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    otofa otoferlin a [ Danio rerio (zebrafish) ]

    Gene ID: 557476, updated on 2-Nov-2024

    Summary

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    Official Symbol
    otofaprovided by ZNC
    Official Full Name
    otoferlin aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-7778
    See related
    Ensembl:ENSDARG00000030832 AllianceGenome:ZFIN:ZDB-GENE-030131-7778
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    otof; fj34b10; wu:fj34b10; si:dkey-181f18.3
    Summary
    Predicted to enable AP-2 adaptor complex binding activity and calcium ion binding activity. Acts upstream of or within several processes, including response to auditory stimulus; sensory perception of sound; and startle response. Predicted to be located in several cellular components, including Golgi membrane; basolateral plasma membrane; and endoplasmic reticulum membrane. Predicted to be active in presynaptic active zone membrane and synaptic vesicle membrane. Is expressed in nervous system; otic vesicle; and trigeminal placode. 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]
    Orthologs
    human mouse all
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    Genomic context

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    See otofa in Genome Data Viewer
    Location:
    chromosome: 20
    Exon count:
    50
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 20 NC_007131.7 (31076259..31212903)
    105 previous assembly GRCz10 (GCF_000002035.5) 20 NC_007131.6 (31173357..31310109)

    Chromosome 20 - NC_007131.7Genomic Context describing neighboring genes Neighboring gene fibronectin type III domain containing 1 Neighboring gene ciliary microtubule inner protein 2C Neighboring gene protein disulfide isomerase family A, member 6 Neighboring gene hippocalcin-like 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Identification of the hair cell soma-1 antigen, HCS-1, as otoferlin. Goodyear RJ, et al. J Assoc Res Otolaryngol, 2010 Dec. PMID 20809368, Free PMC Article
    2. Balancing cell numbers during organogenesis: Six1a differentially affects neurons and sensory hair cells in the inner ear. Bricaud O, et al. Dev Biol, 2011 Sep 1. PMID 21745464, Free PMC Article
    3. Otoferlin deficiency in zebrafish results in defects in balance and hearing: rescue of the balance and hearing phenotype with full-length and truncated forms of mouse otoferlin. Chatterjee P, et al. Mol Cell Biol, 2015 Mar. PMID 25582200, Free PMC Article
    4. Clarin-1 acts as a modulator of mechanotransduction activity and presynaptic ribbon assembly. Ogun O, et al. J Cell Biol, 2014 Nov 10. PMID 25365995, Free PMC Article
    5. Loss of Rbm24a causes defective hair cell development in the zebrafish inner ear and neuromasts. Cheng X, et al. J Genet Genomics, 2020 Jul 20. PMID 33036919

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Otoferlin Depletion Results in Abnormal Synaptic Ribbons and Altered Intracellular Calcium Levels in Zebrafish.
      Title: Otoferlin Depletion Results in Abnormal Synaptic Ribbons and Altered Intracellular Calcium Levels in Zebrafish.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables AP-2 adaptor complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within neuromuscular process controlling balance IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in plasma membrane organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within response to auditory stimulus IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within sensory perception of sound IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within startle response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in synaptic vesicle exocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in synaptic vesicle priming IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptic vesicle recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within synaptic vesicle recycling IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    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 cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma 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 synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in synaptic vesicle membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    otoferlin
    Names
    fer-1-like protein 2

    NCBI Reference Sequences (RefSeq)

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    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_001030112.2 → NP_001025283.1  otoferlin

      See identical proteins and their annotated locations for NP_001025283.1

      Status: PROVISIONAL

      Source sequence(s)
      AL929014, BX000361
      UniProtKB/Swiss-Prot
      Q5SPC5
      Related
      ENSDARP00000007932.8, ENSDART00000008840.9
      Conserved Domains (9) summary
      cd04011
      Location:256 → 367
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:968 → 1105
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:423 → 572
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:1488 → 1611
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3 → 130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:1728 → 1861
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:851 → 925
      FerB; FerB (NUC096) domain
      pfam08151
      Location:365 → 415
      FerI; FerI (NUC094) domain
      pfam16165
      Location:1871 → 1987
      Ferlin_C; Ferlin C-terminus

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007131.7 Reference GRCz11 Primary Assembly

      Range
      31076259..31212903
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009294732.4 → XP_009293007.1  otoferlin isoform X1

      UniProtKB/TrEMBL
      A0A8M3AT93
      Conserved Domains (9) summary
      cd04011
      Location:256 → 367
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:968 → 1105
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:423 → 572
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:1540 → 1663
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3 → 130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:1780 → 1913
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:851 → 925
      FerB; FerB (NUC096) domain
      pfam08151
      Location:365 → 415
      FerI; FerI (NUC094) domain
      pfam16165
      Location:1923 → 2035
      Ferlin_C; Ferlin C-terminus

    2. XM_009294733.4 → XP_009293008.1  otoferlin isoform X2

      UniProtKB/TrEMBL
      A0A8M3AKW3
      Conserved Domains (9) summary
      cd04011
      Location:256 → 367
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:968 → 1105
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:423 → 572
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:1540 → 1663
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3 → 130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:1780 → 1913
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:851 → 925
      FerB; FerB (NUC096) domain
      pfam08151
      Location:365 → 415
      FerI; FerI (NUC094) domain
      pfam16165
      Location:1923 → 2035
      Ferlin_C; Ferlin C-terminus

    3. XM_009294738.4 → XP_009293013.1  otoferlin isoform X6

      UniProtKB/TrEMBL
      A0A8M3AWA4
      Conserved Domains (9) summary
      cd04011
      Location:256 → 367
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:968 → 1105
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:423 → 572
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:1530 → 1653
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3 → 130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:1770 → 1903
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:851 → 925
      FerB; FerB (NUC096) domain
      pfam08151
      Location:365 → 415
      FerI; FerI (NUC094) domain
      pfam16165
      Location:1913 → 2025
      Ferlin_C; Ferlin C-terminus

