U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    Otof otoferlin [ Mus musculus (house mouse) ]

    Gene ID: 83762, updated on 27-Nov-2024

    Summary

    Official Symbol
    Otofprovided by MGI
    Official Full Name
    otoferlinprovided by MGI
    Primary source
    MGI:MGI:1891247
    See related
    Ensembl:ENSMUSG00000062372 AllianceGenome:MGI:1891247
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Summary
    Enables AP-2 adaptor complex binding activity and calcium ion binding activity. Involved in synaptic vesicle priming. Located in endoplasmic reticulum and presynaptic active zone membrane. Is active in cochlear hair cell ribbon synapse and synaptic vesicle membrane. Is expressed in brain; pons mantle layer; and rest of cerebellum ventricular layer. Used to study autosomal recessive nonsyndromic deafness 9. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness 9. Orthologous to human OTOF (otoferlin). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in CNS E18 (RPKM 4.0), cortex adult (RPKM 3.4) and 9 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Otof in Genome Data Viewer
    Location:
    5 B1; 5 16.48 cM
    Exon count:
    49
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (30524410..30620073, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (30367066..30462730, complement)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene selenoprotein I Neighboring gene predicted gene 16288 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:30645501-30645684 Neighboring gene dynein regulatory complex subunit 1 Neighboring gene STARR-seq mESC enhancer starr_12752 Neighboring gene ciliary microtubule inner protein 2C Neighboring gene calcium and integrin binding family member 4 Neighboring gene predicted gene, 40272

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC183613

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables AP-2 adaptor complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables AP-2 adaptor complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables calcium ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in plasma membrane organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    acts_upstream_of_or_within startle response ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    involved_in synaptic vesicle exocytosis EXP
    Inferred from Experiment
    more info
    PubMed 
    involved_in synaptic vesicle exocytosis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within synaptic vesicle exocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in synaptic vesicle exocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in synaptic vesicle priming IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in synaptic vesicle priming IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in synaptic vesicle priming IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in synaptic vesicle recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in apical part of cell ISO
    Inferred from Sequence Orthology
    more info
     
    located_in basal part of cell ISO
    Inferred from Sequence Orthology
    more info
     
    located_in basolateral plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
     
    located_in clathrin-sculpted glutamate transport vesicle membrane TAS
    Traceable Author Statement
    more info
     
    is_active_in cochlear hair cell ribbon synapse EXP
    Inferred from Experiment
    more info
    PubMed 
    is_active_in cochlear hair cell ribbon synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cochlear hair cell ribbon synapse IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in presynaptic active zone membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in presynaptic active zone membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in synaptic vesicle membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in synaptic vesicle membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    otoferlin
    Names
    fer-1-like protein 2
    protein pachanga

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001100395.1NP_001093865.1  otoferlin isoform 1

      See identical proteins and their annotated locations for NP_001093865.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) contains multiple coding region differences resulting in different 3' coding region and 3' UTR, compared to variant 2. It encodes isoform 1, which is shorter and has a distinct C-terminus, compared to isoform 2.
      Source sequence(s)
      AC157761, AK033317, AK046460, AK147256
      Consensus CDS
      CCDS51452.1
      UniProtKB/TrEMBL
      A0A0R4J1K2, B7ZN98
      Related
      ENSMUSP00000110395.3, ENSMUST00000114747.9
      Conserved Domains (10) summary
      cd04011
      Location:265376
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:9741111
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:432581
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:14881611
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:17281861
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:857931
      FerB; FerB (NUC096) domain
      pfam08151
      Location:374424
      FerI; FerI (NUC094) domain
      pfam16165
      Location:18711987
      Ferlin_C; Ferlin C-terminus
      cl14603
      Location:11571234
      C2; C2 domain
    2. NM_001286421.1NP_001273350.1  otoferlin isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 2. It encodes isoform 3, which is shorter than isoform 2.
      Source sequence(s)
      AK033317, AK046460, AK147256
      UniProtKB/TrEMBL
      B7ZN98
      Related
      ENSMUST00000150734.8
      Conserved Domains (10) summary
      cd04011
      Location:250361
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:9591096
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:417566
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:14731596
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:17131846
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:842916
      FerB; FerB (NUC096) domain
      pfam08151
      Location:359409
      FerI; FerI (NUC094) domain
      pfam16165
      Location:18561942
      Ferlin_C; Ferlin C-terminus
      cl14603
      Location:11421219
      C2; C2 domain
    3. NM_001313767.1NP_001300696.1  otoferlin isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice junction in the 3' end and lacks the penultimate exon compared to variant 2. It encodes isoform 4, which lacks an internal segment and has a shorter and distinct C-terminus compared to isoform 2.
      Source sequence(s)
      AC157761, AC175379, AC242405
      UniProtKB/TrEMBL
      A0A2Z2CEU0, B7ZN98
      Conserved Domains (10) summary
      cd04011
      Location:250361
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:9591096
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:417566
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:14731596
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:17131846
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:842916
      FerB; FerB (NUC096) domain
      pfam08151
      Location:359409
      FerI; FerI (NUC094) domain
      pfam16165
      Location:18561972
      Ferlin_C; Ferlin C-terminus
      cl14603
      Location:11421219
      C2; C2 domain
    4. NM_031875.2NP_114081.2  otoferlin isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).
      Source sequence(s)
      AC175379, AK033317, AK046460, AK147256
      Consensus CDS
      CCDS19157.1
      UniProtKB/Swiss-Prot
      A3KLM3, B2RWU0, Q8CCE7, Q9ESF1, Q9ESF2
      UniProtKB/TrEMBL
      E9PYR6
      Related
      ENSMUSP00000073803.7, ENSMUST00000074171.10
      Conserved Domains (9) summary
      cd04011
      Location:250361
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:9591096
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:417566
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:14931616
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:17331866
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:842916
      FerB; FerB (NUC096) domain
      pfam08151
      Location:359409
      FerI; FerI (NUC094) domain
      pfam16165
      Location:18761994
      Ferlin_C; Ferlin C-terminus

