ERCC6 (ERCC excision repair 6, chromatin remodeling factor) - Rat Genome Database

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Gene: ERCC6 (ERCC excision repair 6, chromatin remodeling factor) Canis lupus familiaris
Analyze
Symbol: ERCC6
Name: ERCC excision repair 6, chromatin remodeling factor
RGD ID: 12279392
Description: ENCODES a protein that exhibits DNA helicase activity (ortholog); RNA polymerase binding (ortholog); sequence-specific DNA binding (ortholog); INVOLVED IN DNA damage response (ortholog); DNA protection (ortholog); DNA repair (ortholog); PARTICIPATES IN altered nucleotide excision repair pathway; nucleotide excision repair pathway; ASSOCIATED WITH age related macular degeneration 5 (ortholog); arthrogryposis multiplex congenita (ortholog); cataract (ortholog); FOUND IN B-WICH complex (ortholog); nuclear body (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: DNA excision repair protein ERCC-6; excision repair cross-complementing rodent repair deficiency, complementation group 6
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1281,358,383 - 1,432,276 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl281,361,107 - 1,427,162 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha281,593,582 - 1,667,457 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0281,534,813 - 1,608,719 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl281,534,813 - 1,608,641 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1281,333,055 - 1,406,921 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0281,370,132 - 1,444,015 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0281,502,030 - 1,575,915 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
base-excision repair  (IEA)
chromatin remodeling  (IEA)
DNA damage checkpoint signaling  (IEA)
DNA damage response  (IEA,ISO)
DNA protection  (ISO)
DNA repair  (IEA,ISO)
double-strand break repair via classical nonhomologous end joining  (IEA)
double-strand break repair via synthesis-dependent strand annealing  (IEA)
intrinsic apoptotic signaling pathway in response to DNA damage  (IEA,ISO)
JNK cascade  (IEA,ISO)
multicellular organism growth  (IEA,ISO)
negative regulation of double-strand break repair via nonhomologous end joining  (IEA)
neurogenesis  (IEA)
neuron differentiation  (IEA)
neuron projection development  (IEA)
photoreceptor cell maintenance  (IEA,ISO)
positive regulation of defense response to virus by host  (ISO)
positive regulation of DNA repair  (IEA)
positive regulation of DNA-templated transcription, elongation  (IEA)
positive regulation of double-strand break repair via homologous recombination  (IEA)
positive regulation of gene expression  (ISO)
positive regulation of peptidyl-serine phosphorylation of STAT protein  (ISO)
positive regulation of transcription by RNA polymerase III  (IEA)
positive regulation of transcription initiation by RNA polymerase II  (IEA,ISO)
pyrimidine dimer repair  (IEA,ISO)
reciprocal meiotic recombination  (IEA)
regulation of DNA-templated transcription elongation  (IEA)
regulation of transcription elongation by RNA polymerase II  (ISO)
response to gamma radiation  (IEA,ISO)
response to oxidative stress  (IEA,ISO)
response to superoxide  (IEA,ISO)
response to toxic substance  (IEA,ISO)
response to UV  (IEA,ISO)
response to UV-B  (IEA,ISO)
response to X-ray  (IEA,ISO)
single strand break repair  (IEA)
transcription elongation by RNA polymerase I  (IEA,ISO)
transcription-coupled nucleotide-excision repair  (IEA,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
ERCC6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1281,358,383 - 1,432,276 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl281,361,107 - 1,427,162 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha281,593,582 - 1,667,457 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0281,534,813 - 1,608,719 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl281,534,813 - 1,608,641 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1281,333,055 - 1,406,921 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0281,370,132 - 1,444,015 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0281,502,030 - 1,575,915 (-)NCBIUU_Cfam_GSD_1.0
ERCC6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381049,434,881 - 49,539,538 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1049,454,168 - 49,539,538 (-)EnsemblGRCh38hg38GRCh38
GRCh371050,642,927 - 50,747,584 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361050,336,715 - 50,417,078 (-)NCBINCBI36Build 36hg18NCBI36
Build 341050,336,714 - 50,417,078NCBI
Celera1044,250,656 - 44,333,241 (-)NCBICelera
Cytogenetic Map10q11.23NCBI
HuRef1044,927,342 - 45,011,950 (-)NCBIHuRef
CHM1_11050,944,706 - 51,029,274 (-)NCBICHM1_1
T2T-CHM13v2.01050,283,667 - 50,388,257 (-)NCBIT2T-CHM13v2.0
