Human Gene RTTN (uc002lkq.1) Description and Page Index
  Description: Homo sapiens rotatin (RTTN), mRNA.
RefSeq Summary (NM_173630): This gene encodes a large protein whose specific function is unknown. Absence of the orthologous protein in mouse results in embryonic lethality with deficient axial rotation, abnormal differentiation of the neural tube, and randomized looping of the heart tube during development. In human, mutations in this gene are associated with polymicrogyria with seizures. In human fibroblasts this protein localizes at the ciliary basal bodies. Given the intracellular localization of this protein and the phenotypic effects of mutations, this gene is suspected of playing a role in the maintenance of normal ciliary structure which in turn effects the developmental process of left-right organ specification, axial rotation, and perhaps notochord development. [provided by RefSeq, Jan 2013].
Transcript (Including UTRs)
   Position: hg19 chr18:67,833,670-67,872,962 Size: 39,293 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr18:67,834,151-67,872,894 Size: 38,744 Coding Exon Count: 13 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:67,833,670-67,872,962)mRNA (may differ from genome)Protein (601 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMGIPubMedStanford SOURCEUniProtKB

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RTTN
CDC HuGE Published Literature: RTTN
Positive Disease Associations: Hemoglobin A, Glycosylated
Related Studies:
  1. Hemoglobin A, Glycosylated
    James B Meigs et al. BMC medical genetics 2007, Genome-wide association with diabetes-related traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903298]
    Framingham 100K SNP data is a resource for association tests of known and novel genes with diabetes and related traits posted at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite. Framingham 100K data replicate the TCF7L2 association with diabetes.

-  MalaCards Disease Associations
  MalaCards Gene Search: RTTN
Diseases sorted by gene-association score: microcephaly, short stature, and polymicrogyria with seizures* (1650), polymicrogyria (19), microcephaly (5), seckel syndrome (4), growth hormone deficiency, isolated, type ia (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.61 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 99.44 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -18.6068-0.274 Picture PostScript Text
3' UTR -90.33481-0.188 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:
PF14726 - Rotatin, an armadillo repeat protein, centriole functioning

SCOP Domains:
48371 - ARM repeat

ModBase Predicted Comparative 3D Structure on Q86VV8-2
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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
  BC047602 - Homo sapiens rotatin, mRNA (cDNA clone IMAGE:5556040), partial cds.
CR749799 - Homo sapiens mRNA; cDNA DKFZp686B07186 (from clone DKFZp686B07186).
BC143723 - Homo sapiens cDNA clone IMAGE:9052237.
BC156291 - Synthetic construct Homo sapiens clone IMAGE:100061722, MGC:190083 rotatin (RTTN) mRNA, encodes complete protein.
AK096404 - Homo sapiens cDNA FLJ39085 fis, clone NT2RP7019064.

-  Other Names for This Gene
  Alternate Gene Symbols: AK096404, Q86VV8-2
UCSC ID: uc002lkq.1
RefSeq Accession: NM_173630
Protein: Q86VV8-2, splice isoform of Q86VV8

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK096404.1
exon count: 13CDS single in 3' UTR: no RNA size: 2361
ORF size: 1806CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 3812.00frame shift in genome: no % Coverage: 99.75
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: 485# 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.