Dclre1c DNA cross-link repair 1C [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Dclre1cprovided by RGD
Official Full Name: DNA cross-link repair 1Cprovided by RGD
Primary source: RGD:708574
See related: EnsemblRapid:ENSRNOG00000015980 AllianceGenome:RGD:708574
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Snm1l
Summary: Predicted to enable 5'-3' DNA exonuclease activity; damaged DNA binding activity; and single-stranded DNA endodeoxyribonuclease activity. Predicted to be involved in double-strand break repair via nonhomologous end joining; interstrand cross-link repair; and telomere maintenance. Predicted to act upstream of or within several processes, including B cell differentiation; DNA metabolic process; and response to ionizing radiation. Predicted to be located in Golgi apparatus and nucleoplasm. Predicted to be part of nonhomologous end joining complex. Human ortholog(s) of this gene implicated in Omenn syndrome; common variable immunodeficiency; severe combined immunodeficiency; and severe combined immunodeficiency with sensitivity to ionizing radiation. Orthologous to human DCLRE1C (DNA cross-link repair 1C). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Biased expression in Thymus (RPKM 492.9), Spleen (RPKM 85.8) and 5 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 17q12.3

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	17	NC_086035.1 (79684988..79718399, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	17	NC_051352.1 (74775828..74810089, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	17	NC_005116.4 (78782512..78812140, complement)

Chromosome 17 - NC_086035.1 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 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

BE111954 (e-PCR)
- UniSTS:261173

AI072301 (e-PCR)
- UniSTS:244947

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 damaged DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables single-stranded DNA endodeoxyribonuclease activity	IEA Inferred from Electronic Annotation more info
enables single-stranded DNA endodeoxyribonuclease activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in B cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within B cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within DNA recombination	ISO Inferred from Sequence Orthology more info
involved_in V(D)J recombination	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within V(D)J recombination	ISO Inferred from Sequence Orthology more info
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within chromosome organization	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within double-strand break repair	ISO Inferred from Sequence Orthology 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 response to ionizing radiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within response to ionizing radiation	ISO Inferred from Sequence Orthology more info
involved_in telomere maintenance	IBA Inferred from Biological aspect of Ancestor more info
involved_in telomere maintenance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within telomere maintenance	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
part_of nonhomologous end joining complex	IEA Inferred from Electronic Annotation more info
part_of nonhomologous end joining complex	ISO Inferred from Sequence Orthology more info
part_of nonhomologous end joining complex	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation 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: protein artemis

Names: DNA cross-link repair 1C protein; SNM1-like protein

NP_671486.2

EC 3.1.-.-

XP_038951343.1

EC 3.1.-.-

XP_063132185.1

EC 3.1.-.-

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)

NM_147145.2 → NP_671486.2 protein artemis

See identical proteins and their annotated locations for NP_671486.2

Status: PROVISIONAL

Source sequence(s)

BC083546

UniProtKB/Swiss-Prot

Q5XIX3, Q8K4H7

UniProtKB/TrEMBL

A0A8L2QAU1

Related

ENSRNOP00000102035.1, ENSRNOT00000163213.1

Conserved Domains (2) summary

pfam07522
Location:239 → 343

DRMBL; DNA repair metallo-beta-lactamase

cd16297
Location:1 → 171

artemis-SNM1C-like_MBL-fold; artemis-SNM1C and related proteins; MBL-fold metallo-hydrolase domain

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_086035.1 Reference GRCr8

Range

79684988..79718399 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063276115.1 → XP_063132185.1 protein artemis isoform X1

UniProtKB/TrEMBL

A6JM16
XM_039095415.2 → XP_038951343.1 protein artemis isoform X1

UniProtKB/TrEMBL

A6JM16

Conserved Domains (3) summary

pfam07522
Location:93 → 197

DRMBL; DNA repair metallo-beta-lactamase

NF033845
Location:275 → 520

MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

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