Protein:XPC |
Protein Summary |
 Gene summary |
| Gene name: XPC | ASpdb.0 ID: 7508 | Gene | Gene symbol | XPC | Gene ID | 7508 |
| Gene name | XPC complex subunit, DNA damage recognition and repair factor |
| Synonyms | RAD4|XP3|XPCC|p125 |
| Cytomap | 3p25.1 |
| Type of gene | protein-coding |
| Description | DNA repair protein complementing XP-C cellsmutant xeroderma pigmentosum group Cxeroderma pigmentosum, complementation group C |
| Modification date | 20240403 |
| UniProtAcc | Q01831 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | XPC | GO:0000109 | nucleotide-excision repair complex | 11259578 |
| Gene | XPC | GO:0003684 | damaged DNA binding | 12509299 |
| Gene | XPC | GO:0003697 | single-stranded DNA binding | 12509299 |
| Gene | XPC | GO:0003713 | transcription coactivator activity | 29973595|31527837 |
| Gene | XPC | GO:0005634 | nucleus | 18682493 |
| Gene | XPC | GO:0005654 | nucleoplasm | - |
| Gene | XPC | GO:0005730 | nucleolus | - |
| Gene | XPC | GO:0005737 | cytoplasm | 18682493 |
| Gene | XPC | GO:0005739 | mitochondrion | - |
| Gene | XPC | GO:0005829 | cytosol | - |
| Gene | XPC | GO:0005886 | plasma membrane | - |
| Gene | XPC | GO:0006289 | nucleotide-excision repair | 8168482|9734359|11259578|19941824 |
| Gene | XPC | GO:0043231 | intracellular membrane-bounded organelle | - |
| Gene | XPC | GO:0044877 | protein-containing complex binding | 11259578 |
| Gene | XPC | GO:0045893 | positive regulation of DNA-templated transcription | 29973595|31527837 |
| Gene | XPC | GO:0070914 | UV-damage excision repair | 8077226 |
| Gene | XPC | GO:0071942 | XPC complex | 11279143|31527837 |
| Gene | XPC | GO:0140612 | DNA damage sensor activity | 10873465|19941824 |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| Q01831-1 | Q01831-1_2obh_D.pdb | 2OBH | X-ray | 1.8 | D | 847 | 863 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| Q01831 | XPC | Q01831-1 | Q01831-2 | 940 | 903 | 136 | 172 | Deletion | none | none | 135 | 135 |
| Q01831 | XPC | Q01831-1 | Q01831-3 | 940 | 140 | 138 | 140 | Substitution | ELS | VKR | 138 | 140 |
| Q01831 | XPC | Q01831-1 | Q01831-3 | 940 | 140 | 141 | 940 | Deletion | none | none | 140 | 140 |
| Multiple sequence alignment of our canonical and alternatively spliced XPC |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of XPC |
| UniProt-id | ENSG | ENST | ENSP |
| Q01831-1 | ENSG00000154767.15 | ENST00000285021.12 | ENSP00000285021.8 |
| Q01831-3 | ENSG00000154767.15 | ENST00000476581.6 | ENSP00000424548.1 |
| UniProt-id | NM ID | NP ID |
| Q01831-1 | NM_004628.4 | NP_004619.3 |
| Amino acid sequences of our canonical and alternatively spliced XPC |
| accession_id | Protein sequence |
| Q01831-1 | MARKRAAGGEPRGRELRSQKSKAKSKARREEEEEDAFEDEKPPKKSLLSKVSQGKRKRGCSHPGGSADGPAKKKVAKVTVKSENLKVIKD EALSDGDDLRDFPSDLKKAHHLKRGATMNEDSNEEEEESENDWEEVEELSEPVLGDVRESTAFSRSLLPVKPVEIEIETPEQAKTRERSE KIKLEFETYLRRAMKRFNKGVHEDTHKVHLLCLLANGFYRNNICSQPDLHAIGLSIIPARFTRVLPRDVDTYYLSNLVKWFIGTFTVNAE LSASEQDNLQTTLERRFAIYSARDDEELVHIFLLILRALQLLTRLVLSLQPIPLKSATAKGKKPSKERLTADPGGSSETSSQVLENHTKP KTSKGTKQEETFAKGTCRPSAKGKRNKGGRKKRSKPSSSEEDEGPGDKQEKATQRRPHGRERRVASRVSYKEESGSDEAGSGSDFELSSG EASDPSDEDSEPGPPKQRKAPAPQRTKAGSKSASRTHRGSHRKDPSLPAASSSSSSSKRGKKMCSDGEKAEKRSIAGIDQWLEVFCEQEE KWVCVDCVHGVVGQPLTCYKYATKPMTYVVGIDSDGWVRDVTQRYDPVWMTVTRKCRVDAEWWAETLRPYQSPFMDREKKEDLEFQAKHM DQPLPTAIGLYKNHPLYALKRHLLKYEAIYPETAAILGYCRGEAVYSRDCVHTLHSRDTWLKKARVVRLGEVPYKMVKGFSNRARKARLA EPQLREENDLGLFGYWQTEEYQPPVAVDGKVPRNEFGNVYLFLPSMMPIGCVQLNLPNLHRVARKLDIDCVQAITGFDFHGGYSHPVTDG YIVCEEFKDVLLTAWENEQAVIERKEKEKKEKRALGNWKLLAKGLLIRERLKRRYGPKSEAAAPHTDAGGGLSSDEEEGTSSQAEAARIL |
