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ERCC6 ERCC excision repair 6, chromatin remodeling factor [ Homo sapiens (human) ]

Gene ID: 2074, updated on 7-Oct-2018

Summary

Official Symbol
ERCC6provided by HGNC
Official Full Name
ERCC excision repair 6, chromatin remodeling factorprovided by HGNC
Primary source
HGNC:HGNC:3438
See related
Ensembl:ENSG00000225830 MIM:609413; Vega:OTTHUMG00000018195
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CSB; CKN2; COFS; ARMD5; COFS1; POF11; RAD26; UVSS1; CSB-PGBD3
Summary
This gene encodes a DNA-binding protein that is important in transcription-coupled excision repair. The encoded protein has ATP-stimulated ATPase activity, interacts with several transcription and excision repair proteins, and may promote complex formation at DNA repair sites. Mutations in this gene are associated with Cockayne syndrome type B and cerebrooculofacioskeletal syndrome 1. Alternative splicing occurs between a splice site from exon 5 of this gene to the 3' splice site upstream of the open reading frame (ORF) of the adjacent gene, piggyback-derived-3 (GeneID:267004), which activates the alternative polyadenylation site downstream of the piggyback-derived-3 ORF. The resulting transcripts encode a fusion protein that shares sequence with the product of each individual gene. [provided by RefSeq, Mar 2016]
Expression
Ubiquitous expression in thyroid (RPKM 2.7), skin (RPKM 2.1) and 25 other tissues See more
Orthologs

Genomic context

See ERCC6 in Genome Data Viewer
Location:
10q11.23
Exon count:
23
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 10 NC_000010.11 (49454480..49539538, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (50662526..50747169, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene dorsal root ganglia homeobox Neighboring gene heat shock protein family D (Hsp60) member 1 pseudogene 17 Neighboring gene piggyBac transposable element derived 3 Neighboring gene high mobility group box 1 pseudogene 50 Neighboring gene solute carrier family 18 member A3 Neighboring gene choline O-acetyltransferase

