Otof otoferlin [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Otofprovided by RGD
Official Full Name: otoferlinprovided by RGD
Primary source: RGD:620646
See related: EnsemblRapid:ENSRNOG00000009967 AllianceGenome:RGD:620646
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable AP-2 adaptor complex binding activity and calcium ion binding activity. Involved in cochlea development. Located in apical part of cell and basal part of cell. Biomarker of hypothyroidism. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness 9. Orthologous to human OTOF (otoferlin). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Brain (RPKM 20.4), Adrenal (RPKM 2.2) and 1 other tissue See more
Orthologs: human mouse all
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Genomic context

Location:: 6q14

Exon count:: 48

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (31647869..31744476)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (25928018..26024631)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (27328343..27424864)

Chromosome 6 - NC_086024.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

otoferlin, through GAD65, modulates GABAergic activity.
Title: Function coupling of otoferlin with GAD65 acts to modulate GABAergic activity.
a direct role for otoferlin in exocytosis and modulation of calcium-dependent membrane fusion
Title: Calcium regulates molecular interactions of otoferlin with soluble NSF attachment protein receptor (SNARE) proteins required for hair cell exocytosis.
otoferlin-AP-2 interaction drives Ca(2+)- and stimulus-dependent compensating clathrin-mediated endocytosis in mature inner hair
Title: Otoferlin couples to clathrin-mediated endocytosis in mature cochlear inner hair cells.
Otof CA domain differs structurally and functionally from other C(2) domains
Title: The crystal structure of the C₂A domain of otoferlin reveals an unconventional top loop region.
Using a rodent cochlear cDNA library Rab8b is identified as an interacting partner of otoferlin.
Title: Rab8b GTPase, a protein transport regulator, is an interacting partner of otoferlin, defective in a human autosomal recessive deafness form.
Otoferlin mRNA and protein was detected in mature outer hair cells of low-frequency processing cochlear turns and in auditory nerve fibres. In outer, inner and vestibular hair cells
Title: Differential expression of otoferlin in brain, vestibular system, immature and mature cochlea of the rat.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

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	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	ISO Inferred from Sequence Orthology 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
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cochlea development	IEP Inferred from Expression Pattern more info	PubMed
involved_in plasma membrane organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in sensory perception of sound	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within synaptic vesicle exocytosis	ISO Inferred from Sequence Orthology more info
involved_in synaptic vesicle exocytosis	ISO Inferred from Sequence Orthology more info
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 priming	ISO Inferred from Sequence Orthology more info
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	IDA Inferred from Direct Assay more info	PubMed
located_in basal part of cell	IDA Inferred from Direct Assay more info	PubMed
located_in basolateral plasma membrane	IEA Inferred from Electronic Annotation more info
located_in cell projection	IEA Inferred from Electronic Annotation more info
is_active_in cochlear hair cell ribbon synapse	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in 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	ISO Inferred from Sequence Orthology more info
is_active_in synaptic vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in synaptic vesicle membrane	ISO Inferred from Sequence Orthology more info
located_in synaptic vesicle membrane	ISO Inferred from Sequence Orthology 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)

NM_001276720.1 → NP_001263649.1 otoferlin

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006

UniProtKB/TrEMBL

A0A0G2K867, A6HAD6

Related

ENSRNOP00000074490.1, ENSRNOT00000091159.3

Conserved Domains (10) summary

cd04011
Location:251 → 362

C2B_Ferlin; C2 domain second repeat in Ferlin

cd04017
Location:960 → 1097

C2D_Ferlin; C2 domain fourth repeat in Ferlin

cd04018
Location:418 → 567

C2C_Ferlin; C2 domain third repeat in Ferlin

cd04037
Location:1494 → 1617

C2E_Ferlin; C2 domain fifth repeat in Ferlin

cd08373
Location:3 → 130

C2A_Ferlin; C2 domain first repeat in Ferlin

cd08374
Location:1734 → 1867

C2F_Ferlin; C2 domain sixth repeat in Ferlin

pfam08150
Location:843 → 917

FerB; FerB (NUC096) domain

pfam08151
Location:360 → 410

FerI; FerI (NUC094) domain

pfam16165
Location:1877 → 1963

Ferlin_C; Ferlin C-terminus

cl14603
Location:1143 → 1220

C2; C2 domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086024.1 Reference GRCr8

Range

31647869..31744476

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063262553.1 → XP_063118623.1 otoferlin isoform X2

