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otofa otoferlin a [ Danio rerio (zebrafish) ]

Gene ID: 557476, updated on 4-Jan-2025

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, Jan 2025]
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
    UniProtKB/TrEMBL
    A0A8M9P2M0
    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, A0A8M9P2M0
    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, A0A8M9P2M0
    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, A0A8M9P2M0
    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
    A0A8M9P2M0, 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, A0A8M9P2M0
    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, A0A8M9P2M0
    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, A0A8M9P2M0
    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, A0A8M9P2M0
    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, A0A8M9P2M0, 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, A0A8M9P2M0
    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
    A0A8M9P2M0, 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

    UniProtKB/Swiss-Prot
    Q5SPC5
    UniProtKB/TrEMBL
    A0A8M9P2M0
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5SPC5.1 GenPept UniProtKB/Swiss-Prot:Q5SPC5

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