Ercc6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391432,235,248 - 32,302,947 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1432,235,478 - 32,302,947 (+)EnsemblGRCm39 Ensembl
GRCm381432,513,291 - 32,580,990 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1432,513,521 - 32,580,990 (+)EnsemblGRCm38mm10GRCm38
MGSCv371433,326,707 - 33,394,175 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361431,342,530 - 31,409,998 (+)NCBIMGSCv36mm8
Celera1428,771,098 - 28,837,767 (+)NCBICelera
Cytogenetic Map14BNCBI
cM Map1419.4NCBI
Ercc6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8167,771,311 - 7,841,895 (+)NCBIGRCr8
mRatBN7.2167,764,983 - 7,835,587 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl167,765,013 - 7,835,587 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx167,780,912 - 7,847,534 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0168,925,860 - 8,992,482 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0167,779,882 - 7,846,470 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0168,734,028 - 8,804,610 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl168,734,035 - 8,804,610 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01610,699,983 - 10,770,565 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4168,024,881 - 8,091,587 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1168,024,868 - 8,088,560 (+)NCBI
Celera167,365,531 - 7,432,176 (-)NCBICelera
Cytogenetic Map16p16NCBI
Ercc6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955556748,231 - 813,133 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955556745,175 - 812,215 (+)NCBIChiLan1.0ChiLan1.0
ERCC6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2861,722,441 - 61,811,183 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11061,721,084 - 61,812,606 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01044,703,720 - 44,784,948 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
Ercc6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721379,558,979 - 79,640,918 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936728761,804 - 844,690 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936728706,499 - 843,447 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ERCC6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1490,002,024 - 90,075,898 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11489,998,125 - 90,075,911 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21497,907,746 - 97,985,104 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Ercc6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624928463,279 - 530,115 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624928458,651 - 532,201 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in ERCC6
542 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium 6 6
Low 5 5 16 6 6 6 6 6 6 8 10 6
Below cutoff

Sequence


RefSeq Acc Id: ENSCAFT00000010674   ⟹   ENSCAFP00000009895
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl281,361,107 - 1,427,162 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000063880   ⟹   ENSCAFP00000062955
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl281,361,107 - 1,427,162 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000065020   ⟹   ENSCAFP00000059117
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl281,361,107 - 1,427,162 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000066484   ⟹   ENSCAFP00000060317
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl281,361,107 - 1,427,162 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000071152   ⟹   ENSCAFP00000060621
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl281,361,107 - 1,427,162 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000073646   ⟹   ENSCAFP00000063972
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl281,361,107 - 1,427,162 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000082164   ⟹   ENSCAFP00000046280
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl281,361,107 - 1,427,162 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000084031   ⟹   ENSCAFP00000062952
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl281,361,107 - 1,427,162 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845037026   ⟹   ENSCAFP00845028993
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl281,534,813 - 1,608,641 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845037377   ⟹   ENSCAFP00845029280
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl281,534,826 - 1,608,641 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845037594   ⟹   ENSCAFP00845029454
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl281,534,826 - 1,608,641 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845037794   ⟹   ENSCAFP00845029612
