Human Gene TSFM (uc001sqh.3)
  Description: Homo sapiens Ts translation elongation factor, mitochondrial (TSFM), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.
RefSeq Summary (NM_001172696): This gene encodes a mitochondrial translation elongation factor. The encoded protein is an enzyme that catalyzes the exchange of guanine nucleotides on the translation elongation factor Tu during the elongation step of mitchondrial protein translation. Mutations in this gene are associated with combined oxidative phosphorylation deficiency-3 syndrome. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Mar 2010].
Transcript (Including UTRs)
   Position: hg19 chr12:58,176,528-58,191,370 Size: 14,843 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr12:58,176,585-58,190,366 Size: 13,782 Coding Exon Count: 7 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:58,176,528-58,191,370)mRNA (may differ from genome)Protein (346 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMalacardsMGIOMIM
PubMedReactomeUniProtKBWikipediaBioGrid 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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TSFM
CDC HuGE Published Literature: TSFM

-  MalaCards Disease Associations
  MalaCards Gene Search: TSFM
Diseases sorted by gene-association score: combined oxidative phosphorylation deficiency 3* (1691), dilated cardiomyopathy* (103), central nervous system mesenchymal non-meningothelial tumor (7), extraosseous ewing's sarcoma (6), horner's syndrome (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 5.95 RPKM in Adrenal Gland
Total median expression: 110.01 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 -15.1057-0.265 Picture PostScript Text
3' UTR -230.311004-0.229 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:
PF00889 - Elongation factor TS

SCOP Domains:
46934 - UBA-like
54713 - Elongation factor Ts (EF-Ts), dimerisation domain

ModBase Predicted Comparative 3D Structure on P43897-2
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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
  AK308981 - Homo sapiens cDNA, FLJ99022.
KM576716 - Homo sapiens clone METTL21B-TSFM_M2-T2-T5out mRNA sequence.
LF384691 - JP 2014500723-A/192194: Polycomb-Associated Non-Coding RNAs.
AK313453 - Homo sapiens cDNA, FLJ93997.
AK304621 - Homo sapiens cDNA FLJ50108 complete cds, highly similar to Elongation factor Ts, mitochondrial precursor.
BC022862 - Homo sapiens Ts translation elongation factor, mitochondrial, mRNA (cDNA clone MGC:23697 IMAGE:4076880), complete cds.
AK295323 - Homo sapiens cDNA FLJ60259 complete cds, highly similar to Elongation factor Ts, mitochondrial precursor.
BC093068 - Homo sapiens Ts translation elongation factor, mitochondrial, mRNA (cDNA clone MGC:111185 IMAGE:30722527), complete cds.
AF110399 - Homo sapiens elongation factor Ts mRNA, nuclear gene encoding mitochondrial protein, complete cds.
KJ898158 - Synthetic construct Homo sapiens clone ccsbBroadEn_07552 TSFM gene, encodes complete protein.
KR711974 - Synthetic construct Homo sapiens clone CCSBHm_00034394 TSFM (TSFM) mRNA, encodes complete protein.
L37936 - Human nuclear-encoded mitochondrial elongation factor Ts (EF-Ts) mRNA, 3' end of cds.
LF324076 - JP 2014500723-A/131579: Polycomb-Associated Non-Coding RNAs.
LF324075 - JP 2014500723-A/131578: Polycomb-Associated Non-Coding RNAs.
LF324074 - JP 2014500723-A/131577: Polycomb-Associated Non-Coding RNAs.
LF324071 - JP 2014500723-A/131574: Polycomb-Associated Non-Coding RNAs.
LF324070 - JP 2014500723-A/131573: Polycomb-Associated Non-Coding RNAs.
LF324069 - JP 2014500723-A/131572: Polycomb-Associated Non-Coding RNAs.
MA620268 - JP 2018138019-A/192194: Polycomb-Associated Non-Coding RNAs.
MA559653 - JP 2018138019-A/131579: Polycomb-Associated Non-Coding RNAs.
MA559652 - JP 2018138019-A/131578: Polycomb-Associated Non-Coding RNAs.
MA559651 - JP 2018138019-A/131577: Polycomb-Associated Non-Coding RNAs.
MA559648 - JP 2018138019-A/131574: Polycomb-Associated Non-Coding RNAs.
MA559647 - JP 2018138019-A/131573: Polycomb-Associated Non-Coding RNAs.
MA559646 - JP 2018138019-A/131572: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P43897 (Reactome details) participates in the following event(s):

R-HSA-5419269 TSFM binds TUFM displacing GDP
R-HSA-5419268 TUFM binds GTP displacing TSFM
R-HSA-5389840 Mitochondrial translation elongation
R-HSA-5368287 Mitochondrial translation
R-HSA-72766 Translation
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001172696, NP_001166167, P43897-2
UCSC ID: uc001sqh.3
RefSeq Accession: NM_001172696
Protein: P43897-2, splice isoform of P43897 CCDS: CCDS53809.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene TSFM:
ataxias (Hereditary Ataxia Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001172696.1
exon count: 7CDS single in 3' UTR: no RNA size: 2102
ORF size: 1041CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2244.00frame shift in genome: no % Coverage: 100.00
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.