DCLRE1B DNA cross-link repair 1B [Homo sapiens (human)] - Gene

Summary

Official Symbol: DCLRE1Bprovided by HGNC
Official Full Name: DNA cross-link repair 1Bprovided by HGNC
Primary source: HGNC:HGNC:17641
See related: Ensembl:ENSG00000118655 MIM:609683; AllianceGenome:HGNC:17641
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: DKCB8; SNM1B; SNMIB; APOLLO
Summary: DNA interstrand cross-links prevent strand separation, thereby physically blocking transcription, replication, and segregation of DNA. DCLRE1B is one of several evolutionarily conserved genes involved in repair of interstrand cross-links (Dronkert et al., 2000 [PubMed 10848582]).[supplied by OMIM, Mar 2008]
Expression: Ubiquitous expression in bone marrow (RPKM 3.3), appendix (RPKM 3.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p13.2

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (113904619..113914086)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (113916281..113925748)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (114447241..114456708)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

DNA-PK controls Apollo's access to leading-end telomeres.
Title: DNA-PK controls Apollo's access to leading-end telomeres.
DCLRE1B/Apollo germline mutations associated with renal cell carcinoma impair telomere protection.
Title: DCLRE1B/Apollo germline mutations associated with renal cell carcinoma impair telomere protection.
DCLRE1B promotes tumor progression and predicts immunotherapy response through METTL3-mediated m6A modification in pancreatic cancer.
Title: DCLRE1B promotes tumor progression and predicts immunotherapy response through METTL3-mediated m6A modification in pancreatic cancer.
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.
A phosphate binding pocket is a key determinant of exo- versus endo-nucleolytic activity in the SNM1 nuclease family.
Title: A phosphate binding pocket is a key determinant of exo- versus endo-nucleolytic activity in the SNM1 nuclease family.
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.
The SNM1B/APOLLO DNA nuclease functions in resolution of replication stress and maintenance of common fragile site stability.
Title: The SNM1B/APOLLO DNA nuclease functions in resolution of replication stress and maintenance of common fragile site stability.
the N-terminal region of Snm1B forms a complex containing PSF2 and Mus81, while the C-terminal region is important for PSF2-mediated chromatin association.
Title: Snm1B interacts with PSF2.
The nuclease hSNM1B/Apollo is linked to the Fanconi anemia pathway via its interaction with FANCP/SLX4.
Title: The nuclease hSNM1B/Apollo is linked to the Fanconi anemia pathway via its interaction with FANCP/SLX4.
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.

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

Associated conditions

Description	Tests
Dyskeratosis congenita, autosomal recessive 8 MedGen: C5774257 OMIM: 620133 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Large-scale genotyping identifies 41 new loci associated with breast cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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' 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 protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
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
involved_in interstrand cross-link repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protection from non-homologous end joining at telomere	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in telomere capping	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in telomere maintenance	IBA Inferred from Biological aspect of Ancestor more info
involved_in telomere maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in telomere maintenance via telomere lengthening	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in telomeric 3' overhang formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in telomeric loop formation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome, telomeric region	HDA more info	PubMed
colocalizes_with chromosome, telomeric region	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome, telomeric region	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: 5' exonuclease Apollo

Names: DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae); PSO2 homolog; SNM1 homolog B; beta-lactamase DCLRE1B

NP_001306875.1

EC 3.5.2.6

NP_001306876.1

EC 3.5.2.6

NP_001350619.1

EC 3.5.2.6

NP_001350620.1

EC 3.5.2.6

NP_073747.1

EC 3.5.2.6

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

NG_057565.1 RefSeqGene

Range

5708..14468

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1219

mRNA and Protein(s)

NM_001319946.2 → NP_001306875.1 5' exonuclease Apollo isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate 5' exon compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).

Source sequence(s)

AI669133, CR936679, DR005221

Conserved Domains (3) summary

cd11662
Location:370 → 403

apollo_TRF2_binding; TRF2-binding region of apollo and similar proteins

pfam07522
Location:90 → 173

DRMBL; DNA repair metallo-beta-lactamase

cl23716
Location:1 → 25

metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain
NM_001319947.2 → NP_001306876.1 5' exonuclease Apollo isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).

Source sequence(s)

AI669133, BC029687, DA414122

UniProtKB/Swiss-Prot

Q9H816

Conserved Domains (3) summary

cd11662
Location:370 → 403

apollo_TRF2_binding; TRF2-binding region of apollo and similar proteins

pfam07522
Location:90 → 173

DRMBL; DNA repair metallo-beta-lactamase

cl23716
Location:1 → 25

metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain
NM_001363690.2 → NP_001350619.1 5' exonuclease Apollo isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (4) includes alternate splicing in the 3' coding region, which results in a frameshift compared to variant 1. The encoded isoform (c) has a shorter and distinct C-terminus compared to isoform a.

Source sequence(s)

AL137856

Conserved Domains (2) summary

cd16273
Location:6 → 151

SNM1A-1C-like_MBL-fold; SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain

pfam07522
Location:216 → 299

DRMBL; DNA repair metallo-beta-lactamase
NM_001363691.2 → NP_001350620.1 5' exonuclease Apollo isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' and 3' coding regions, compared to variant 1. The encoded isoform (d) has a shorter N-terminus and a shorter distinct C-terminus, compared to isoform a.

Source sequence(s)

AF306691, AI669133, AL137856

Conserved Domains (2) summary

pfam07522
Location:90 → 173

DRMBL; DNA repair metallo-beta-lactamase

cl23716
Location:1 → 25

metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain
NM_022836.4 → NP_073747.1 5' exonuclease Apollo isoform a

See identical proteins and their annotated locations for NP_073747.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AI669133, BC029687, DR005221

Consensus CDS

CCDS866.1

UniProtKB/Swiss-Prot

Q9H816, Q9H9E5

UniProtKB/TrEMBL

A0A3B3ITQ0

Related

ENSP00000498042.1, ENST00000650450.2

Conserved Domains (3) summary

cd11662
Location:496 → 529

apollo_TRF2_binding; TRF2-binding region of apollo and similar proteins

cd16273
Location:6 → 151

SNM1A-1C-like_MBL-fold; SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain

pfam07522
Location:216 → 299

DRMBL; DNA repair metallo-beta-lactamase