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Aliases for RTTN Gene

Aliases for RTTN Gene

External Ids for RTTN Gene

Previous GeneCards Identifiers for RTTN Gene

  • GC18M067493
  • GC18M067730
  • GC18M065820
  • GC18M065822
  • GC18M064389

Summaries for RTTN Gene

Entrez Gene Summary for RTTN Gene

  • 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]

GeneCards Summary for RTTN Gene

RTTN (Rotatin) is a Protein Coding gene. Diseases associated with RTTN include Polymicrogyria With Seizures and Polymicrogyria. GO annotations related to this gene include binding.

UniProtKB/Swiss-Prot for RTTN Gene

  • Involved in the genetic cascade that governs left-right specification. Plays a role in the maintenance of a normal ciliary structure. Required for correct asymmetric expression of NODAL, LEFTY and PITX2.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RTTN Gene

Genomics for RTTN Gene

Regulatory Elements for RTTN Gene

Enhancers for RTTN Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH18G070418 1.8 FANTOM5 Ensembl ENCODE dbSUPER 11.2 -216.4 -216380 8.2 PKNOX1 FOXA2 FEZF1 YY1 TCF12 ZNF766 GATA2 FOS JUNB PPARG SOCS6 RTTN LARP7P3 CD226 RPS2P6
GH18G070375 1.5 Ensembl ENCODE dbSUPER 11.1 -175.1 -175100 11.2 HNRNPUL1 PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 YY1 FOS SOCS6 RTTN LINC01910 LIVAR
GH18G070432 1.4 Ensembl ENCODE dbSUPER 11.3 -227.8 -227756 1.9 ARID4B THRB ZNF48 RAD21 RARA RFX5 ZNF143 MIXL1 THAP11 ZNF654 RTTN LARP7P3 RPS2P6 LOC105376872
GH18G070370 1.4 Ensembl ENCODE dbSUPER 10.5 -166.7 -166679 4.3 TBP FOXA2 SIN3A RAD21 BRCA1 RFX5 ZNF366 RCOR1 FOS CREM RTTN LINC01910 LIVAR
GH18G070294 1.4 Ensembl ENCODE dbSUPER 10.5 -90.1 -90092 2.8 MLX ARID4B SIN3A SP5 REST PPARG SSRP1 MIER3 SMARCA4 PBX2 RTTN LINC01909 SOCS6 GC18P070327
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RTTN on UCSC Golden Path with GeneCards custom track

Promoters for RTTN Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000104814 145 2000 MLX CREB3L1 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3

Genomic Location for RTTN Gene

Chromosome:
18
Start:
70,003,031 bp from pter
End:
70,205,945 bp from pter
Size:
202,915 bases
Orientation:
Minus strand

Genomic View for RTTN Gene

Genes around RTTN on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RTTN Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RTTN Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RTTN Gene

Proteins for RTTN Gene

  • Protein details for RTTN Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86VV8-RTTN_HUMAN
    Recommended name:
    Rotatin
    Protein Accession:
    Q86VV8
    Secondary Accessions:
    • Q68CS9
    • Q6ZRL8
    • Q6ZTK3
    • Q86TG4
    • Q8N8N8
    • Q8TBQ4
    • Q96IN9
    • Q9UFJ4

    Protein attributes for RTTN Gene

    Size:
    2226 amino acids
    Molecular mass:
    248630 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAC86583.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAC87292.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAC87292.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305}; Sequence=CAH18659.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for RTTN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RTTN Gene

Post-translational modifications for RTTN Gene

  • Ubiquitination at Lys1528
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RTTN Gene

Domains & Families for RTTN Gene

Protein Domains for RTTN Gene

Suggested Antigen Peptide Sequences for RTTN Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RTTN: view

No data available for Gene Families and UniProtKB/Swiss-Prot for RTTN Gene

Function for RTTN Gene

Molecular function for RTTN Gene

UniProtKB/Swiss-Prot Function:
Involved in the genetic cascade that governs left-right specification. Plays a role in the maintenance of a normal ciliary structure. Required for correct asymmetric expression of NODAL, LEFTY and PITX2.
genes like me logo Genes that share phenotypes with RTTN: view

