Human Gene APLF (uc002ser.1)
  Description: Homo sapiens aprataxin and PNKP like factor (APLF), mRNA.
RefSeq Summary (NM_173545): C2ORF13 is a component of the cellular response to chromosomal DNA single- and double-strand breaks (Iles et al., 2007 [PubMed 17353262]).[supplied by OMIM, Mar 2008].
Transcript (Including UTRs)
   Position: hg19 chr2:68,760,751-68,805,313 Size: 44,563 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr2:68,765,007-68,805,267 Size: 40,261 Coding Exon Count: 5 

Page IndexSequence and LinksPrimersCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:68,760,751-68,805,313)mRNA (may differ from genome)Protein (237 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMGIOMIMPubMedBioGrid CRISPR DB

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 2.43 RPKM in Testis
Total median expression: 33.51 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 -112.30365-0.308 Picture PostScript Text
3' UTR -6.1046-0.133 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.

-  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 orthologGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGD FlyBase  
 Protein Sequence Protein Sequence  
 Alignment Alignment  

-  Descriptions from all associated GenBank mRNAs
  JF432390 - Synthetic construct Homo sapiens clone IMAGE:100073592 aprataxin and PNKP like factor (C2orf13) gene, encodes complete protein.
KJ895795 - Synthetic construct Homo sapiens clone ccsbBroadEn_05189 APLF gene, encodes complete protein.
BC030711 - Homo sapiens chromosome 2 open reading frame 13, mRNA (cDNA clone IMAGE:4822182).
AK122915 - Homo sapiens cDNA FLJ16593 fis, clone TESTI4004722, highly similar to Mus musculus G protein-coupled receptor 73 (Gpr73).
AK290841 - Homo sapiens cDNA FLJ77093 complete cds.
AK308186 - Homo sapiens cDNA, FLJ98134.
BC041144 - Homo sapiens aprataxin and PNKP like factor, mRNA (cDNA clone MGC:47799 IMAGE:6042653), complete cds.

-  Other Names for This Gene
  Alternate Gene Symbols: AK122915, NM_173545, NP_775816
UCSC ID: uc002ser.1
RefSeq Accession: NM_173545

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK122915.1
exon count: 6CDS single in 3' UTR: no RNA size: 3310
ORF size: 714CDS single in intron: no Alignment % ID: 99.91
txCdsPredict score: 1398.00frame shift in genome: no % Coverage: 33.96
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.