Dclre1b DNA cross-link repair 1B [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Dclre1bprovided by RGD
Official Full Name: DNA cross-link repair 1Bprovided by RGD
Primary source: RGD:1310343
See related: EnsemblRapid:ENSRNOG00000019367 AllianceGenome:RGD:1310343
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable several functions, including 5'-3' DNA exonuclease activity; beta-lactamase activity; and protein homodimerization activity. Predicted to be involved in DNA metabolic process. Predicted to be located in centrosome; chromosome, telomeric region; and nuclear body. Human ortholog(s) of this gene implicated in dyskeratosis congenita. Orthologous to human DCLRE1B (DNA cross-link repair 1B). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Spleen (RPKM 70.0), Thymus (RPKM 66.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q34

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (193998350..194006873, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (191309909..191318399, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (206285085..206293599, complement)

Chromosome 2 - NC_086020.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

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Markers

AA957141 (e-PCR)
- UniSTS:248103

RH133747 (e-PCR)
- UniSTS:217030

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 5'-3' DNA exonuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables 5'-3' exonuclease activity	IEA Inferred from Electronic Annotation more info
enables 5'-3' exonuclease activity	ISO Inferred from Sequence Orthology more info
enables 5'-3' exonuclease activity	ISS Inferred from Sequence or Structural Similarity more info
enables beta-lactamase activity	IEA Inferred from Electronic Annotation more info
enables beta-lactamase activity	ISO Inferred from Sequence Orthology more info
enables beta-lactamase activity	ISS Inferred from Sequence or Structural Similarity more info
enables damaged DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables exonuclease activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in biological_process	ND No biological Data available 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
involved_in interstrand cross-link repair	IEA Inferred from Electronic Annotation more info
involved_in interstrand cross-link repair	ISO Inferred from Sequence Orthology more info
involved_in protection from non-homologous end joining at telomere	IEA Inferred from Electronic Annotation more info
involved_in protection from non-homologous end joining at telomere	ISO Inferred from Sequence Orthology more info
involved_in protection from non-homologous end joining at telomere	ISS Inferred from Sequence or Structural Similarity more info
involved_in telomere capping	ISO Inferred from Sequence Orthology more info
involved_in telomere maintenance	IBA Inferred from Biological aspect of Ancestor more info
involved_in telomere maintenance	ISO Inferred from Sequence Orthology more info
involved_in telomere maintenance	ISS Inferred from Sequence or Structural Similarity more info
involved_in telomere maintenance via telomere lengthening	IEA Inferred from Electronic Annotation more info
involved_in telomere maintenance via telomere lengthening	ISO Inferred from Sequence Orthology more info
involved_in telomeric 3' overhang formation	IEA Inferred from Electronic Annotation more info
involved_in telomeric 3' overhang formation	ISO Inferred from Sequence Orthology more info
involved_in telomeric 3' overhang formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in telomeric loop formation	IEA Inferred from Electronic Annotation more info
involved_in telomeric loop formation	ISO Inferred from Sequence Orthology more info
involved_in telomeric loop formation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in centrosome	IEA Inferred from Electronic Annotation more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in centrosome	ISS Inferred from Sequence or Structural Similarity more info
located_in chromosome, telomeric region	IEA Inferred from Electronic Annotation more info
located_in chromosome, telomeric region	ISO Inferred from Sequence Orthology more info
located_in chromosome, telomeric region	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nuclear body	IEA Inferred from Electronic Annotation more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: 5' exonuclease Apollo

Names: DNA cross-link repair 1B protein; SNM1 homolog B; beta-lactamase MBLAC2

NP_001020858.2

EC 3.5.2.6

NP_001376151.1

EC 3.5.2.6

XP_006233142.1

EC 3.5.2.6

XP_038958331.1

EC 3.5.2.6

XP_038958333.1

EC 3.5.2.6

XP_038958334.1

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.

mRNA and Protein(s)

NM_001025687.2 → NP_001020858.2 5' exonuclease Apollo

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/Swiss-Prot

Q4KLY6

UniProtKB/TrEMBL

A6K3M4, G3V8I3

Related

ENSRNOP00000026213.7, ENSRNOT00000026213.8

Conserved Domains (3) summary

cd11662
Location:492 → 524

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 → 298

DRMBL; DNA repair metallo-beta-lactamase
NM_001389222.1 → NP_001376151.1 5' exonuclease Apollo

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/Swiss-Prot

Q4KLY6

UniProtKB/TrEMBL

A6K3M4, G3V8I3

Conserved Domains (3) summary

cd11662
Location:492 → 524

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 → 298

DRMBL; DNA repair metallo-beta-lactamase

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086020.1 Reference GRCr8

Range

193998350..194006873 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006233080.5 → XP_006233142.1 5' exonuclease Apollo isoform X1

UniProtKB/Swiss-Prot

Q4KLY6

Conserved Domains (3) summary

cd11662
Location:431 → 463

apollo_TRF2_binding; TRF2-binding region of apollo and similar proteins

pfam07522
Location:155 → 237

DRMBL; DNA repair metallo-beta-lactamase

cl23716
Location:6 → 119

metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain
XM_039102403.2 → XP_038958331.1 5' exonuclease Apollo isoform X2

UniProtKB/TrEMBL

A6K3M5

Conserved Domains (2) summary

cd11662
Location:356 → 388

apollo_TRF2_binding; TRF2-binding region of apollo and similar proteins

pfam07522
Location:80 → 162

DRMBL; DNA repair metallo-beta-lactamase
XM_039102405.2 → XP_038958333.1 5' exonuclease Apollo isoform X3

UniProtKB/TrEMBL

A0A0G2K494

Conserved Domains (1) summary

cd16273
Location:6 → 151

SNM1A-1C-like_MBL-fold; SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain
XM_039102406.2 → XP_038958334.1 5' exonuclease Apollo isoform X4

UniProtKB/TrEMBL

A0A0G2K494

Conserved Domains (1) summary

cd16273
Location:6 → 151

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