependent recruitment of SNM1A to DNA repair complexes by a ubiquitin-binding zinc finger.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
    10. These findings suggest that SNM1A acts with ATM to promote the G1 cell cycle checkpoint.
      Title: SNM1A acts downstream of ATM to promote the G1 cell cycle checkpoint.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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

    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

    Homology

    Clone Names

    • FLJ97135, KIAA0086

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 5'-3' DNA exonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 5'-3' DNA exonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables beta-lactamase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables damaged DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in double-strand break repair via nonhomologous end joining IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in interstrand cross-link repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    DNA cross-link repair 1A protein
    Names
    DNA-crosslink repair gene SNM1
    SNM1 homolog A
    beta-lactamase DCLRE1A
    NP_001258745.1
    NP_055696.3
    XP_006718153.1
    XP_011538731.1
    XP_054223311.1
    XP_054223312.1

    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.

    mRNA and Protein(s)

    1. NM_001271816.2 → NP_001258745.1  DNA cross-link repair 1A protein

      See identical proteins and their annotated locations for NP_001258745.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      D42045, DB224073
      Consensus CDS
      CCDS7584.1
      UniProtKB/Swiss-Prot
      D3DRC1, Q14701, Q6P5Y3, Q6PJP8, Q6PKL4
      Related
      ENSP00000358311.1, ENST00000369305.1
      Conserved Domains (2) summary
      cd16298
      Location:689 → 844
      SNM1A-like_MBL-fold; 5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain
      pfam07522
      Location:914 → 1019
      DRMBL; DNA repair metallo-beta-lactamase

    2. NM_014881.5 → NP_055696.3  DNA cross-link repair 1A protein

      See identical proteins and their annotated locations for NP_055696.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      D42045
      Consensus CDS
      CCDS7584.1
      UniProtKB/Swiss-Prot
      D3DRC1, Q14701, Q6P5Y3, Q6PJP8, Q6PKL4
      Related
      ENSP00000355185.2, ENST00000361384.7
      Conserved Domains (2) summary
      cd16298
      Location:689 → 844
      SNM1A-like_MBL-fold; 5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain
      pfam07522
      Location:914 → 1019
      DRMBL; DNA repair metallo-beta-lactamase

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      113834725..113854394 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011540429.2 → XP_011538731.1  DNA cross-link repair 1A protein isoform X1

      See identical proteins and their annotated locations for XP_011538731.1

      UniProtKB/Swiss-Prot
      D3DRC1, Q14701, Q6P5Y3, Q6PJP8, Q6PKL4
      Conserved Domains (2) summary
      cd16298
      Location:689 → 844
      SNM1A-like_MBL-fold; 5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain
      pfam07522
      Location:914 → 1019
      DRMBL; DNA repair metallo-beta-lactamase

    2. XM_006718090.2 → XP_006718153.1  DNA cross-link repair 1A protein isoform X1

      See identical proteins and their annotated locations for XP_006718153.1

      UniProtKB/Swiss-Prot
      D3DRC1, Q14701, Q6P5Y3, Q6PJP8, Q6PKL4
      Conserved Domains (2) summary
      cd16298
      Location:689 → 844
      SNM1A-like_MBL-fold; 5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain
      pfam07522
      Location:914 → 1019
      DRMBL; DNA repair metallo-beta-lactamase

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      114726307..114745963 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367336.1 → XP_054223311.1  DNA cross-link repair 1A protein isoform X1

    2. XM_054367337.1 → XP_054223312.1  DNA cross-link repair 1A protein isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6PJP8.3 GenPept UniProtKB/Swiss-Prot:Q6PJP8

    Gene LinkOut

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