| Q01831-2 | MARKRAAGGEPRGRELRSQKSKAKSKARREEEEEDAFEDEKPPKKSLLSKVSQGKRKRGCSHPGGSADGPAKKKVAKVTVKSENLKVIKD EALSDGDDLRDFPSDLKKAHHLKRGATMNEDSNEEEEESENDWEEAKTRERSEKIKLEFETYLRRAMKRFNKGVHEDTHKVHLLCLLANG FYRNNICSQPDLHAIGLSIIPARFTRVLPRDVDTYYLSNLVKWFIGTFTVNAELSASEQDNLQTTLERRFAIYSARDDEELVHIFLLILR ALQLLTRLVLSLQPIPLKSATAKGKKPSKERLTADPGGSSETSSQVLENHTKPKTSKGTKQEETFAKGTCRPSAKGKRNKGGRKKRSKPS SSEEDEGPGDKQEKATQRRPHGRERRVASRVSYKEESGSDEAGSGSDFELSSGEASDPSDEDSEPGPPKQRKAPAPQRTKAGSKSASRTH RGSHRKDPSLPAASSSSSSSKRGKKMCSDGEKAEKRSIAGIDQWLEVFCEQEEKWVCVDCVHGVVGQPLTCYKYATKPMTYVVGIDSDGW VRDVTQRYDPVWMTVTRKCRVDAEWWAETLRPYQSPFMDREKKEDLEFQAKHMDQPLPTAIGLYKNHPLYALKRHLLKYEAIYPETAAIL GYCRGEAVYSRDCVHTLHSRDTWLKKARVVRLGEVPYKMVKGFSNRARKARLAEPQLREENDLGLFGYWQTEEYQPPVAVDGKVPRNEFG NVYLFLPSMMPIGCVQLNLPNLHRVARKLDIDCVQAITGFDFHGGYSHPVTDGYIVCEEFKDVLLTAWENEQAVIERKEKEKKEKRALGN WKLLAKGLLIRERLKRRYGPKSEAAAPHTDAGGGLSSDEEEGTSSQAEAARILAASWPQNREDEEKQKLKGGPKKTKREKKAAASHLFPF |
| Q01831-3 | MARKRAAGGEPRGRELRSQKSKAKSKARREEEEEDAFEDEKPPKKSLLSKVSQGKRKRGCSHPGGSADGPAKKKVAKVTVKSENLKVIKD |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| XPC (go to UniProt):Q01831 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Q01831 | Region | 111 | 136 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=136;End=172 |
| Q01831 | Region | 327 | 519 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=141;End=940 |
| Q01831 | Region | 496 | 734 | Note=Interaction with RAD23B | Type=Deletion;Start=141;End=940 |
| Q01831 | Region | 607 | 766 | Note=Minimal sensor domain involved in damage recognition | Type=Deletion;Start=141;End=940 |
| Q01831 | Region | 607 | 741 | Note=DNA-binding%3B preference for heteroduplex DNA | Type=Deletion;Start=141;End=940 |
| Q01831 | Region | 767 | 831 | Note=DNA-binding%3B preference for single stranded DNA%3B required for formation of stable nucleoprotein complex | Type=Deletion;Start=141;End=940 |
| Q01831 | Region | 816 | 940 | Note=Interaction with ERCC2 and GTF2H1;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12509233;Dbxref=PMID:12509233 | Type=Deletion;Start=141;End=940 |
| Q01831 | Region | 847 | 866 | Note=Interaction with CETN2 | Type=Deletion;Start=141;End=940 |
| Q01831 | Region | 866 | 940 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=141;End=940 |
| Q01831 | Motif | 390 | 395 | Note=Nuclear localization signal;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=141;End=940 |
| Q01831 | Compositional bias | 121 | 136 | Note=Acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=136;End=172 |
| Q01831 | Compositional bias | 342 | 359 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=141;End=940 |
| Q01831 | Compositional bias | 393 | 438 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=141;End=940 |
| Q01831 | Compositional bias | 496 | 510 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=141;End=940 |
| Q01831 | Compositional bias | 905 | 919 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=141;End=940 |
Gene Isoform Structures and Expression Levels for XPC |
| Gene structures of our canonical and alternative spliced genes of XPC * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of Q01831-1 |
| 3D view using mol* of Q01831-2 |
| 3D view using mol* of Q01831-3 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of Q01831-1 |
