Human Gene RTTN (uc010xfb.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 chr18:67,671,043-67,872,962 Size: 201,920 Total Exon Count: 48 Strand: -
Coding Region
   Position: hg19 chr18:67,671,387-67,806,886 Size: 135,500 Coding Exon Count: 29 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:67,671,043-67,872,962)mRNA (may differ from genome)Protein (1314 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCHPRDLynxMGIneXtProtPubMed
Stanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: RTTN_HUMAN
DESCRIPTION: RecName: Full=Rotatin;
FUNCTION: Involved in the genetic cascade that governs left-right specification. Required for correct asymmetric expression of NODAL, LEFTY and PITX2 (By similarity).
SEQUENCE CAUTION: Sequence=BAC86583.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAC87292.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAC87292.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing; Sequence=CAH18659.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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 -807.542621-0.308 Picture PostScript Text
3' UTR -95.52344-0.278 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
  InterPro Domains: Graphical view of domain structure
IPR011989 - ARM-like
IPR016024 - ARM-type_fold

SCOP Domains:
48371 - ARM repeat

ModBase Predicted Comparative 3D Structure on Q86VV8
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
  Biological Process:
GO:0007275 multicellular organism development
GO:0007368 determination of left/right symmetry
GO:0044782 cilium organization

Cellular Component:
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005856 cytoskeleton
GO:0005929 cilium
GO:0036064 ciliary basal body
GO:0042995 cell projection


-  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).
AK126538 - Homo sapiens cDNA FLJ44574 fis, clone UTERU3018081.
AK128137 - Homo sapiens cDNA FLJ46258 fis, clone TESTI4024245.
BC143723 - Homo sapiens cDNA clone IMAGE:9052237.
BC156291 - Synthetic construct Homo sapiens clone IMAGE:100061722, MGC:190083 rotatin (RTTN) mRNA, encodes complete protein.
BC026879 - Homo sapiens, clone IMAGE:4455574, mRNA, partial cds.
BC007359 - Homo sapiens rotatin, mRNA (cDNA clone IMAGE:3622437), partial cds.
BC046931 - Homo sapiens rotatin, mRNA (cDNA clone IMAGE:3623202), partial cds.
AL117635 - Homo sapiens mRNA; cDNA DKFZp434G145 (from clone DKFZp434G145).
BC046222 - Homo sapiens rotatin, mRNA (cDNA clone IMAGE:6198495), partial cds.
AK129866 - Homo sapiens cDNA FLJ26356 fis, clone HRT05041.
BC013774 - Homo sapiens rotatin, mRNA (cDNA clone IMAGE:4385350), partial cds.
JX424573 - Homo sapiens RTTN mRNA, partial cds.
AK096404 - Homo sapiens cDNA FLJ39085 fis, clone NT2RP7019064.

-  Other Names for This Gene
  Alternate Gene Symbols: BC143723, Q68CS9, Q6ZRL8, Q6ZTK3, Q86TG4, Q86VV8, Q8N8N8, Q8TBQ4, Q96IN9, Q9UFJ4, RTTN_HUMAN
UCSC ID: uc010xfb.1
RefSeq Accession: NM_173630
Protein: Q86VV8 (aka RTTN_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC143723.1
exon count: 48CDS single in 3' UTR: no RNA size: 6725
ORF size: 3945CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 5863.00frame shift in genome: no % Coverage: 99.96
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.