    4. XM_021468441.2 → XP_021324116.1  otoferlin isoform X5

      UniProtKB/TrEMBL
      A0A8M9PPD5
      Conserved Domains (9) summary
      cd04011
      Location:256 → 367
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:968 → 1105
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:423 → 572
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:1530 → 1653
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3 → 130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:1770 → 1903
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:851 → 925
      FerB; FerB (NUC096) domain
      pfam08151
      Location:365 → 415
      FerI; FerI (NUC094) domain
      pfam16165
      Location:1913 → 2031
      Ferlin_C; Ferlin C-terminus

    5. XM_009294740.4 → XP_009293015.1  otoferlin isoform X8

      UniProtKB/TrEMBL
      A0A8M3AKW9
      Conserved Domains (9) summary
      cd04011
      Location:256 → 367
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:968 → 1105
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:423 → 572
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:1512 → 1635
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3 → 130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:1752 → 1885
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:851 → 925
      FerB; FerB (NUC096) domain
      pfam08151
      Location:365 → 415
      FerI; FerI (NUC094) domain
      pfam16165
      Location:1895 → 2007
      Ferlin_C; Ferlin C-terminus

    6. XM_009294739.4 → XP_009293014.1  otoferlin isoform X7

      UniProtKB/TrEMBL
      A0A8M3AT99
      Conserved Domains (9) summary
      cd04011
      Location:256 → 367
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:968 → 1105
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:423 → 572
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:1516 → 1639
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3 → 130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:1756 → 1889
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:851 → 925
      FerB; FerB (NUC096) domain
      pfam08151
      Location:365 → 415
      FerI; FerI (NUC094) domain
      pfam16165
      Location:1899 → 2011
      Ferlin_C; Ferlin C-terminus

    7. XM_009294742.4 → XP_009293017.1  otoferlin isoform X9

      UniProtKB/TrEMBL
      A0A8M3B468
      Conserved Domains (9) summary
      cd04011
      Location:256 → 367
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:968 → 1105
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:423 → 572
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:1488 → 1611
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3 → 130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:1728 → 1861
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:851 → 925
      FerB; FerB (NUC096) domain
      pfam08151
      Location:365 → 415
      FerI; FerI (NUC094) domain
      pfam16165
      Location:1871 → 1983
      Ferlin_C; Ferlin C-terminus

    8. XM_009294734.4 → XP_009293009.1  otoferlin isoform X3

      UniProtKB/TrEMBL
      A0A8M3B462
      Conserved Domains (9) summary
      cd04011
      Location:256 → 367
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:968 → 1105
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:423 → 572
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:1540 → 1663
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3 → 130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:1780 → 1913
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:851 → 925
      FerB; FerB (NUC096) domain
      pfam08151
      Location:365 → 415
      FerI; FerI (NUC094) domain
      pfam16165
      Location:1923 → 2039
      Ferlin_C; Ferlin C-terminus

    9. XM_009294744.4 → XP_009293019.1  otoferlin isoform X12

      UniProtKB/TrEMBL
      A0A8M3ALL1, X1WB77
      Related
      ENSDARP00000118166.2, ENSDART00000136255.4
      Conserved Domains (9) summary
      cd04011
      Location:256 → 367
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:968 → 1105
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:423 → 572
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:1488 → 1611
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3 → 130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:1728 → 1861
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:851 → 925
      FerB; FerB (NUC096) domain
      pfam08151
      Location:365 → 415
      FerI; FerI (NUC094) domain
      pfam16165
      Location:1871 → 1987
      Ferlin_C; Ferlin C-terminus

    10. XM_009294736.4 → XP_009293011.1  otoferlin isoform X4

      See identical proteins and their annotated locations for XP_009293011.1

      UniProtKB/TrEMBL
      A0A8M3ALK6
      Conserved Domains (9) summary
      cd04011
      Location:256 → 367
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:968 → 1105
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:423 → 572
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:1540 → 1663
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3 → 130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:1780 → 1913
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:851 → 925
      FerB; FerB (NUC096) domain
      pfam08151
      Location:365 → 415
      FerI; FerI (NUC094) domain
      pfam16165
      Location:1923 → 2039
      Ferlin_C; Ferlin C-terminus

    11. XM_021468443.2 → XP_021324118.1  otoferlin isoform X11

      UniProtKB/TrEMBL
      A0A8M9PBS5
      Conserved Domains (9) summary
      cd04011
      Location:256 → 367
      C2B_Ferlin; C2 domain second repeat in Ferlin
      cd04017
      Location:968 → 1105
      C2D_Ferlin; C2 domain fourth repeat in Ferlin
      cd04018
      Location:423 → 572
      C2C_Ferlin; C2 domain third repeat in Ferlin
      cd04037
      Location:1516 → 1639
      C2E_Ferlin; C2 domain fifth repeat in Ferlin
      cd08373
      Location:3 → 130
      C2A_Ferlin; C2 domain first repeat in Ferlin
      cd08374
      Location:1756 → 1889
      C2F_Ferlin; C2 domain sixth repeat in Ferlin
      pfam08150
      Location:851 → 925
      FerB; FerB (NUC096) domain
      pfam08151
      Location:365 → 415
      FerI; FerI (NUC094) domain
      pfam16165
      Location:1899 → 2017
      Ferlin_C; Ferlin C-terminus

    12. XM_068215466.1 → XP_068071567.1  otoferlin isoform X10

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5SPC5.1 GenPept UniProtKB/Swiss-Prot:Q5SPC5

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