Human Gene TCAF2 (uc011ktm.2)
  Description: Homo sapiens family with sequence similarity 115, member C (TCAF2), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr7:143,318,542-143,422,176 Size: 103,635 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr7:143,320,869-143,421,823 Size: 100,955 Coding Exon Count: 6 

Page IndexSequence and LinksPrimersGene AllelesRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:143,318,542-143,422,176)mRNA (may differ from genome)Protein (845 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkH-INV
LynxMGIOMIMPubMedTreefamUniProtKB
BioGrid 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


+  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: 3.94 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 41.46 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -21.1069-0.306 Picture PostScript Text
3' UTR -86.02353-0.244 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:
PF13402 - Peptidase M60, enhancin and enhancin-like
PF17291 - N-terminal domain of M60-like peptidases

ModBase Predicted Comparative 3D Structure on A6NFQ2-2
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK098041 - Homo sapiens cDNA FLJ40722 fis, clone THYMU2028629.
AL832734 - Homo sapiens mRNA; cDNA DKFZp686F2013 (from clone DKFZp686F2013).
BC113530 - Homo sapiens family with sequence similarity 115, member C, mRNA (cDNA clone MGC:142090 IMAGE:8322582), complete cds.
BC117233 - Homo sapiens family with sequence similarity 115, member C, mRNA (cDNA clone MGC:150842 IMAGE:40125784), complete cds.
AY167570 - Homo sapiens unknown mRNA.
AK315909 - Homo sapiens cDNA, FLJ78808 complete cds, highly similar to Mus musculus experimental autoimmune prostatitis antigen 2 (Eapa2), mRNA.
AK297123 - Homo sapiens cDNA FLJ58905 complete cds, moderately similar to Mus musculus experimental autoimmune prostatitis antigen 2 (Eapa2), mRNA.
BC033189 - Homo sapiens cDNA clone IMAGE:4622649, partial cds.
BC010225 - Homo sapiens hypothetical LOC154761, mRNA (cDNA clone IMAGE:4150153), with apparent retained intron.
HQ258592 - Synthetic construct Homo sapiens clone IMAGE:100073128 family with sequence similarity 115, member C (FAM115C), transcript variant 1 (FAM115C) gene, encodes complete protein.
HQ258634 - Synthetic construct Homo sapiens clone IMAGE:100073190 family with sequence similarity 115, member C (FAM115C), transcript variant 1 (FAM115C) gene, encodes complete protein.
EU832016 - Synthetic construct Homo sapiens clone HAIB:100067045; DKFZo004B1024 family with sequence similarity 139, member A protein (FAM139A) gene, encodes complete protein.
EU831922 - Synthetic construct Homo sapiens clone HAIB:100066951; DKFZo008B1023 family with sequence similarity 139, member A protein (FAM139A) gene, encodes complete protein.
KJ906482 - Synthetic construct Homo sapiens clone ccsbBroadEn_16152 FAM115C gene, encodes complete protein.
AK296318 - Homo sapiens cDNA FLJ57809 complete cds.
AK090395 - Homo sapiens mRNA for FLJ00264 protein.
JD305891 - Sequence 286915 from Patent EP1572962.
JD099578 - Sequence 80602 from Patent EP1572962.
JD322083 - Sequence 303107 from Patent EP1572962.
JD399054 - Sequence 380078 from Patent EP1572962.
JD151415 - Sequence 132439 from Patent EP1572962.
JD324738 - Sequence 305762 from Patent EP1572962.
JD364800 - Sequence 345824 from Patent EP1572962.
JD524509 - Sequence 505533 from Patent EP1572962.
JD302656 - Sequence 283680 from Patent EP1572962.
JD053176 - Sequence 34200 from Patent EP1572962.
JD126873 - Sequence 107897 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NFQ2-2, AY167570, FAM115C, FAM139A, NM_173678, NP_775949
UCSC ID: uc011ktm.2
RefSeq Accession: NM_173678
Protein: A6NFQ2-2, splice isoform of A6NFQ2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AY167570.1
exon count: 7CDS single in 3' UTR: no RNA size: 2955
ORF size: 2538CDS single in intron: no Alignment % ID: 99.90
txCdsPredict score: 5276.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 2
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 386# 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.