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • B-WICH complex positively regulates rRNA expression, organism-specific biosystem (from REACTOME)
    B-WICH complex positively regulates rRNA expression, organism-specific biosystemThe B-WICH complex is a large 3 Mdalton complex containing SMARCA5 (SNF2H), BAZ1B (WSTF), ERCC6 (CSB), MYO1C (Nuclear myosin 1c) (Cavellan et al. 2006, Percipalle et al. 2006, Vintermist et al. 2001,...
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • Dual incision in TC-NER, organism-specific biosystem (from REACTOME)
    Dual incision in TC-NER, organism-specific biosystemIn transcription-coupled nucleotide excision repair (TC-NER), similar to global genome nucleotide excision repair (GG-NER), the oligonucleotide that contains the lesion is excised from the open bubbl...
  • ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression, organism-specific biosystem (from REACTOME)
    ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression, organism-specific biosystemAbout half of the rRNA genes in the genome are actively expressed, being transcribed by RNA polymerase I (reviewed in Nemeth and Langst 2008, Bartova et al. 2010, Goodfellow and Zomerdijk 2012, Grumm...
  • Epigenetic regulation of gene expression, organism-specific biosystem (from REACTOME)
    Epigenetic regulation of gene expression, organism-specific biosystemEpigenetic processes regulate gene expression by modulating the frequency, rate, or extent of gene expression in a mitotically or meiotically heritable way that does not entail a change in the DNA se...
  • Formation of TC-NER Pre-Incision Complex, organism-specific biosystem (from REACTOME)
    Formation of TC-NER Pre-Incision Complex, organism-specific biosystemFormation of TC-NER pre-incision complex is initiated when the RNA polymerase II (RNA Pol II) complex stalls at a DNA damage site. The stalling is caused by misincorporation of a ribonucleotide oppos...
  • Gap-filling DNA repair synthesis and ligation in TC-NER, organism-specific biosystem (from REACTOME)
    Gap-filling DNA repair synthesis and ligation in TC-NER, organism-specific biosystemIn transcription-coupled nucleotide excision repair (TC-NER), similar to global genome nucleotide excision repair (GG-NER), DNA polymerases delta or epsilon, or the Y family DNA polymerase kappa, fil...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Nucleotide Excision Repair, organism-specific biosystem (from REACTOME)
    Nucleotide Excision Repair, organism-specific biosystemNucleotide excision repair (NER) was first described in the model organism E. coli in the early 1960s as a process whereby bulky base damage is enzymatically removed from DNA, facilitating the recove...
  • Nucleotide excision repair, organism-specific biosystem (from KEGG)
    Nucleotide excision repair, organism-specific biosystemNucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the ...
  • Nucleotide excision repair, conserved biosystem (from KEGG)
    Nucleotide excision repair, conserved biosystemNucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the ...
  • Positive epigenetic regulation of rRNA expression, organism-specific biosystem (from REACTOME)
    Positive epigenetic regulation of rRNA expression, organism-specific biosystemTranscription of rRNA genes is controlled by epigenetic activation and repression (reviewed in Percipalle and Farrants 2006, McStay and Grummt 2008, Goodfellow and Zomerdijk 2012, Grummt and Langst 2...
  • RNA Polymerase I Promoter Clearance, organism-specific biosystem (from REACTOME)
    RNA Polymerase I Promoter Clearance, organism-specific biosystemPromoter clearance is one of the rate-limiting steps in Polymerase I transcription. This step is composed of three phases, promoter opening, transcription initiation and promoter escape.
  • RNA Polymerase I Transcription, organism-specific biosystem (from REACTOME)
    RNA Polymerase I Transcription, organism-specific biosystemThe rRNA genes are transcribed by RNA polymerase I, one of three eukaryotic nuclear RNA polymerases. The polymerase is a multisubunit complex, composed of two large subunits (the most conserved porti...
  • RNA Polymerase I Transcription Initiation, organism-specific biosystem (from REACTOME)
    RNA Polymerase I Transcription Initiation, organism-specific biosystemDuring initiation the double-stranded DNA must be melted and transcription begins. SL1 forms and interacts with UBF-1 and the rDNA promoter. It is this platform that will recruit active RNA polymeras...
  • RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription, organism-specific biosystem (from REACTOME)
    RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription, organism-specific biosystemTranscription by RNA Polymerase I, RNA Polymerase III and transcription from mitochondrial promoters.
  • Transcription-Coupled Nucleotide Excision Repair (TC-NER), organism-specific biosystem (from REACTOME)
    Transcription-Coupled Nucleotide Excision Repair (TC-NER), organism-specific biosystemDNA damage in transcribed strands of active genes is repaired through a specialized nucleotide excision repair (NER) pathway known as transcription-coupled nucleotide excision repair (TC-NER). TC-NER...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ77465, MGC26346

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
NOT DNA helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-dependent ATPase activity IDA
Inferred from Direct Assay
more info
PubMed 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
protein C-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein N-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein tyrosine kinase activator activity IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
DNA duplex unwinding IEA
Inferred from Electronic Annotation
more info
 
activation of JNKK activity IEA
Inferred from Electronic Annotation
more info
 
activation of JUN kinase activity IEA
Inferred from Electronic Annotation
more info
 
base-excision repair IMP
Inferred from Mutant Phenotype
more info
PubMed 
intrinsic apoptotic signaling pathway in response to DNA damage IEA
Inferred from Electronic Annotation
more info
 
multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
photoreceptor cell maintenance IEA
Inferred from Electronic Annotation
more info
 
positive regulation of DNA-templated transcription, elongation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of gene expression, epigenetic TAS
Traceable Author Statement
more info
 
positive regulation of protein tyrosine kinase activity IEA
Inferred from Electronic Annotation
more info
 
pyrimidine dimer repair IEA
Inferred from Electronic Annotation
more info
 
regulation of DNA-templated transcription, elongation IDA
Inferred from Direct Assay
more info
PubMed 
response to UV IDA
Inferred from Direct Assay
more info
PubMed 
response to UV-B IEA
Inferred from Electronic Annotation
more info
 
response to X-ray IEA
Inferred from Electronic Annotation
more info
 
response to gamma radiation IEA
Inferred from Electronic Annotation
more info
 
response to oxidative stress IDA
Inferred from Direct Assay
more info
PubMed 
response to oxidative stress IGI
Inferred from Genetic Interaction
more info
PubMed 
response to superoxide IEA
Inferred from Electronic Annotation
more info
 
