Human Gene TTC21A (uc003cjf.2) Description and Page Index
  Description: Homo sapiens tetratricopeptide repeat domain 21A (TTC21A), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr3:39,174,212-39,180,394 Size: 6,183 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr3:39,174,597-39,180,279 Size: 5,683 Coding Exon Count: 10 

Page IndexSequence and LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:39,174,212-39,180,394)mRNA (may differ from genome)Protein (441 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIOMIMPubMed
Stanford SOURCEUniProtKB

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TTC21A
CDC HuGE Published Literature: TTC21A
Positive Disease Associations: Thyrotropin
Related Studies:
  1. Thyrotropin
    Shih-Jen Hwang et al. BMC medical genetics 2007, A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903292]
    Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.

-  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: 44.81 RPKM in Testis
Total median expression: 134.11 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 -125.00385-0.325 Picture PostScript Text
3' UTR -31.74115-0.276 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:
PF13174 - Tetratricopeptide repeat
PF14559 - Tetratricopeptide repeat

SCOP Domains:
81901 - HCP-like
48439 - Protein prenylyltransferase
48452 - TPR-like

ModBase Predicted Comparative 3D Structure on Q8NDW8-3
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     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  HM005525 - Homo sapiens clone HTL-T-212 testicular tissue protein Li 212 mRNA, complete cds.
AJ487015 - Homo sapiens mRNA for TRP domain containing protein (STI2 gene).
BC129948 - Homo sapiens tetratricopeptide repeat domain 21A, mRNA (cDNA clone MGC:156293 IMAGE:40126472), complete cds.
AK302408 - Homo sapiens cDNA FLJ61471 complete cds, highly similar to Homo sapiens tetratricopeptide repeat domain 21A (TTC21A), mRNA.
AK302465 - Homo sapiens cDNA FLJ58738 complete cds, highly similar to Homo sapiens tetratricopeptide repeat domain 21A (TTC21A), mRNA.
AK093313 - Homo sapiens cDNA FLJ35994 fis, clone TESTI2014838.
AX748048 - Sequence 1573 from Patent EP1308459.
AK098528 - Homo sapiens cDNA FLJ25662 fis, clone TST01417.
BX647142 - Homo sapiens mRNA; cDNA DKFZp686P18239 (from clone DKFZp686P18239).
AK299774 - Homo sapiens cDNA FLJ57790 complete cds, moderately similar to Homo sapiens tetratricopeptide repeat domain 21A (TTC21A), mRNA.
JD103230 - Sequence 84254 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BX647142, NM_001105513, NP_001098983, Q8NDW8-3, STI2
UCSC ID: uc003cjf.2
RefSeq Accession: NM_001105513
Protein: Q8NDW8-3, splice isoform of Q8NDW8

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BX647142.1
exon count: 10CDS single in 3' UTR: no RNA size: 1846
ORF size: 1326CDS single in intron: no Alignment % ID: 99.73
txCdsPredict score: 2630.00frame shift in genome: no % Coverage: 98.75
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: 331# 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.