Human Phenotype Ontology for RTTN Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for RTTN Gene

Localization for RTTN Gene

Subcellular locations from UniProtKB/Swiss-Prot for RTTN Gene

Cytoplasm, cytoskeleton, cilium basal body. Note=Colocalizes with the basal bodies at the primary cilium.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RTTN gene
Compartment Confidence
cytoskeleton 5
plasma membrane 3
mitochondrion 2

Gene Ontology (GO) - Cellular Components for RTTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005813 centrosome IEA --
GO:0005856 cytoskeleton IEA --
GO:0005929 cilium IEA --
GO:0036064 ciliary basal body IDA,IEA 22939636
genes like me logo Genes that share ontologies with RTTN: view

Pathways & Interactions for RTTN Gene

No Data Available

Interacting Proteins for RTTN Gene

Selected Interacting proteins: Q86VV8-RTTN_HUMAN for RTTN Gene via IID

Gene Ontology (GO) - Biological Process for RTTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0044782 cilium organization IEA --
genes like me logo Genes that share ontologies with RTTN: view

No data available for Pathways by source and SIGNOR curated interactions for RTTN Gene

Drugs & Compounds for RTTN Gene

No Compound Related Data Available

Transcripts for RTTN Gene

Unigene Clusters for RTTN Gene

Rotatin:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for RTTN Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^
SP1: -
SP2:
SP3:
SP4:
SP5:

ExUns: 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^ 43a · 43b ^ 44 ^ 45a · 45b ^ 46 ^ 47a · 47b ^
SP1: - -
SP2:
SP3: -
SP4:
SP5: -

ExUns: 48 ^ 49 ^ 50a · 50b · 50c
SP1:
SP2:
SP3:
SP4: -
SP5:

Relevant External Links for RTTN Gene

GeneLoc Exon Structure for
RTTN
ECgene alternative splicing isoforms for
RTTN

Expression for RTTN Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RTTN Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RTTN Gene



Protein tissue co-expression partners for RTTN Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RTTN Gene:

RTTN

SOURCE GeneReport for Unigene cluster for RTTN Gene:

Hs.654809

Evidence on tissue expression from TISSUES for RTTN Gene

  • Nervous system(4.3)
  • Kidney(4.1)
  • Pancreas(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RTTN Gene

Germ Layers:
  • ectoderm
Systems:
  • nervous
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • head
  • skull
genes like me logo Genes that share expression patterns with RTTN: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for RTTN Gene

Orthologs for RTTN Gene

This gene was present in the common ancestor of chordates.

Orthologs for RTTN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RTTN 34 35
  • 99.1 (n)
dog
(Canis familiaris)
Mammalia RTTN 34 35
  • 87.62 (n)
mouse
(Mus musculus)
Mammalia Rttn 34 16 35
  • 83.88 (n)
cow
(Bos Taurus)
Mammalia RTTN 34 35
  • 83.76 (n)
rat
(Rattus norvegicus)
Mammalia Rttn 34
  • 83.39 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 76 (a)
OneToMany
-- 35
  • 69 (a)
OneToMany
-- 35
  • 57 (a)
OneToMany
-- 35
  • 55 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia RTTN 35
  • 65 (a)
OneToOne
chicken
(Gallus gallus)
Aves RTTN 34 35
  • 69.45 (n)
lizard
(Anolis carolinensis)
Reptilia RTTN 35
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rttn 34
  • 61.53 (n)
zebrafish
(Danio rerio)
Actinopterygii rttn 34 35
  • 55.72 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 26 (a)
OneToOne
Species where no ortholog for RTTN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RTTN Gene

ENSEMBL:
Gene Tree for RTTN (if available)
TreeFam:
Gene Tree for RTTN (if available)