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| pLDDT distribution across the protein length of Q01831-2 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of Q01831-1 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| Q01831-1 | 0.985 | 188 | 1.007 | 874.65 | 0.631 | 0.672 | 0.846 | 0.32 | 1.03 | 0.31 | 0.927 | 118,119,120,121,122,123,124,126,127,129,130,131,64 1,642,643,644,647,648,649,652,653,654,655,656,657, 678,681,683,685,686,688,689,692,693,709,710,730,73 2,761,762,763,764,773,795,796,797,799,809 |
| Q01831-2 | 0.974 | 93 | 0.928 | 218.834 | 0.489 | 0.699 | 0.971 | 0.077 | 1.221 | 0.063 | 0.375 | 376,377,378,379,380,738,739,740,741,743,744,747,75 5,771,772,773,774 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of Q01831-1_Q01831-1_2obh_D.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q01831-1_2obh_D_Q01831-2.pdb |
| 3D view using mol* of Q01831-1_2obh_D_Q01831-3.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q01831-1_Q01831-2.pdb |
| 3D view using mol* of Q01831-1_Q01831-3.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/Q01831-1_vs_Q01831-2.png |
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| ./stats/secondary_structure/figure/Q01831-1_vs_Q01831-3.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/Q01831-1_vs_Q01831-2.png |
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| ./stats/relative_asa/Q01831-1_vs_Q01831-3.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Q01831 | Region | 496 | 734 | Note=Interaction with RAD23B | Type=Deletion;Start=141;End=940 |
| Q01831 | Region | 816 | 940 | Note=Interaction with ERCC2 and GTF2H1;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12509233;Dbxref=PMID:12509233 | Type=Deletion;Start=141;End=940 |
| Q01831 | Region | 847 | 866 | Note=Interaction with CETN2 | Type=Deletion;Start=141;End=940 |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to XPC |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to XPC |
| Previous studies relating to the alternative splicing of XPC and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| XPC | 12177305 | The human XPC DNA repair gene: arrangement, splice site information content and influence of a single nucleotide polymorphism in a splice acceptor site on alternative splicing and function. | XPC DNA repair gene mutations result in the cancer-prone disorder xeroderma pigmentosum. The XPC gene spans 33 kb and has 16 exons (82-882 bp) and 15 introns (0.08-5.4 kb). A 1.6 kb intron was found within exon 5. Sensitive real- time quantitative reverse transcription-polymerase chain reaction methods were developed to measure full-length XPC mRNA (the predominant form) and isoforms that skipped exons 4, 7 or 12. Exon 7 was skipped in approximately 0.07% of XPC mRNAs, consistent with the high information content of the exon 7 splice acceptor and donor sites (12.3 and 10.4 bits). In contrast, exon 4 was skipped in approximately 0.7% of the XPC mRNAs, consistent with the low information content of the exon 4 splice acceptor (-0.1 bits). A new common C/A single nucleotide polymorphism in the XPC intron 11 splice acceptor site (58% C in 97 normals) decreased its information content from 7.5 to 5.1 bits. Fibroblasts homozygous for A/A had significantly higher levels (approximately 2.6-fold) of the XPC mRNA isoform that skipped exon 12 than those homozygous for C/C. This abnormally spliced XPC mRNA isoform has diminished DNA repair function and may contribute to cancer susceptibility. | D009369 | Neoplasms |
Clinically important variants in XPC |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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