UniProtKB/TrEMBL

A6HAD6
XM_063262552.1 → XP_063118622.1 otoferlin isoform X1

UniProtKB/TrEMBL

A6HAD6
XM_006239833.4 → XP_006239895.1 otoferlin isoform X5

See identical proteins and their annotated locations for XP_006239895.1

UniProtKB/Swiss-Prot

Q9ERC5

UniProtKB/TrEMBL

A6HAD6

Related

ENSRNOP00000046997.2, ENSRNOT00000044278.6

Conserved Domains (10) summary

cd04011
Location:266 → 377

C2B_Ferlin; C2 domain second repeat in Ferlin

cd04017
Location:975 → 1112

C2D_Ferlin; C2 domain fourth repeat in Ferlin

cd04018
Location:433 → 582

C2C_Ferlin; C2 domain third repeat in Ferlin

cd04037
Location:1489 → 1612

C2E_Ferlin; C2 domain fifth repeat in Ferlin

cd08373
Location:3 → 130

C2A_Ferlin; C2 domain first repeat in Ferlin

cd08374
Location:1729 → 1862

C2F_Ferlin; C2 domain sixth repeat in Ferlin

pfam08150
Location:858 → 932

FerB; FerB (NUC096) domain

pfam08151
Location:375 → 425

FerI; FerI (NUC094) domain

pfam16165
Location:1872 → 1988

Ferlin_C; Ferlin C-terminus

cl14603
Location:1158 → 1235

C2; C2 domain
XM_039113005.2 → XP_038968933.1 otoferlin isoform X2

UniProtKB/TrEMBL

A6HAD6

Related

ENSRNOP00000110964.1, ENSRNOT00000124771.1

Conserved Domains (9) summary

cd04011
Location:266 → 377

C2B_Ferlin; C2 domain second repeat in Ferlin

cd04017
Location:975 → 1112

C2D_Ferlin; C2 domain fourth repeat in Ferlin

cd04018
Location:433 → 582

C2C_Ferlin; C2 domain third repeat in Ferlin

cd04037
Location:1509 → 1632

C2E_Ferlin; C2 domain fifth repeat in Ferlin

cd08373
Location:3 → 130

C2A_Ferlin; C2 domain first repeat in Ferlin

cd08374
Location:1749 → 1882

C2F_Ferlin; C2 domain sixth repeat in Ferlin

pfam08150
Location:857 → 932

FerB; FerB (NUC096) domain

pfam08151
Location:375 → 425

FerI; FerI (NUC094) domain

pfam16165
Location:1892 → 1980

Ferlin_C; Ferlin C-terminus
XM_039113006.2 → XP_038968934.1 otoferlin isoform X2

UniProtKB/TrEMBL

A6HAD6

Conserved Domains (9) summary

cd04011
Location:266 → 377

C2B_Ferlin; C2 domain second repeat in Ferlin

cd04017
Location:975 → 1112

C2D_Ferlin; C2 domain fourth repeat in Ferlin

cd04018
Location:433 → 582

C2C_Ferlin; C2 domain third repeat in Ferlin

cd04037
Location:1509 → 1632

C2E_Ferlin; C2 domain fifth repeat in Ferlin

cd08373
Location:3 → 130

C2A_Ferlin; C2 domain first repeat in Ferlin

cd08374
Location:1749 → 1882

C2F_Ferlin; C2 domain sixth repeat in Ferlin

pfam08150
Location:857 → 932

FerB; FerB (NUC096) domain

pfam08151
Location:375 → 425

FerI; FerI (NUC094) domain

pfam16165
Location:1892 → 1980

Ferlin_C; Ferlin C-terminus
XM_063262557.1 → XP_063118627.1 otoferlin isoform X6

UniProtKB/TrEMBL

A6HAD6
XM_063262555.1 → XP_063118625.1 otoferlin isoform X3

UniProtKB/TrEMBL

A0A0G2K867, A6HAD6
XM_063262556.1 → XP_063118626.1 otoferlin isoform X4

UniProtKB/TrEMBL

A6HAD6
XM_017594387.3 → XP_017449876.1 otoferlin isoform X8

UniProtKB/TrEMBL

A6HAD6
XM_063262558.1 → XP_063118628.1 otoferlin isoform X7

UniProtKB/TrEMBL

A6HAD6
XM_063262559.1 → XP_063118629.1 otoferlin isoform X9