Human Gene TCAF1 (uc003wdo.2)
  Description: Homo sapiens family with sequence similarity 115, member A (TCAF1), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr7:143,548,461-143,599,172 Size: 50,712 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr7:143,551,226-143,573,701 Size: 22,476 Coding Exon Count: 8 

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 (chr7:143,548,461-143,599,172)mRNA (may differ from genome)Protein (921 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHPRDLynxMGIneXtProtOMIM
PubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: F115A_HUMAN
DESCRIPTION: RecName: Full=Protein FAM115A;
SIMILARITY: Belongs to the FAM115 family.
SEQUENCE CAUTION: Sequence=BAA34458.2; 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: 29.75 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 554.54 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 -52.80133-0.397 Picture PostScript Text
3' UTR -702.872765-0.254 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 Q9Y4C2
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:0005515 protein binding
GO:0044325 ion channel binding

Biological Process:
GO:0030336 negative regulation of cell migration
GO:0090314 positive regulation of protein targeting to membrane
GO:1901529 positive regulation of anion channel activity

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  LF207110 - JP 2014500723-A/14613: Polycomb-Associated Non-Coding RNAs.
BC039457 - Homo sapiens cDNA clone IMAGE:5312122.
LF361996 - JP 2014500723-A/169499: Polycomb-Associated Non-Coding RNAs.
LF361997 - JP 2014500723-A/169500: Polycomb-Associated Non-Coding RNAs.
LF361998 - JP 2014500723-A/169501: Polycomb-Associated Non-Coding RNAs.
AF086218 - Homo sapiens full length insert cDNA clone ZC65G07.
DQ786304 - Homo sapiens clone HLS_IMAGE_753138 mRNA sequence.
DQ786274 - Homo sapiens clone HLS_IMAGE_327228 mRNA sequence.
LF361999 - JP 2014500723-A/169502: Polycomb-Associated Non-Coding RNAs.
JD021952 - Sequence 2976 from Patent EP1572962.
JD030682 - Sequence 11706 from Patent EP1572962.
LF362000 - JP 2014500723-A/169503: Polycomb-Associated Non-Coding RNAs.
JD035782 - Sequence 16806 from Patent EP1572962.
LF362001 - JP 2014500723-A/169504: Polycomb-Associated Non-Coding RNAs.
LF362002 - JP 2014500723-A/169505: Polycomb-Associated Non-Coding RNAs.
JD024918 - Sequence 5942 from Patent EP1572962.
JD030659 - Sequence 11683 from Patent EP1572962.
LF362003 - JP 2014500723-A/169506: Polycomb-Associated Non-Coding RNAs.
AB018281 - Homo sapiens KIAA0738 mRNA for KIAA0738 protein.
AK001640 - Homo sapiens cDNA FLJ10778 fis, clone NT2RP4000360, highly similar to Homo sapiens mRNA for KIAA0738 protein.
JD434076 - Sequence 415100 from Patent EP1572962.
JD239029 - Sequence 220053 from Patent EP1572962.
JD038304 - Sequence 19328 from Patent EP1572962.
JD036574 - Sequence 17598 from Patent EP1572962.
JD517781 - Sequence 498805 from Patent EP1572962.
JD366591 - Sequence 347615 from Patent EP1572962.
JD534849 - Sequence 515873 from Patent EP1572962.
JD155914 - Sequence 136938 from Patent EP1572962.
JD105996 - Sequence 87020 from Patent EP1572962.
JD517780 - Sequence 498804 from Patent EP1572962.
JD269614 - Sequence 250638 from Patent EP1572962.
JD230047 - Sequence 211071 from Patent EP1572962.
JD182847 - Sequence 163871 from Patent EP1572962.
JD333387 - Sequence 314411 from Patent EP1572962.
JD268102 - Sequence 249126 from Patent EP1572962.
JD442749 - Sequence 423773 from Patent EP1572962.
JD442748 - Sequence 423772 from Patent EP1572962.
JD045236 - Sequence 26260 from Patent EP1572962.
JD388466 - Sequence 369490 from Patent EP1572962.
JD457201 - Sequence 438225 from Patent EP1572962.
