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Aliases for C9orf142 Gene

Aliases for C9orf142 Gene

  • Chromosome 9 Open Reading Frame 142 2 3 5
  • Paralog Of XRCC4 And XLF 2 3 4
  • XRCC4-Like Small Protein 2 3 4
  • PAXX 3 4
  • XLS 3 4
  • Protein PAXX 3

External Ids for C9orf142 Gene

Previous GeneCards Identifiers for C9orf142 Gene

  • GC09P137163
  • GC09P139006
  • GC09P139886
  • GC09P109345

Summaries for C9orf142 Gene

Entrez Gene Summary for C9orf142 Gene

  • The protein encoded by this gene plays a role in the nonhomologous end joining (NHEJ) pathway of DNA double-strand break repair. The encoded protein may function to stabilize the Ku70/Ku80 heterodimer to facilitate the assembly and maintain the stability of the NHEJ complex. [provided by RefSeq, Jul 2016]

GeneCards Summary for C9orf142 Gene

C9orf142 (Chromosome 9 Open Reading Frame 142) is a Protein Coding gene. GO annotations related to this gene include protein homodimerization activity.

UniProtKB/Swiss-Prot for C9orf142 Gene

  • Involved in non-homologous end joining (NHEJ), a major pathway to repair double-strand breaks in DNA. May act as a scaffold required to stabilize the Ku heterodimer, composed of XRCC5/Ku80 and XRCC6/Ku70, at double-strand break sites and promote the assembly and/or stability of the NHEJ machinery.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for C9orf142 Gene

Genomics for C9orf142 Gene

Regulatory Elements for C9orf142 Gene

Enhancers for C9orf142 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09F136898 0.4 ENCODE 7.4 -93.3 -93302 1.8 CTCF MLLT1 NR3C1 ZNF600 TMEM141 C9orf142 LCNL1 MIR4479 PIR43412
GH09F136900 1 Ensembl ENCODE 6.6 -90.2 -90244 4.0 HDGF ELF3 TBP PKNOX1 RAD21 ZBTB40 KAT2B YY1 EGR1 ZNF207 TRAF2 TMEM141 PHPT1 ANAPC2 ENSG00000238268 LCN12 C9orf142 SAPCD2 MIR4479 PIR43412
GH09F136699 1.4 FANTOM5 Ensembl ENCODE 2.8 -291.6 -291617 2.4 BCOR PKNOX1 ATF1 MXI1 TBL1XR1 MAX RBBP5 RELA ZNF121 POLR2A ANAPC2 CCDC183 RABL6 ABCA2 C9orf142 LCNL1 SEC16A FUT7 AGPAT2 FAM69B
GH09F136990 1.3 FANTOM5 Ensembl ENCODE 2.3 +4.0 3977 11.6 HDGF PKNOX1 ARNT CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 CBX5 ENSG00000238268 LCN12 ABCA2 ANAPC2 PRR31 C9orf139 SNHG7 LCNL1 RABL6 CCDC183
GH09F137173 1 FANTOM5 ENCODE 1.9 +181.2 181240 0.9 ZNF687 ESRRA DPF2 CTBP1 GATA3 POLR2A EZH2 EGR2 TPRN LCNL1 ABCA2 C9orf142 CLIC3 FUT7 GC09M137178 PIR32559 TMEM210
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around C9orf142 on UCSC Golden Path with GeneCards custom track

Promoters for C9orf142 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001475912 -118 1401 HDGF PKNOX1 ARNT CREB3L1 ZFP64 SIN3A DMAP1 ZNF2 FOS KLF13

Genomic Location for C9orf142 Gene

Chromosome:
9
Start:
136,992,418 bp from pter
End:
136,993,984 bp from pter
Size:
1,567 bases
Orientation:
Plus strand

Genomic View for C9orf142 Gene

Genes around C9orf142 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
C9orf142 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for C9orf142 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for C9orf142 Gene

Proteins for C9orf142 Gene

  • Protein details for C9orf142 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BUH6-PAXX_HUMAN
    Recommended name:
    Protein PAXX
    Protein Accession:
    Q9BUH6
    Secondary Accessions:
    • Q8IY19