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl281,534,826 - 1,608,641 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845037979   ⟹   ENSCAFP00845029761
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl281,534,826 - 1,608,641 (-)Ensembl
RefSeq Acc Id: XM_038439778   ⟹   XP_038295706
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0281,534,813 - 1,608,719 (-)NCBI
RefSeq Acc Id: XM_038514398   ⟹   XP_038370326
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1281,333,055 - 1,406,921 (-)NCBI
RefSeq Acc Id: XM_038578050   ⟹   XP_038433978
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0281,502,030 - 1,575,915 (-)NCBI
RefSeq Acc Id: XM_038642209   ⟹   XP_038498137
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0281,370,132 - 1,444,015 (-)NCBI
RefSeq Acc Id: XM_534944   ⟹   XP_534944
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1281,358,383 - 1,432,276 (-)NCBI
Dog10K_Boxer_Tasha281,593,582 - 1,667,457 (-)NCBI
Sequence:
RefSeq Acc Id: XP_534944   ⟸   XM_534944
- UniProtKB: A0A8C0R7I2 (UniProtKB/TrEMBL),   A0A8C0TI63 (UniProtKB/TrEMBL),   A0A8I3PAF3 (UniProtKB/TrEMBL),   A0A8C0NLW5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000062952   ⟸   ENSCAFT00000084031
RefSeq Acc Id: ENSCAFP00000062955   ⟸   ENSCAFT00000063880
RefSeq Acc Id: ENSCAFP00000063972   ⟸   ENSCAFT00000073646
RefSeq Acc Id: ENSCAFP00000009895   ⟸   ENSCAFT00000010674
RefSeq Acc Id: ENSCAFP00000060317   ⟸   ENSCAFT00000066484
RefSeq Acc Id: ENSCAFP00000046280   ⟸   ENSCAFT00000082164
RefSeq Acc Id: ENSCAFP00000059117   ⟸   ENSCAFT00000065020
RefSeq Acc Id: ENSCAFP00000060621   ⟸   ENSCAFT00000071152
RefSeq Acc Id: XP_038370326   ⟸   XM_038514398
RefSeq Acc Id: XP_038498137   ⟸   XM_038642209
RefSeq Acc Id: XP_038295706   ⟸   XM_038439778
- UniProtKB: A0A8C0R7I2 (UniProtKB/TrEMBL),   A0A8C0TI63 (UniProtKB/TrEMBL),   A0A8I3PAF3 (UniProtKB/TrEMBL),   A0A8C0NLW5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038433978   ⟸   XM_038578050
- UniProtKB: A0A8C0NLW5 (UniProtKB/TrEMBL),   A0A8C0R7I2 (UniProtKB/TrEMBL),   A0A8C0TI63 (UniProtKB/TrEMBL),   A0A8I3PAF3 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845029612   ⟸   ENSCAFT00845037794
RefSeq Acc Id: ENSCAFP00845029761   ⟸   ENSCAFT00845037979
RefSeq Acc Id: ENSCAFP00845028993   ⟸   ENSCAFT00845037026
RefSeq Acc Id: ENSCAFP00845029280   ⟸   ENSCAFT00845037377
RefSeq Acc Id: ENSCAFP00845029454   ⟸   ENSCAFT00845037594
Promoters
RGD ID:13688247
Promoter ID:EPDNEW_C6313
Type:multiple initiation site
Name:ERCC6_1
Description:ERCC excision repair 6, chromatin remodeling factor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1281,432,204 - 1,432,264EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000006624 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030017646 UniProtKB/TrEMBL
  ENSCAFG00040022529 UniProtKB/TrEMBL
  ENSCAFG00845020981 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000010674.5 UniProtKB/TrEMBL
  ENSCAFT00000066484.2 UniProtKB/TrEMBL
  ENSCAFT00000071152.2 UniProtKB/TrEMBL
  ENSCAFT00000073646.2 UniProtKB/TrEMBL
  ENSCAFT00000082164.2 UniProtKB/TrEMBL
  ENSCAFT00030032524.1 UniProtKB/TrEMBL
  ENSCAFT00040041803.1 UniProtKB/TrEMBL
  ENSCAFT00040041830.1 UniProtKB/TrEMBL
  ENSCAFT00040041902.1 UniProtKB/TrEMBL
  ENSCAFT00040041989.1 UniProtKB/TrEMBL
  ENSCAFT00040042063.1 UniProtKB/TrEMBL
  ENSCAFT00040042117.1 UniProtKB/TrEMBL
  ENSCAFT00845037026.1 UniProtKB/TrEMBL
  ENSCAFT00845037377 ENTREZGENE
  ENSCAFT00845037377.1 UniProtKB/TrEMBL
  ENSCAFT00845037594.1 UniProtKB/TrEMBL
  ENSCAFT00845037794.1 UniProtKB/TrEMBL
  ENSCAFT00845037979.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.10810 UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/TrEMBL
InterPro Helicase_ATP-bd UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  SNF2-like_sf UniProtKB/TrEMBL
  SNF2_N UniProtKB/TrEMBL
KEGG Report cfa:477747 UniProtKB/TrEMBL
NCBI Gene ERCC6 ENTREZGENE
PANTHER DNA EXCISION REPAIR PROTEIN ERCC-6-RELATED UniProtKB/TrEMBL
  SNF2/RAD54 FAMILY MEMBER UniProtKB/TrEMBL
Pfam Helicase_C UniProtKB/TrEMBL
  SNF2_N UniProtKB/TrEMBL
PROSITE HELICASE_ATP_BIND_1 UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/TrEMBL
SMART DEXDc UniProtKB/TrEMBL
  HELICc UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A0A8C0NLW5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0R7I2 ENTREZGENE
  A0A8C0TFU9_CANLF UniProtKB/TrEMBL
  A0A8C0TI63 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0TIN9_CANLF UniProtKB/TrEMBL
  A0A8C0TJA0_CANLF UniProtKB/TrEMBL
  A0A8C0TLK6_CANLF UniProtKB/TrEMBL
  A0A8C0TM51_CANLF UniProtKB/TrEMBL
  A0A8I3P6E6_CANLF UniProtKB/TrEMBL
  A0A8I3PAF3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PF27_CANLF UniProtKB/TrEMBL
  A0A8I3PN22_CANLF UniProtKB/TrEMBL
  A0A8I3S2G6_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:40445 ENTREZGENE