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

Gene ID: 9937, updated on 27-Nov-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
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Genomic context

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See DCLRE1A in Genome Data Viewer
Location:
10q25.3
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (113834725..113854394, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (114726307..114745963, complement)
RS_2024_09 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. SNM1A is crucial for efficient repair of complex DNA breaks in human cells. Swift LP, et al. Nat Commun, 2024 Jun 25. PMID 38918391, Free PMC Article
  2. Genomic organization of a potential human DNA-crosslink repair gene, KIAA0086. Demuth I, et al. Mutat Res, 1998 Oct 21. PMID 9806498
  3. 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
  4. The hSNM1 protein is a DNA 5'-exonuclease. Hejna J, et al. Nucleic Acids Res, 2007. PMID 17804464, Free PMC Article
  5. 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

See all (46) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SNM1A is crucial for efficient repair of complex DNA breaks in human cells.
    Title: SNM1A is crucial for efficient repair of complex DNA breaks in human cells.
  2. 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.
  3. The SNM1A DNA repair nuclease.
    Title: The SNM1A DNA repair nuclease.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
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)

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_2024_08

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

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