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Entry: Rad10 (PF03834)

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Pfam summary

Description

DNA repair protein rad10

Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain. Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA interstrand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex [3].
 
Literature1. Xu H, Swoboda I, Bhalla PL, Sijbers AM, Zhao C, Ong EK, Hoeijmakers JH, Singh MB; Plant J. 1998;13:823-829.Plant homologue of human excision repair gene ERCC1 points to conservation of DNA repair mechanisms. PUBMED:9681020
2. Park Y, Gerson SL; Annu Rev Med. 2005;56:495-508.DNA repair defects in stem cell function and aging. PUBMED:15660524
3. Tripsianes K, Folkers GE, Zheng C, Das D, Grinstead JS, Kaptein R, Boelens R; Nucleic Acids Res. 2007;35:5789-5798.Analysis of the XPA and ssDNA-binding surfaces on the central domain of human ERCC1 reveals evidence for subfunctionalization. PUBMED:17720715
 
 
InterPro entry IPR004579
 

Alignment

New Hampshire tree

The seed alignment for this family in the PANDIT database contains 7 aligned sequences:

  ERCC1_ARATH/124-191   ERCC1_HUMAN/99-166   O96136_PLAF7/46-113   Q93456_CAEEL/49-118   Q9Y0X3_DROME/61-129   RAD10_YEAST/91-163   SWI10_SCHPO/41-108  

The full alignment for this family in the Pfam database contains 142 aligned sequences

Species in the seed alignment

List of species covered in the seed alignment. The number in brackets denotes the number of sequences taken from each organism.

  Schizosaccharomyces pombe (1);   Drosophila melanogaster (1);   Plasmodium falciparum 3D7 (1);   Arabidopsis thaliana (1);   Saccharomyces cerevisiae (1);   Caenorhabditis elegans (1);   Homo sapiens (1);  

The full alignment covers 91 species.

Pre-computed estimates from Markov codon substitution models (explanation)

Following are maximum-likelihood estimates and log-likelihood scores from codon models M0, M1, M2, M7 and M8, implemented in PAML v.4.1

Model name  

Model M0

Model M1

Model M2

Model M7

Model M8

Log-likelihood score  

-1532.78-1522.043737-1522.043737-1511.583946-1510.916189

Tree Length  

250.78250.77746250.77746250.77746250.77746

κ  

1.601.7111041.7111191.7229891.616768

ω-ratio  

ω=0.00599p0=0.861294 ~ ω0=0.006825
p1=0.138706 ~ ω1=1
p0=0.861292 ~ ω0=0.006825
p1=0.138708 ~ ω1=1
p2=0 ~ ω2=17.745641
ω~Β(0.949849,99)p0=0.999587 ~ ω~Β(1.223628,99)
p1=0.000413 ~ ω=395.252977

P-value for testing  
positive selection  

M1 vs M2: P-value=1
family classification: conserved
M7 vs M8: P-value=0.512858
family classification: conserved

Maximum-likelihood estimates and log-likelihood scores from codon models Nonsynonymous and Dual implemented in HYPHY

Model name  

Model Nonsynonymous

Model Dual

Log-likelihood score  

-1570.13804-1569.95972

Mean ω-ratio  

ω = 0.3024ω = 0.07372

Coeff. of variation  
of ω-ratio  

CVω = 2.46174CVω = 2.74325
 

Annotations

InteractionsThis family has 0 known interactions:

StructuresThis family has 3 structures:
Notation: PDB_ID (PDB chain, PDB residues)

Gene Ontologies
Cellular component
 nucleus[GO:0005634]
Biological Process
 DNA repair[GO:0006281]
Molecular Function
 damaged DNA binding[GO:0003684]
 endonuclease activity[GO:0004519]

KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Carbohydrate Metabolism
Galactose metabolism [KEGG]
Lipid Metabolism
Glycerolipid metabolism [KEGG]
Glycan Biosynthesis and Metabolism
Other glycan degradation [KEGG]
Glycosphingolipid biosynthesis - lacto and neolacto series [KEGG]
Metabolism of Cofactors and Vitamins
Pantothenate and CoA biosynthesis [KEGG]
Genetic Information Processing
Replication and Repair
Nucleotide excision repair [KEGG]
 

Expression data (explanation)

 
Bgee expression data - for genes coding for sequences from seed alignment     Click here for overview of Bgee data

The numbers in brackets correspond to the number of genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Homo sapiens

HumanProteinpedia expression data - for human genes coding for sequences from full alignment     Click here for overview of Human Proteinpedia data

The numbers in brackets correspond to the number of human genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Healthy tissues
Disease tissues

Human disease association

 
Genetic Association Database - data for human genes coding for sequences from full alignment

The numbers in brackets correspond to the number of genes that are associated with the selected family and are associated with the corresponding disease. Click on the disease name to see all the families possibly associated with that disease and click on the genes to see the corresponding genes.

Associated diseases and disorders

Links to OMIM - for human genes coding for sequences from full alignment
 
126380 (1)