    Protein attributes for C9orf142 Gene

    Size:
    204 amino acids
    Molecular mass:
    21640 Da
    Quaternary structure:
    • Homodimer. Interacts with the DNA-bound XRCC5/Ku80 and XRCC6/Ku70 heterodimer (Ku complex); the interaction is direct. Associates with the non-homologous end joining (NHEJ) complex which is at least composed of the core proteins XRCC5/Ku80, XRCC6/Ku70, PRKDC/DNA-PKcs, LIG4 and XRCC4. Additional components of the NHEJ complex include NHEJ1/XLF and C9orf142/PAXX.

    Three dimensional structures from OCA and Proteopedia for C9orf142 Gene

    Alternative splice isoforms for C9orf142 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for C9orf142 Gene

Post-translational modifications for C9orf142 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for C9orf142 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for C9orf142 Gene

Domains & Families for C9orf142 Gene

Protein Domains for C9orf142 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q9BUH6

UniProtKB/Swiss-Prot:

PAXX_HUMAN :
  • The N-terminus (residues 1-113) forms a head domain that is structurally related to those of XRCC4, XLF/NHEJ1, and SASS6.
Domain:
  • The N-terminus (residues 1-113) forms a head domain that is structurally related to those of XRCC4, XLF/NHEJ1, and SASS6.
  • Contains 1 PISA domain.
genes like me logo Genes that share domains with C9orf142: view

No data available for Gene Families and Suggested Antigen Peptide Sequences for C9orf142 Gene

Function for C9orf142 Gene

Molecular function for C9orf142 Gene

UniProtKB/Swiss-Prot Function:
Involved in non-homologous end joining (NHEJ), a major pathway to repair double-strand breaks in DNA. May act as a scaffold required to stabilize the Ku heterodimer, composed of XRCC5/Ku80 and XRCC6/Ku70, at double-strand break sites and promote the assembly and/or stability of the NHEJ machinery.

Gene Ontology (GO) - Molecular Function for C9orf142 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25574025
GO:0032947 protein complex scaffold IDA 25670504
GO:0042803 protein homodimerization activity IDA 25574025
genes like me logo Genes that share ontologies with C9orf142: view
genes like me logo Genes that share phenotypes with C9orf142: view

Animal Model Products

miRNA for C9orf142 Gene

miRTarBase miRNAs that target C9orf142

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for C9orf142 Gene

Localization for C9orf142 Gene

Subcellular locations from UniProtKB/Swiss-Prot for C9orf142 Gene

Nucleus. Note=Predominantly localizes to the nucleus. Accumulates at sites of DNA damage generated by laser microirradiation. {ECO:0000269 PubMed:25574025, ECO:0000269 PubMed:25670504}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for C9orf142 Gene COMPARTMENTS Subcellular localization image for C9orf142 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for C9orf142 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 25574025
GO:0035861 site of double-strand break IDA 25670504
GO:0043564 colocalizes_with Ku70:Ku80 complex IDA 25670504
GO:0070062 extracellular exosome IDA 23376485
GO:0070419 nonhomologous end joining complex IDA 25670504
genes like me logo Genes that share ontologies with C9orf142: view

Pathways & Interactions for C9orf142 Gene

SuperPathways for C9orf142 Gene

No Data Available

Interacting Proteins for C9orf142 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000360682%0d%0a9606.ENSP00000344818%0d%0a
Selected Interacting proteins: Q9BUH6-PAXX_HUMAN ENSP00000360682 for C9orf142 Gene via IID STRING

Gene Ontology (GO) - Biological Process for C9orf142 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006281 DNA repair IEA --
GO:0006303 double-strand break repair via nonhomologous end joining IMP 25574025
GO:0006974 cellular response to DNA damage stimulus IEA,IDA 25574025
GO:0051103 DNA ligation involved in DNA repair IMP 25574025
genes like me logo Genes that share ontologies with C9orf142: view

No data available for Pathways by source and SIGNOR curated interactions for C9orf142 Gene

