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 fibrob... See more...

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 Microcephaly, Short Stature, And Polymicrogyria With Or Without Seizures and Polymicrogyria. Gene Ontology (GO) annotations related to this gene include binding.

UniProtKB/Swiss-Prot Summary 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.

Additional gene information for RTTN Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RTTN Gene

Genomics for RTTN Gene

GeneHancer (GH) Regulatory Elements for RTTN Gene

Promoters and enhancers for RTTN Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18J070204 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 511.3 -0.1 -74 2.8 RXRA FOXK2 ZBTB40 ZNF217 EP300 SIN3A NRF1 TCF12 SP1 NCOR1 RTTN ENSG00000287646 LOC105372180
GH18J070205 Promoter 0.3 Ensembl 500.7 +1.6 1625 0.2 ENSG00000287646 LOC105372180 RTTN piR-50968-053
GH18J070418 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 11.3 -216.5 -216482 8.4 TCF12 JUND FOS REST KDM6A TCF7 MEF2C EP300 TEAD1 FOXA2 SOCS6 RTTN LARP7P3 CD226 RPS2P6 lnc-SOCS6-7 LINC01910
GH18J070294 Promoter/Enhancer 1.4 Ensembl ENCODE dbSUPER 10.5 -90.3 -90310 2.8 POLR2G ZBTB25 MYC TGIF2 SKI TEAD1 ZKSCAN8 MXI1 ZSCAN9 KMT2B RTTN LINC01909 SOCS6 RF00017-2699
GH18J070375 Enhancer 1.3 Ensembl ENCODE dbSUPER 11.1 -175.3 -175307 11.3 EP300 FOXK2 TCF12 POLR2G NCOR1 PHB2 FOS REST KDM6A TCF7 SOCS6 RTTN piR-50437-317 piR-57133-282 LINC01910
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RTTN on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RTTN

Top Transcription factor binding sites by QIAGEN in the RTTN gene promoter:
  • AML1a
  • AREB6
  • C/EBPalpha
  • E47
  • FOXO1
  • FOXO1a
  • NF-kappaB
  • NF-kappaB1
  • POU2F1
  • POU2F1a

Genomic Locations for RTTN Gene

Genomic Locations for RTTN Gene
chr18:70,003,031-70,205,726
(GRCh38/hg38)
Size:
202,696 bases
Orientation:
Minus strand
chr18:67,671,029-67,873,181
(GRCh37/hg19)
Size:
202,153 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
    Miscellaneous:
    • [Isoform 2]: May be due to an intron retention.
    • [Isoform 4]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
    SequenceCaution:
    • Sequence=BAC86583.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAC87292.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAC87292.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305}; Sequence=CAH18659.1; Type=Erroneous initiation; Note=Truncated N-terminus.; 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

Gene Families for RTTN Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for RTTN Gene

Suggested Antigen Peptide Sequences for RTTN Gene

GenScript: Design optimal peptide antigens:
  • Rotatin (RTTN_HUMAN)
genes like me logo Genes that share domains with RTTN: view

No data available for Graphical View of Domain Structure 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.

Phenotypes From GWAS Catalog for RTTN Gene

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

CRISPR Products

miRNA for RTTN Gene

miRTarBase miRNAs that target RTTN

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RTTN

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. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. 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
nucleus 1

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:0005814 centriole IBA 21873635
GO:0005815 microtubule organizing center IEA --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with RTTN: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RTTN Gene

Pathways & Interactions for RTTN Gene

PathCards logo

SuperPathways for RTTN Gene

No Data Available

Gene Ontology (GO) - Biological Process for RTTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007099 centriole replication IBA 21873635
GO:0007275 multicellular organism development IEA --
GO:0007368 determination of left/right symmetry IEA --
GO:0010457 centriole-centriole cohesion IBA 21873635
GO:0032053 ciliary basal body organization IBA 21873635
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

mRNA/cDNA for RTTN Gene

2 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
23 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RTTN

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

Expression for RTTN Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RTTN

SOURCE GeneReport for Unigene cluster for RTTN Gene:

Hs.654809

Evidence on tissue expression from TISSUES for RTTN Gene

  • Nervous system(4.4)
  • Kidney(4.1)
  • Pancreas(4)

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

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

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 31 30
  • 99.1 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RTTN 31 30
  • 87.62 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Rttn 17 31 30
  • 83.88 (n)
cow
(Bos Taurus)
Mammalia RTTN 31 30
  • 83.76 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rttn 30
  • 83.39 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 76 (a)
OneToMany
-- 31
  • 69 (a)
OneToMany
-- 31
  • 57 (a)
OneToMany
-- 31
  • 55 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia RTTN 31
  • 65 (a)
OneToOne
chicken
(Gallus gallus)
Aves RTTN 31 30
  • 69.45 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RTTN 31
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rttn 30
  • 61.53 (n)
zebrafish
(Danio rerio)
Actinopterygii rttn 31 30
  • 55.72 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for RTTN: view image

Paralogs for RTTN Gene

No data available for Paralogs for RTTN Gene

Variants for RTTN Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RTTN Gene

SNP ID Clinical significance and condition Chr 18 pos Variation AA Info Type
668415 Likely Benign: not provided 70,127,728(-) A/G SYNONYMOUS_VARIANT
670493 Benign: not provided 70,121,363(-) T/C INTRON_VARIANT
672895 Likely Benign: not provided 70,199,519(-) G/A INTRON_VARIANT
673109 Benign: not provided 70,205,765(-) G/A
673149 Benign: not provided 70,060,112(-) T/C INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for RTTN Gene

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)

Additional Variant Information for RTTN Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for RTTN Gene

MalaCards: The human disease database

(16) MalaCards diseases for RTTN Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

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.

Additional Disease Information for 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 GM (American journal of human genetics 2012) 3 4 54
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  3. Rotatin is a novel gene required for axial rotation and left-right specification in mouse embryos. (PMID: 11900971) Faisst AM … Gruss P (Mechanisms of development 2002) 2 3 54
  4. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3 54
  5. PPP1R35 is a novel centrosomal protein that regulates centriole length in concert with the microcephaly protein RTTN. (PMID: 30168418) Sydor AM … Mennella V (eLife 2018) 3 54

Products for RTTN Gene

Sources for RTTN Gene