Ercc6 ERCC excision repair 6, chromatin remodeling factor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ercc6provided by RGD
Official Full Name: ERCC excision repair 6, chromatin remodeling factorprovided by RGD
Primary source: RGD:1311509
See related: Ensembl:ENSRNOG00000030017 AllianceGenome:RGD:1311509
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
Summary: Predicted to enable several functions, including ATP binding activity; protein C-terminus binding activity; and protein tyrosine kinase activator activity. Involved in DNA protection; regulation of transcription elongation from RNA polymerase II promoter; and transcription-coupled nucleotide-excision repair. Predicted to be located in nuclear body; nucleolus; and site of DNA damage. Predicted to be part of transcription elongation factor complex. Predicted to be active in nucleus. Used to study Cockayne syndrome B. Biomarker of middle cerebral artery infarction and transient cerebral ischemia. Human ortholog(s) of this gene implicated in several diseases, including Cockayne syndrome (multiple); De Sanctis-Cacchione syndrome; UV-sensitive syndrome; age related macular degeneration 5; and primary ovarian insufficiency 11. Orthologous to human ERCC6 (ERCC excision repair 6, chromatin remodeling factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 77.4), Thymus (RPKM 55.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 16p16

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	16	NC_086034.1 (7771311..7841895)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	16	NC_051351.1 (7764983..7835587)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	16	NC_005115.4 (8734028..8804610)

Chromosome 16 - NC_086034.1 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?

Rat Model of Cockayne Syndrome Neurological Disease.
Title: Rat Model of Cockayne Syndrome Neurological Disease.

Submit: New GeneRIF Correction

General gene information

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Markers

RH143983 (e-PCR)
- UniSTS:233229

RH131315 (e-PCR)
- UniSTS:214598

AW531214 (e-PCR)
- UniSTS:245092

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	ISO Inferred from Sequence Orthology more info
enables ATP-dependent activity, acting on DNA	IBA Inferred from Biological aspect of Ancestor more info
enables ATP-dependent activity, acting on DNA	ISO Inferred from Sequence Orthology more info
enables ATP-dependent chromatin remodeler activity	ISO Inferred from Sequence Orthology more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
NOT enables DNA helicase activity	ISO Inferred from Sequence Orthology more info
enables RNA polymerase binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables protein tyrosine kinase activator activity	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA damage checkpoint signaling	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in DNA protection	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within DNA repair	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within JNK cascade	ISO Inferred from Sequence Orthology more info
involved_in base-excision repair	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair via classical nonhomologous end joining	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within intrinsic apoptotic signaling pathway in response to DNA damage	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within multicellular organism growth	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of double-strand break repair via nonhomologous end joining	ISO Inferred from Sequence Orthology more info
involved_in neurogenesis	ISO Inferred from Sequence Orthology more info
involved_in neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in neuron projection development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within photoreceptor cell maintenance	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA repair	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription, elongation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of defense response to virus by host	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of double-strand break repair via homologous recombination	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of peptidyl-serine phosphorylation of STAT protein	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase III	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription initiation by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pyrimidine dimer repair	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription elongation	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription elongation by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to UV	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to UV-B	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to X-ray	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to gamma radiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to oxidative stress	ISO Inferred from Sequence Orthology more info
involved_in response to oxidative stress	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to superoxide	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to toxic substance	ISO Inferred from Sequence Orthology more info
involved_in single strand break repair	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within transcription elongation by RNA polymerase I	ISO Inferred from Sequence Orthology more info
involved_in transcription-coupled nucleotide-excision repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in transcription-coupled nucleotide-excision repair	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within transcription-coupled nucleotide-excision repair	ISO Inferred from Sequence Orthology more info
involved_in transcription-coupled nucleotide-excision repair	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of B-WICH complex	ISO Inferred from Sequence Orthology more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in site of DNA damage	ISO Inferred from Sequence Orthology more info
part_of transcription elongation factor complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA excision repair protein ERCC-6

Names: excision repair cross-complementation group 6; excision repair cross-complementing rodent repair deficiency, complementation group 6

NP_001100766.1

EC 3.6.4.-

XP_006252796.1

EC 3.6.4.-

XP_006252797.1

EC 3.6.4.-

XP_006252798.1

EC 3.6.4.-

XP_006252799.1

EC 3.6.4.-

XP_006252800.1

EC 3.6.4.-

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_001107296.1 → NP_001100766.1 DNA excision repair protein ERCC-6

See identical proteins and their annotated locations for NP_001100766.1

Status: PROVISIONAL

Source sequence(s)

CH474046

UniProtKB/TrEMBL

A6KFV6, D3ZS47

Related

ENSRNOP00000063005.1, ENSRNOT00000064255.2

Conserved Domains (3) summary

COG0553
Location:483 → 911

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd00046
Location:474 → 587

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00079
Location:734 → 864

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

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_086034.1 Reference GRCr8

Range

7771311..7841895

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006252734.5 → XP_006252796.1 DNA excision repair protein ERCC-6 isoform X1

See identical proteins and their annotated locations for XP_006252796.1

UniProtKB/TrEMBL

A0A0G2JTU1

Related

ENSRNOP00000068845.1

Conserved Domains (3) summary

cd00046
Location:521 → 671

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00079
Location:824 → 954

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

pfam00176
Location:504 → 806

SNF2_N; SNF2 family N-terminal domain
XM_006252737.5 → XP_006252799.1 DNA excision repair protein ERCC-6 isoform X2

Conserved Domains (3) summary

COG0553
Location:505 → 948

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd00046
Location:496 → 618

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00079
Location:771 → 901

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
XM_006252736.5 → XP_006252798.1 DNA excision repair protein ERCC-6 isoform X1

See identical proteins and their annotated locations for XP_006252798.1

UniProtKB/TrEMBL

A0A0G2JTU1

Conserved Domains (3) summary

cd00046
Location:521 → 671

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00079
Location:824 → 954

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

pfam00176
Location:504 → 806

SNF2_N; SNF2 family N-terminal domain
XM_006252735.5 → XP_006252797.1 DNA excision repair protein ERCC-6 isoform X1

See identical proteins and their annotated locations for XP_006252797.1

UniProtKB/TrEMBL

A0A0G2JTU1

Conserved Domains (3) summary

cd00046
Location:521 → 671

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00079
Location:824 → 954

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

pfam00176
Location:504 → 806

SNF2_N; SNF2 family N-terminal domain
XM_006252738.4 → XP_006252800.1 DNA excision repair protein ERCC-6 isoform X3

Conserved Domains (3) summary

cd00046
Location:294 → 444

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00079
Location:597 → 727

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

pfam00176
Location:277 → 579

SNF2_N; SNF2 family N-terminal domain