Human Gene TCAF2 (uc003wdi.2)
  Description: Homo sapiens family with sequence similarity 115, member C (TCAF2), transcript variant 3, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr7:143,416,776-143,427,173 Size: 10,398 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr7:143,416,996-143,424,760 Size: 7,765 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:143,416,776-143,427,173)mRNA (may differ from genome)Protein (638 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsH-INV
LynxMGIneXtProtOMIMPubMedUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: F115C_HUMAN
DESCRIPTION: RecName: Full=Protein FAM115C; AltName: Full=Protein FAM139A;
SIMILARITY: Belongs to the FAM115 family.
SEQUENCE CAUTION: Sequence=BAC03376.1; Type=Erroneous initiation;

-  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 -105.60220-0.480 Picture PostScript Text
3' UTR -701.082413-0.291 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
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0044325 ion channel binding

Biological Process:
GO:0010360 negative regulation of anion channel activity
GO:0030335 positive regulation of cell migration
GO:0090314 positive regulation of protein targeting to membrane

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030054 cell junction


-  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.
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.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NFQ2, AK090395, B4DK02, F115C_HUMAN, FAM115C, FAM139A, NM_001130026, NP_001123498, Q14D25, Q17RQ4, Q8IWQ0, Q8NF84
UCSC ID: uc003wdi.2
RefSeq Accession: NM_001130026
Protein: A6NFQ2 (aka F115C_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK090395.1
exon count: 6CDS single in 3' UTR: no RNA size: 4677
ORF size: 1917CDS single in intron: no Alignment % ID: 99.85
txCdsPredict score: 3816.00frame shift in genome: no % Coverage: 92.15
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.