Transcripts for C9orf142 Gene

Unigene Clusters for C9orf142 Gene

Chromosome 9 open reading frame 142:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for C9orf142 Gene

No ASD Table

Relevant External Links for C9orf142 Gene

GeneLoc Exon Structure for
C9orf142
ECgene alternative splicing isoforms for
C9orf142

Expression for C9orf142 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for C9orf142 Gene

Protein differential expression in normal tissues from HIPED for C9orf142 Gene

This gene is overexpressed in Tlymphocyte (21.6), Peripheral blood mononuclear cells (13.1), and CD8 Tcells (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for C9orf142 Gene



Protein tissue co-expression partners for C9orf142 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of C9orf142 Gene:

C9orf142

SOURCE GeneReport for Unigene cluster for C9orf142 Gene:

Hs.409582
genes like me logo Genes that share expression patterns with C9orf142: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for C9orf142 Gene

Orthologs for C9orf142 Gene

This gene was present in the common ancestor of chordates.

Orthologs for C9orf142 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia C9H9orf142 34
  • 99.39 (n)
C9ORF142 35
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia C9H9orf142 34
  • 85.67 (n)
C9orf142 35
  • 79 (a)
OneToOne
cow
(Bos Taurus)
Mammalia C11H9ORF142 35
  • 84 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia RGD1306215 34
  • 82.72 (n)
mouse
(Mus musculus)
Mammalia BC029214 34 16 35
  • 79.33 (n)
oppossum
(Monodelphis domestica)
Mammalia C9orf142 35
  • 53 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia C9orf142 35
  • 50 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia C9orf142 35
  • 34 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii C5H9orf142 35
  • 30 (a)
OneToOne
Species where no ortholog for C9orf142 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for C9orf142 Gene

ENSEMBL:
Gene Tree for C9orf142 (if available)
TreeFam:
Gene Tree for C9orf142 (if available)

Paralogs for C9orf142 Gene

No data available for Paralogs for C9orf142 Gene

Variants for C9orf142 Gene

Sequence variations from dbSNP and Humsavar for C9orf142 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs10781530 -- 136,991,496(+) AGGCA(A/C)GTAGG upstream-variant-2KB
rs10870156 -- 136,991,087(+) AAAGG(A/G)TGTGC upstream-variant-2KB
rs10870157 -- 136,991,310(+) GCCTC(C/T)GCCTG upstream-variant-2KB
rs10870158 -- 136,991,368(+) TAGCA(A/C)CCGCT upstream-variant-2KB
rs10870159 -- 136,992,590(+) GTAGG(C/G)GTGCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for C9orf142 Gene

Variant ID Type Subtype PubMed ID
dgv13007n54 CNV loss 21841781
esv2422220 CNV deletion 17116639
nsv469918 CNV loss 18288195
nsv524322 CNV loss 19592680
nsv615991 CNV loss 21841781
nsv818738 CNV gain 17921354
nsv951206 CNV deletion 24416366

Variation tolerance for C9orf142 Gene

Residual Variation Intolerance Score: 40.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.35; 41.75% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for C9orf142 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
C9orf142

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for C9orf142 Gene

Disorders for C9orf142 Gene

Relevant External Links for C9orf142

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
C9orf142

No disorders were found for C9orf142 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for C9orf142 Gene

Publications for C9orf142 Gene

  1. DNA repair. PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair. (PMID: 25574025) Ochi T. … Jackson S.P. (Science 2015) 2 3 4 64
  2. XLS (c9orf142) is a new component of mammalian DNA double-stranded break repair. (PMID: 25941166) Craxton A. … Malewicz M. (Cell Death Differ. 2015) 2 3 4 64
  3. Interactome analysis identifies a new paralogue of XRCC4 in non- homologous end joining DNA repair pathway. (PMID: 25670504) Xing M. … Xu D. (Nat. Commun. 2015) 3 4 64
  4. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. (PMID: 25609649) Li X. … Chen J. (Mol. Syst. Biol. 2015) 3 64
  5. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein M.Y. … Mann M. (Cell 2015) 3 64

Products for C9orf142 Gene

Sources for C9orf142 Gene

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