Mouse Gene Otof (ENSMUST00000114747.8) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus otoferlin (Otof), transcript variant 4, mRNA. (from RefSeq NM_001313767)
Gencode Transcript: ENSMUST00000114747.8
Gencode Gene: ENSMUSG00000062372.13
Transcript (Including UTRs)
   Position: mm10 chr5:30,367,062-30,461,902 Size: 94,841 Total Exon Count: 47 Strand: -
Coding Region
   Position: mm10 chr5:30,367,860-30,461,798 Size: 93,939 Coding Exon Count: 47 

Page IndexSequence and LinksPrimersCTDRNA StructureOther Species
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:30,367,062-30,461,902)mRNA (may differ from genome)Protein (1992 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsPubMed
SOURCEUniProtKBWikipedia

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -43.00104-0.413 Picture PostScript Text
3' UTR -262.60798-0.329 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.

-  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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsembl   
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Descriptions from all associated GenBank mRNAs
  AK147256 - Mus musculus adult male brain UNDEFINED_CELL_LINE cDNA, RIKEN full-length enriched library, clone:M5C1003C04 product:otoferlin, full insert sequence.
AK147434 - Mus musculus cDNA, RIKEN full-length enriched library, clone:M5C1041A07 product:otoferlin, full insert sequence.
AF183183 - Mus musculus cochlear otoferlin (Otof) mRNA, complete cds.
AF183184 - Mus musculus brain otoferlin (Otof) mRNA, complete cds.
BC145107 - Mus musculus otoferlin, mRNA (cDNA clone MGC:178663 IMAGE:9053655), complete cds.
BC145108 - Mus musculus cDNA clone IMAGE:9053656.
BC150702 - Mus musculus otoferlin, mRNA (cDNA clone MGC:183613 IMAGE:9087613), complete cds.
AY586513 - Mus musculus otoferlin (Otof) mRNA, complete cds.
KX060996 - Mus musculus strain C57/N otoferlin (Otof) mRNA, complete cds.
AK046460 - Mus musculus adult male corpora quadrigemina cDNA, RIKEN full-length enriched library, clone:B230387J08 product:otoferlin, full insert sequence.
AK033317 - Mus musculus 15 days embryo male testis cDNA, RIKEN full-length enriched library, clone:8030492G06 product:otoferlin, full insert sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: A0A0R4J1K2, NM_001313767, uc008wvl.1, uc008wvl.2
UCSC ID: uc008wvl.2
RefSeq Accession: NM_001100395
CCDS: CCDS19157.1, CCDS51452.1

-  Gene Model Information
  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.