JD558806 - Sequence 539830 from Patent EP1572962.
JD430984 - Sequence 412008 from Patent EP1572962.
JD326927 - Sequence 307951 from Patent EP1572962.
JD530631 - Sequence 511655 from Patent EP1572962.
JD294069 - Sequence 275093 from Patent EP1572962.
JD199024 - Sequence 180048 from Patent EP1572962.
JD327186 - Sequence 308210 from Patent EP1572962.
JD472276 - Sequence 453300 from Patent EP1572962.
JD299120 - Sequence 280144 from Patent EP1572962.
JD241736 - Sequence 222760 from Patent EP1572962.
JD063421 - Sequence 44445 from Patent EP1572962.
JD356100 - Sequence 337124 from Patent EP1572962.
JD066355 - Sequence 47379 from Patent EP1572962.
JD486684 - Sequence 467708 from Patent EP1572962.
AK291605 - Homo sapiens cDNA FLJ76313 complete cds.
JD315129 - Sequence 296153 from Patent EP1572962.
JD102424 - Sequence 83448 from Patent EP1572962.
AK299911 - Homo sapiens cDNA FLJ58406 complete cds, weakly similar to Mus musculus experimental autoimmune prostatitis antigen 2 (Eapa2), mRNA.
JD253211 - Sequence 234235 from Patent EP1572962.
JD333721 - Sequence 314745 from Patent EP1572962.
JD236952 - Sequence 217976 from Patent EP1572962.
JD073163 - Sequence 54187 from Patent EP1572962.
JD133584 - Sequence 114608 from Patent EP1572962.
JD099672 - Sequence 80696 from Patent EP1572962.
JD099671 - Sequence 80695 from Patent EP1572962.
AK294312 - Homo sapiens cDNA FLJ56782 complete cds, moderately similar to Mus musculus experimental autoimmune prostatitis antigen 2 (Eapa2), mRNA.
LF362004 - JP 2014500723-A/169507: Polycomb-Associated Non-Coding RNAs.
JD341212 - Sequence 322236 from Patent EP1572962.
BC000609 - Homo sapiens family with sequence similarity 115, member A, mRNA (cDNA clone MGC:1890 IMAGE:3346754), complete cds.
AB383971 - Synthetic construct DNA, clone: pF1KSDA0738, Homo sapiens FAM115A gene for FAM115A protein, complete cds, without stop codon, in Flexi system.
LF362005 - JP 2014500723-A/169508: Polycomb-Associated Non-Coding RNAs.
LF362006 - JP 2014500723-A/169509: Polycomb-Associated Non-Coding RNAs.
LF362008 - JP 2014500723-A/169511: Polycomb-Associated Non-Coding RNAs.
JD108243 - Sequence 89267 from Patent EP1572962.
JD462051 - Sequence 443075 from Patent EP1572962.
JD157323 - Sequence 138347 from Patent EP1572962.
MA442687 - JP 2018138019-A/14613: Polycomb-Associated Non-Coding RNAs.
MA597573 - JP 2018138019-A/169499: Polycomb-Associated Non-Coding RNAs.
MA597574 - JP 2018138019-A/169500: Polycomb-Associated Non-Coding RNAs.
MA597575 - JP 2018138019-A/169501: Polycomb-Associated Non-Coding RNAs.
MA597576 - JP 2018138019-A/169502: Polycomb-Associated Non-Coding RNAs.
MA597577 - JP 2018138019-A/169503: Polycomb-Associated Non-Coding RNAs.
MA597578 - JP 2018138019-A/169504: Polycomb-Associated Non-Coding RNAs.
MA597579 - JP 2018138019-A/169505: Polycomb-Associated Non-Coding RNAs.
MA597580 - JP 2018138019-A/169506: Polycomb-Associated Non-Coding RNAs.
MA597581 - JP 2018138019-A/169507: Polycomb-Associated Non-Coding RNAs.
MA597582 - JP 2018138019-A/169508: Polycomb-Associated Non-Coding RNAs.
MA597583 - JP 2018138019-A/169509: Polycomb-Associated Non-Coding RNAs.
MA597585 - JP 2018138019-A/169511: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K6E0, F115A_HUMAN, FAM115A, KIAA0738, NM_014719, NP_001193870, Q75KM8, Q75KM9, Q7L665, Q9BW63, Q9Y4C2
UCSC ID: uc003wdo.2
RefSeq Accession: NM_014719
Protein: Q9Y4C2 (aka F115A_HUMAN)
CCDS: CCDS56514.1, CCDS5886.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014719.2
exon count: 9CDS single in 3' UTR: no RNA size: 5682
ORF size: 2766CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 5732.00frame shift in genome: no % Coverage: 99.68
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.