Paralogs for RTTN Gene

No data available for Paralogs for RTTN Gene

Variants for RTTN Gene

Sequence variations from dbSNP and Humsavar for RTTN Gene

SNP ID Clin Chr 18 pos Sequence Context AA Info Type
rs201884120 Pathogenic, Microcephaly, short stature, and polymicrogyria with or without seizures (MSSP) [MIM:614833] 70,205,267(+) TCTTG(C/T)AGAGA nc-transcript-variant, upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs318240757 Pathogenic, Microcephaly, short stature, and polymicrogyria with or without seizures (MSSP) [MIM:614833] 70,135,273(-) TCCTT(A/T)ATATT nc-transcript-variant, reference, missense
rs775277800 Pathogenic 70,166,989(+) CAAGG(C/G/T)TTGGT nc-transcript-variant, reference, missense, utr-variant-5-prime
rs780270096 Pathogenic 70,028,797(+) CACCA(C/T)CCTCC nc-transcript-variant, reference, missense
rs864321620 Pathogenic 70,135,176(-) GAGAT(A/G)TAAGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RTTN Gene

Variant ID Type Subtype PubMed ID
esv32736 CNV gain+loss 17666407
esv3396488 CNV insertion 20981092
esv3583135 CNV loss 25503493
esv3642981 CNV loss 21293372
nsv1113934 CNV deletion 24896259
nsv510465 OTHER sequence alteration 20534489
nsv577546 CNV loss 21841781
nsv833686 CNV gain 17160897

Variation tolerance for RTTN Gene

Residual Variation Intolerance Score: 5.17% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.65; 72.74% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RTTN Gene

Human Gene Mutation Database (HGMD)
RTTN
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RTTN

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RTTN Gene

Disorders for RTTN Gene

MalaCards: The human disease database

(6) MalaCards diseases for RTTN Gene - From: OMIM, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
polymicrogyria with seizures
  • microcephalic primordial dwarfism due to rttn deficiency
polymicrogyria
  • pmg
heterotopia, periventricular
  • heterotopia, periventricular, ehlers-danlos variant
microcephaly
  • microcephalus
growth hormone deficiency, isolated, type ia
  • isolated growth hormone deficiency, type ia
- elite association - COSMIC cancer census association via MalaCards
Search RTTN in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RTTN_HUMAN
  • Microcephaly, short stature, and polymicrogyria with or without seizures (MSSP) [MIM:614833]: A disease characterized by many irregular small gyri in the brain surface and fusion of the molecular layer over multiple small gyri, which gives a festooned appearance to the cortical surface, without abnormal neuronal migration. Polymicrogyria is a heterogeneous disorder, considered to be the result of postmigratory abnormal cortical organization. MSSP patients have moderate to severe mental retardation, poor speech, dysarthria and seizures. {ECO:0000269 PubMed:22939636}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for RTTN

Genetic Association Database (GAD)
RTTN
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RTTN
genes like me logo Genes that share disorders with RTTN: view

No data available for Genatlas for RTTN Gene

Publications for RTTN Gene

  1. RTTN mutations link primary cilia function to organization of the human cerebral cortex. (PMID: 22939636) Kheradmand Kia S. … Mancini G.M. (Am. J. Hum. Genet. 2012) 3 4 64
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  3. Rotatin is a novel gene required for axial rotation and left-right specification in mouse embryos. (PMID: 11900971) Faisst A.M. … Gruss P. (Mech. Dev. 2002) 2 3 64
  4. Kelch Domain of Gigaxonin Interacts with Intermediate Filament Proteins Affected in Giant Axonal Neuropathy. (PMID: 26460568) Johnson-Kerner B.L. … Wichterle H. (PLoS ONE 2015) 3 64
  5. RTTN Mutations Cause Primary Microcephaly and Primordial Dwarfism in Humans. (PMID: 26608784) Shamseldin H. … Alkuraya F.S. (Am. J. Hum. Genet. 2015) 3 64

Products for RTTN Gene

Sources for RTTN Gene

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