Human Gene OTOL1 (uc011bpb.2) Description and Page Index
  Description: Homo sapiens otolin 1 (OTOL1), mRNA.
RefSeq Summary (NM_001080440): This gene encodes a secreted glycoprotein with a C-terminal complement Cq1-like globular domain that belongs to the C1q/tumor necrosis factor-related protein (CTRP) family. The encoded protein is expressed in the inner ear and forms a multimeric complex called the otoconia, together with cerebellin-1 and otoconin-90, as part of the otoconial membrane. It contains extensive posttranslational modifications including hydroxylated prolines and glycosylated lysines. Naturally occurring mutations in this gene are associated with abnormal otoconia formation and balance deficits resulting from vestibular dysfunction. [provided by RefSeq, Jul 2017]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments. ##Evidence-Data-START## Transcript exon combination :: DW009679.1, DW009680.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA2145544, SAMEA2154361 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000327928.4/ ENSP00000330808.4 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr3:161,214,596-161,221,730 Size: 7,135 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr3:161,214,596-161,221,730 Size: 7,135 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsGene AllelesRNA-Seq Expression
Microarray ExpressionProtein StructureOther SpeciesGO AnnotationsOther NamesModel Information
Methods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:161,214,596-161,221,730)mRNA (may differ from genome)Protein (477 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
HGNCHPRDLynxMGIneXtProtPubMed
Stanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: OTOL1_HUMAN
DESCRIPTION: RecName: Full=Otolin-1; Flags: Precursor;
SUBUNIT: Interacts with OC90 (By similarity).
SUBCELLULAR LOCATION: Secreted (By similarity).
SIMILARITY: Belongs to the OTOL1 family.
SIMILARITY: Contains 1 C1q domain.
SIMILARITY: Contains 3 collagen-like domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): OTOL1
CDC HuGE Published Literature: OTOL1
Positive Disease Associations: Attention Deficit Disorder with Hyperactivity , Behavior , Body Weight Changes , Body Weights and Measures , Cholesterol , Cholesterol, HDL , Frontal Lobe , Glucose , Hemoglobin A, Glycosylated , Intra-Abdominal Fat , Respiratory Function Tests , Subcutaneous Fat
Related Studies:
  1. Attention Deficit Disorder with Hyperactivity
    Jessica Lasky-Su et al. American journal of medical genetics. Part B, Neuropsychiatric genetics 2008, Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations., American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetic. [PubMed 18821565]
  2. Behavior
    Jessica Lasky-Su et al. American journal of medical genetics. Part B, Neuropsychiatric genetics 2008, Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations., American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetic. [PubMed 18821565]
  3. Body Weight Changes
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
           more ... click here to view the complete list

+  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: 0.05 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 0.13 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.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001073 - C1q
IPR008160 - Collagen
IPR008983 - Tumour_necrosis_fac-like

Pfam Domains:
PF00386 - C1q domain
PF01391 - Collagen triple helix repeat (20 copies)

SCOP Domains:
49842 - TNF-like

ModBase Predicted Comparative 3D Structure on A6NHN0
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005576 extracellular region
GO:0005581 collagen trimer


-  Other Names for This Gene
  Alternate Gene Symbols: A6NHN0, NM_001080440, NP_001073909, OTOL1_HUMAN
UCSC ID: uc011bpb.2
RefSeq Accession: NM_001080440
Protein: A6NHN0 (aka OTOL1_HUMAN)
CCDS: CCDS46948.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001080440.1
exon count: 4CDS single in 3' UTR: no RNA size: 1434
ORF size: 1434CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2856.00frame shift in genome: no % Coverage: 100.00
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.