Human Gene PAXX (uc004cki.3)
  Description: Homo sapiens chromosome 9 open reading frame 142 (PAXX), mRNA.
RefSeq Summary (NM_183241): 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].
Transcript (Including UTRs)
   Position: hg19 chr9:139,886,870-139,888,428 Size: 1,559 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr9:139,886,896-139,888,257 Size: 1,362 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:139,886,870-139,888,428)mRNA (may differ from genome)Protein (204 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHPRDLynxMalacardsMGIneXtProt
OMIMPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CI142_HUMAN
DESCRIPTION: RecName: Full=Uncharacterized protein C9orf142;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PAXX
Diseases sorted by gene-association score: achromatopsia (1)

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 61.31 RPKM in Spleen
Total median expression: 1264.40 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -15.5026-0.596 Picture PostScript Text
3' UTR -55.71171-0.326 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF15384 - PAXX, PAralog of XRCC4 and XLF, also called C9orf142

ModBase Predicted Comparative 3D Structure on Q9BUH6
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0032947 protein complex scaffold
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity

Biological Process:
GO:0006281 DNA repair
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0006974 cellular response to DNA damage stimulus
GO:0051103 DNA ligation involved in DNA repair

Cellular Component:
GO:0005634 nucleus
GO:0035861 site of double-strand break
GO:0070419 nonhomologous end joining complex
GO:0043564 Ku70:Ku80 complex


-  Descriptions from all associated GenBank mRNAs
  BC002613 - Homo sapiens chromosome 9 open reading frame 142, mRNA (cDNA clone MGC:2999 IMAGE:3161564), complete cds.
JD554929 - Sequence 535953 from Patent EP1572962.
CU678068 - Synthetic construct Homo sapiens gateway clone IMAGE:100022342 5' read C9orf142 mRNA.
HQ447605 - Synthetic construct Homo sapiens clone IMAGE:100070950; CCSB013390_01 chromosome 9 open reading frame 142 (C9orf142) gene, encodes complete protein.
KJ896019 - Synthetic construct Homo sapiens clone ccsbBroadEn_05413 C9orf142 gene, encodes complete protein.
BC038191 - Homo sapiens chromosome 9 open reading frame 142, mRNA (cDNA clone IMAGE:3873974), partial cds.
JD446646 - Sequence 427670 from Patent EP1572962.
JD475393 - Sequence 456417 from Patent EP1572962.
JD318731 - Sequence 299755 from Patent EP1572962.
JD082272 - Sequence 63296 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: C9orf142, CI142_HUMAN, NM_183241, NP_899064, Q8IY19, Q9BUH6
UCSC ID: uc004cki.3
RefSeq Accession: NM_183241
Protein: Q9BUH6 (aka CI142_HUMAN)
CCDS: CCDS7020.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_183241.1
exon count: 7CDS single in 3' UTR: no RNA size: 851
ORF size: 615CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1430.00frame shift in genome: no % Coverage: 95.42
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.