response to toxic substance IEA
Inferred from Electronic Annotation
more info
 
transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
PubMed 
transcription elongation from RNA polymerase I promoter IEA
Inferred from Electronic Annotation
more info
 
transcription-coupled nucleotide-excision repair IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription-coupled nucleotide-excision repair TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IEA
Inferred from Electronic Annotation
more info
 
transcription elongation factor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
DNA excision repair protein ERCC-6; ERCC6-PGBD3 fusion protein
Names
ATP-dependent helicase ERCC6
Chimeric CSB-PGBD3 protein
Chimeric ERCC6-PGBD3 protein
Cockayne syndrome group B protein
cockayne syndrome protein CSB
excision repair cross-complementation group 6
excision repair cross-complementing rodent repair deficiency, complementation group 6
NP_000115.1
NP_001263987.1
NP_001263988.1
NP_001333369.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_009442.1 RefSeqGene

    Range
    4979..89622
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_465

mRNA and Protein(s)

  1. NM_000124.3NP_000115.1  DNA excision repair protein ERCC-6 isoform 2

    See identical proteins and their annotated locations for NP_000115.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longer protein (isoform 2).
    Source sequence(s)
    AB209504, AC073366, AL138760, DA457690, L04791
    Consensus CDS
    CCDS7229.1
    UniProtKB/Swiss-Prot
    Q03468
    UniProtKB/TrEMBL
    Q59FF6
    Related
    ENSP00000348089.5, OTTHUMP00000019581, ENST00000355832.9, OTTHUMT00000047990
    Conserved Domains (3) summary
    cd00046
    Location:527677
    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:830960
    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:510812
    SNF2_N; SNF2 family N-terminal domain
  2. NM_001277058.1NP_001263987.1  ERCC6-PGBD3 fusion protein isoform 1

    See identical proteins and their annotated locations for NP_001263987.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) contains an alternate 3' terminal exon, compared to variant 3. It is generated as a result of splicing of ERCC6 exon 5 to the 3' splice site upstream of the PGBD3 ORF that activates the alternative polyadenylation site downstream of the PGBD3 ORF. The resulting protein (isoform 1, ERCC6-PGBD3 fusion protein) is shorter and has a distinct C-terminus, compared to isoform 2.
    Source sequence(s)
    AC073366, AK291018, AL138760
    Consensus CDS
    CCDS60529.1
    UniProtKB/Swiss-Prot
    P0DP91
    UniProtKB/TrEMBL
    A8K4Q3
    Related
    ENSP00000387966.2, OTTHUMP00000245834, ENST00000447839.6, OTTHUMT00000413018
    Conserved Domains (1) summary
    pfam13843
    Location:609967
    DDE_Tnp_1_7; Transposase IS4
  3. NM_001277059.1NP_001263988.1  ERCC6-PGBD3 fusion protein isoform 1

    See identical proteins and their annotated locations for NP_001263988.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and contains an alternate 3' terminal exon, compared to variant 3. It is generated as a result of splicing of ERCC6 exon 5 to the 3' splice site upstream of the PGBD3 ORF that activates the alternative polyadenylation site downstream of the PGBD3 ORF. The resulting protein (isoform 1, ERCC6-PGBD3 fusion protein) is shorter and has a distinct C-terminus, compared to isoform 2.
    Source sequence(s)
    AK291018, AL138760, BC034479
    Consensus CDS
    CCDS60529.1
    UniProtKB/Swiss-Prot
    P0DP91
    UniProtKB/TrEMBL
    A8K4Q3
    Related
    ENSP00000423550.1, OTTHUMP00000245835, ENST00000515869.1, OTTHUMT00000413019
    Conserved Domains (1) summary
    pfam13843
    Location:609967
    DDE_Tnp_1_7; Transposase IS4
  4. NM_001346440.1NP_001333369.1  DNA excision repair protein ERCC-6 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4 ) uses an alternate splice site in the 5' UTR, compared to variant 3, and encodes isoform 2. Variants 3 and 4 encode the same protein (isoform 2).
    Source sequence(s)
    AC073366, AL138760, DA457690, L04791
    Consensus CDS
    CCDS7229.1
    UniProtKB/Swiss-Prot
    Q03468

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p12 Primary Assembly

    Range
    49454480..49539538 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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