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      30524410..30620073 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006504206.4XP_006504269.1  otoferlin isoform X2

      UniProtKB/Swiss-Prot
      A3KLM3, B2RWU0, Q8CCE7, Q9ESF1, Q9ESF2
      Conserved Domains (9) summary
      cd04011
      Location:250361
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:9591096
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:417566
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:14931616
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:17331866
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:842916
      FerB; FerB (NUC096) domain
      pfam08151
      Location:359409
      FerI; FerI (NUC094) domain
      pfam16165
      Location:18761994
      Ferlin_C; Ferlin C-terminus
    2. XM_006504209.5XP_006504272.1  otoferlin isoform X5

      UniProtKB/Swiss-Prot
      A3KLM3, B2RWU0, Q8CCE7, Q9ESF1, Q9ESF2
      Conserved Domains (9) summary
      cd04011
      Location:73184
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:782919
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:240389
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:13161439
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08374
      Location:15561689
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:665739
      FerB; FerB (NUC096) domain
      pfam08151
      Location:182232
      FerI; FerI (NUC094) domain
      pfam16165
      Location:16991817
      Ferlin_C; Ferlin C-terminus
      cl14603
      Location:9651042
      C2; C2 domain
    3. XM_017321186.2XP_017176675.1  otoferlin isoform X3

      UniProtKB/Swiss-Prot
      A3KLM3, B2RWU0, Q8CCE7, Q9ESF1, Q9ESF2
      Conserved Domains (9) summary
      cd04011
      Location:250361
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:9591096
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:417566
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:14931616
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:17331866
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:842916
      FerB; FerB (NUC096) domain
      pfam08151
      Location:359409
      FerI; FerI (NUC094) domain
      pfam16165
      Location:18761944
      Ferlin_C; Ferlin C-terminus
    4. XM_017321185.2XP_017176674.1  otoferlin isoform X1

      UniProtKB/Swiss-Prot
      A3KLM3, B2RWU0, Q8CCE7, Q9ESF1, Q9ESF2
      UniProtKB/TrEMBL
      E9PYR6
      Conserved Domains (9) summary
      cd04011
      Location:250361
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:9591096
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:417566
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:14931616
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:17331866
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:842916
      FerB; FerB (NUC096) domain
      pfam08151
      Location:359409
      FerI; FerI (NUC094) domain
      pfam16165
      Location:18761994
      Ferlin_C; Ferlin C-terminus
    5. XM_006504208.5XP_006504271.1  otoferlin isoform X4

      UniProtKB/Swiss-Prot
      A3KLM3, B2RWU0, Q8CCE7, Q9ESF1, Q9ESF2
      Conserved Domains (9) summary
      cd04011
      Location:250361
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:9591096
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:417566
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:14931616
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:17331866
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:842916
      FerB; FerB (NUC096) domain
      pfam08151
      Location:359409
      FerI; FerI (NUC094) domain
      pfam16165
      Location:18761938
      Ferlin_C; Ferlin C-terminus
    6. XM_011240802.3XP_011239104.1  otoferlin isoform X6

      Conserved Domains (6) summary
      cd04011
      Location:250361
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:9591096
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:417566
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd08373
      Location:3130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      pfam08150
      Location:842916
      FerB; FerB (NUC096) domain
      pfam08151
      Location:359409
      FerI; FerI (NUC094) domain

    RNA

    1. XR_001784761.3 RNA Sequence

    2. XR_376842.4 RNA Sequence

    3. XR_376841.4 RNA Sequence