Ercc4l1 (excision repair cross-complementing rodent repair deficiency, complementation group 4-like 1) - Rat Genome Database

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Gene: Ercc4l1 (excision repair cross-complementing rodent repair deficiency, complementation group 4-like 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Ercc4l1 (Ensembl: Ercc4)
Name: excision repair cross-complementing rodent repair deficiency, complementation group 4-like 1 (Ensembl:ERCC excision repair 4, endonuclease catalytic subunit)
RGD ID: 1304845
Description: Predicted to enable damaged DNA binding activity; single-stranded DNA binding activity; and single-stranded DNA endodeoxyribonuclease activity. Predicted to be involved in double-strand break repair via homologous recombination; nucleotide-excision repair involved in interstrand cross-link repair; and resolution of meiotic recombination intermediates. Predicted to be part of nucleotide-excision repair factor 1 complex. Human ortholog(s) of this gene implicated in Fanconi anemia complementation group Q; XFE progeroid syndrome; pancreatic cancer; polyneuropathy due to drug; and xeroderma pigmentosum (multiple). Orthologous to human ERCC4 (ERCC excision repair 4, endonuclease catalytic subunit); PARTICIPATES IN nucleotide excision repair pathway; INTERACTS WITH bisphenol A; indole-3-methanol.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: DNA repair endonuclease XPF; DNA repair endonuclease XPF-like; Ercc4; excision repair cross-complementing rodent repair deficiency, complementation group 4; LOC100909753; LOC103693257; LOC360465
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8101,462,146 - 1,500,409 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl101,462,197 - 1,490,393 (+)EnsemblGRCr8
mRatBN7.210954,927 - 983,651 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10954,977 - 983,174 (+)EnsemblmRatBN7.2
Rnor_6.010975,653 - 1,010,029 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01011,655,960 - 11,690,620 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera1023,398 - 46,137 (+)NCBICelera
RGSC_v3.110875,554 - 909,421 (+)NCBI
Cytogenetic Map10q11NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
7. Xeroderma pigmentosum group F caused by a defect in a structure-specific DNA repair endonuclease. Sijbers AM, etal., Cell. 1996 Sep 6;86(5):811-22.

Genomics

Variants

.
Variants in Ercc4l1
320 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10130004247Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
1549898Neuinf3Neuroinflammation QTL 326.4nervous system integrity trait (VT:0010566)MHC Class II RT1A-positive spinal cord ventral horn area to total spinal cord ventral horn area ratio (CMO:0001980)1015893911Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10117749933Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
7 1 18 49 66 137 94 11 48 36 32 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000004563   ⟹   ENSRNOP00000004563
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl102,925,592 - 2,955,525 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000089404   ⟹   ENSRNOP00000074477
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10954,977 - 983,174 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000103966   ⟹   ENSRNOP00000083739
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl102,925,592 - 2,955,539 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000108933   ⟹   ENSRNOP00000087150
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10955,010 - 969,352 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000118820   ⟹   ENSRNOP00000083462
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl102,920,455 - 2,955,539 (-)Ensembl
mRatBN7.2 Ensembl10954,977 - 970,153 (+)Ensembl
RefSeq Acc Id: XM_063270016   ⟹   XP_063126086
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8101,462,146 - 1,500,409 (+)NCBI
Protein Sequences
Protein RefSeqs XP_063126086 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000074477
  ENSRNOP00000074477.3
  ENSRNOP00000083462.2
Ensembl Acc Id: ENSRNOP00000087150   ⟸   ENSRNOT00000108933
Ensembl Acc Id: ENSRNOP00000074477   ⟸   ENSRNOT00000089404
Ensembl Acc Id: ENSRNOP00000083462   ⟸   ENSRNOT00000118820
RefSeq Acc Id: XP_063126086   ⟸   XM_063270016
- UniProtKB: A0A0G2K855 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000083739   ⟸   ENSRNOT00000103966
Ensembl Acc Id: ENSRNOP00000004563   ⟸   ENSRNOT00000004563

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K855-F1-model_v2 AlphaFold A0A0G2K855 1-914 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304845 AgrOrtholog
Ensembl Genes ENSRNOG00000065745 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000070542 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000089404 ENTREZGENE
  ENSRNOT00000089404.3 UniProtKB/TrEMBL
  ENSRNOT00000118820.2 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.10130 UniProtKB/TrEMBL
  5' to 3' exonuclease, C-terminal subdomain UniProtKB/TrEMBL
InterPro ERCC4_domain UniProtKB/TrEMBL
  Restrct_endonuc-II-like UniProtKB/TrEMBL
  RuvA_2-like UniProtKB/TrEMBL
  XPF UniProtKB/TrEMBL
  XPF_nuclease UniProtKB/TrEMBL
NCBI Gene Ercc4l1 ENTREZGENE
PANTHER DNA REPAIR ENDONUCLEASE XPF UniProtKB/TrEMBL
  DNA REPAIR ENDONUCLEASE XPF UniProtKB/TrEMBL
Pfam ERCC4 UniProtKB/TrEMBL
PhenoGen Ercc4l1 PhenoGen
RatGTEx ENSRNOG00000065745 RatGTEx
  ENSRNOG00000070542 RatGTEx
SMART ERCC4 UniProtKB/TrEMBL
Superfamily-SCOP Restriction endonuclease-like UniProtKB/TrEMBL
  RuvA domain 2-like UniProtKB/TrEMBL
UniProt A0A0G2K855 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZX01_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Ercc4l1  excision repair cross-complementing rodent repair deficiency, complementation group 4-like 1  LOC103693257  DNA repair endonuclease XPF-like  Data merged from RGD:9450399 737654 PROVISIONAL
2015-07-29 Ercc4l1  excision repair cross-complementing rodent repair deficiency, complementation group 4-like 1  LOC100909753  DNA repair endonuclease XPF-like  Data merged from RGD:6502047 737654 PROVISIONAL
2014-08-25 LOC103693257  DNA repair endonuclease XPF-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-07-05 LOC100909753  DNA repair endonuclease XPF-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-29 Ercc4l1  excision repair cross-complementing rodent repair deficiency, complementation group 4-like 1  Ercc4_predicted  excision repair cross-complementing rodent repair deficiency, complementation group 4 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Ercc4_predicted  excision repair cross-complementing rodent repair deficiency, complementation group 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED