Otof (otoferlin) - Rat Genome Database
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Gene: Otof (otoferlin) Rattus norvegicus
Analyze
Symbol: Otof
Name: otoferlin
RGD ID: 620646
Description: Predicted to have AP-2 adaptor complex binding activity and calcium ion binding activity. Involved in cochlea development. Localizes to several cellular components, including apical part of cell; basal part of cell; and endoplasmic reticulum. Biomarker of hypothyroidism. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness 9. Orthologous to human OTOF (otoferlin); PARTICIPATES IN auditory mechanotransduction pathway; INTERACTS WITH 6-propyl-2-thiouracil; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: fer-1-like protein 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2625,928,018 - 26,024,631 (+)NCBI
Rnor_6.0 Ensembl627,328,406 - 27,424,864 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0627,328,343 - 27,424,864 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0637,140,727 - 37,237,155 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4625,912,607 - 26,008,137 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1626,003,001 - 26,007,276 (+)NCBI
Celera625,406,310 - 25,502,501 (+)NCBICelera
Cytogenetic Map6q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Brandt N, etal., J Neurosci. 2007 Mar 21;27(12):3174-86.
2. Duncker SV, etal., J Neurosci. 2013 May 29;33(22):9508-19. doi: 10.1523/JNEUROSCI.5689-12.2013.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Heidrych P, etal., Hum Mol Genet. 2008 Dec 1;17(23):3814-21. doi: 10.1093/hmg/ddn279. Epub 2008 Sep 4.
5. Longo-Guess C, etal., Hear Res. 2007 Dec;234(1-2):21-8. Epub 2007 Sep 29.
6. Mahdieh N, etal., Int J Pediatr Otorhinolaryngol. 2012 Nov;76(11):1610-5. doi: 10.1016/j.ijporl.2012.07.030. Epub 2012 Aug 18.
7. Marlin S, etal., Biochem Biophys Res Commun. 2010 Apr 9;394(3):737-42. doi: 10.1016/j.bbrc.2010.03.062. Epub 2010 Mar 16.
8. Matsunaga T, etal., Clin Genet. 2012 Nov;82(5):425-32. doi: 10.1111/j.1399-0004.2012.01897.x. Epub 2012 Jun 1.
9. MGD data from the GO Consortium
10. Migliosi V, etal., J Med Genet. 2002 Jul;39(7):502-6.
11. NCBI rat LocusLink and RefSeq merged data July 26, 2002
12. OMIM Disease Annotation Pipeline
13. Online Mendelian Inheritance in Man, OMIM (TM).
14. RGD automated data pipeline
15. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. RGD automated import pipeline for gene-chemical interactions
17. RGD comprehensive gene curation
18. Rodriguez-Ballesteros M, etal., Hum Mutat. 2003 Dec;22(6):451-6.
19. Roux I, etal., Cell. 2006 Oct 20;127(2):277-89.
20. Safieddine S, etal., Annu Rev Neurosci. 2012;35:509-28. doi: 10.1146/annurev-neuro-061010-113705.
21. Schug N, etal., Eur J Neurosci. 2006 Dec;24(12):3372-80.
22. Tekin M, etal., Am J Med Genet A. 2005 Sep 15;138(1):6-10.
23. Yasunaga S, etal., Am J Hum Genet 2000 Sep;67(3):591-600. Epub 2000 Jul 19.
24. Yasunaga S, etal., Nat Genet. 1999 Apr;21(4):363-9.
Additional References at PubMed
PMID:15632090   PMID:18287496   PMID:20562868   PMID:21216247   PMID:24478316   PMID:25609709   PMID:25701657   PMID:27458190  


Genomics

Comparative Map Data
Otof
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2625,928,018 - 26,024,631 (+)NCBI
Rnor_6.0 Ensembl627,328,406 - 27,424,864 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0627,328,343 - 27,424,864 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0637,140,727 - 37,237,155 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4625,912,607 - 26,008,137 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1626,003,001 - 26,007,276 (+)NCBI
Celera625,406,310 - 25,502,501 (+)NCBICelera
Cytogenetic Map6q14NCBI
OTOF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl226,457,203 - 26,558,756 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl226,457,203 - 26,558,698 (-)EnsemblGRCh38hg38GRCh38
GRCh38226,457,203 - 26,558,756 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37226,680,071 - 26,781,566 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh37226,680,071 - 26,781,624 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36226,533,575 - 26,635,070 (-)NCBINCBI36hg18NCBI36
Build 34226,591,722 - 26,612,561NCBI
Celera226,523,620 - 26,625,188 (-)NCBI
Cytogenetic Map2p23.3NCBI
HuRef226,419,277 - 26,520,993 (-)NCBIHuRef
CHM1_1226,610,235 - 26,711,604 (-)NCBICHM1_1
Otof
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39530,524,410 - 30,620,073 (-)NCBIGRCm39mm39
GRCm38530,367,066 - 30,462,730 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl530,367,062 - 30,461,932 (-)EnsemblGRCm38mm10GRCm38
MGSCv37530,669,351 - 30,764,305 (-)NCBIGRCm37mm9NCBIm37
MGSCv36530,646,656 - 30,738,483 (-)NCBImm8
Celera527,843,111 - 27,940,114 (-)NCBICelera
Cytogenetic Map5B1NCBI
Otof
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554698,481,231 - 8,569,265 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554698,480,099 - 8,569,215 (-)NCBIChiLan1.0ChiLan1.0
OTOF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A26,548,972 - 26,566,606 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A26,546,959 - 26,647,278 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A26,454,010 - 26,555,642 (-)NCBIMhudiblu_PPA_v0panPan3
OTOF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1720,518,813 - 20,614,750 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11720,518,480 - 20,619,713 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Otof
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364935,916,113 - 5,999,867 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OTOF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3112,478,027 - 112,581,100 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13112,478,188 - 112,581,105 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23119,511,861 - 119,546,848 (-)NCBISscrofa10.2Sscrofa10.2susScr3
OTOF
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11481,080,077 - 81,187,769 (+)NCBI
ChlSab1.1 Ensembl1481,080,462 - 81,186,697 (+)Ensembl
Otof
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247388,599,815 - 8,690,382 (-)NCBI

Position Markers
D6Got19  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0627,388,742 - 27,388,896NCBIRnor6.0
Rnor_5.0637,201,033 - 37,201,187UniSTSRnor5.0
RGSC_v3.4625,972,823 - 25,972,978RGDRGSC3.4
RGSC_v3.4625,972,824 - 25,972,978UniSTSRGSC3.4
RGSC_v3.1625,975,777 - 25,975,931RGD
Celera625,466,376 - 25,466,530UniSTS
RH 3.4 Map694.9RGD
RH 3.4 Map694.9UniSTS
RH 2.0 Map6226.2RGD
Cytogenetic Map6q14UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6135623029Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6135623029Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6135623029Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6135623029Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6135623029Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6141917988Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6142388212Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6142388212Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142388212Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6142388212Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6142388212Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6143665660Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6143665660Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6143665660Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6144015370Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6144570292Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
1359023Bp272Blood pressure QTL 2722.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6112039328706721Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6112039346120393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)71017386255173862Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295834367603Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295857516539Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)61941788764417887Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62151530265784818Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:63
Count of miRNA genes:57
Interacting mature miRNAs:63
Transcripts:ENSRNOT00000044278
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium 7
Low 2 51 6
Below cutoff 2 4 6 1 3 1 4 4 6 24 11 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000044278   ⟹   ENSRNOP00000046997
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl627,328,515 - 27,424,052 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091159   ⟹   ENSRNOP00000074490
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl627,328,406 - 27,424,864 (+)Ensembl
RefSeq Acc Id: NM_001276720   ⟹   NP_001263649
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2625,928,055 - 26,024,631 (+)NCBI
Rnor_6.0627,328,406 - 27,424,864 (+)NCBI
Rnor_5.0637,140,727 - 37,237,155 (+)NCBI
Celera625,406,310 - 25,502,501 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006239833   ⟹   XP_006239895
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2625,928,020 - 26,024,631 (+)NCBI
Rnor_6.0627,328,343 - 27,424,864 (+)NCBI
Rnor_5.0637,140,727 - 37,237,155 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008764534   ⟹   XP_008762756
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0627,328,343 - 27,422,131 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008764535   ⟹   XP_008762757
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0627,328,343 - 27,424,864 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594387   ⟹   XP_017449876
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2625,928,020 - 26,024,631 (+)NCBI
Rnor_6.0627,328,343 - 27,424,864 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594388   ⟹   XP_017449877
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0627,385,801 - 27,422,131 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039113005   ⟹   XP_038968933
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2625,928,020 - 26,024,631 (+)NCBI
RefSeq Acc Id: XM_039113006   ⟹   XP_038968934
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2625,928,020 - 26,024,631 (+)NCBI
RefSeq Acc Id: XM_039113008   ⟹   XP_038968936
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2625,928,020 - 26,024,631 (+)NCBI
RefSeq Acc Id: XM_039113009   ⟹   XP_038968937
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2625,928,164 - 26,024,631 (+)NCBI
RefSeq Acc Id: XM_039113010   ⟹   XP_038968938
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2625,998,160 - 26,024,631 (+)NCBI
RefSeq Acc Id: XM_039113011   ⟹   XP_038968939
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2625,928,018 - 26,011,217 (+)NCBI
RefSeq Acc Id: XR_005505593
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2625,928,020 - 26,019,853 (+)NCBI
RefSeq Acc Id: XR_005505594
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2625,928,018 - 26,012,620 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001263649   ⟸   NM_001276720
- UniProtKB: A0A0G2K867 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239895   ⟸   XM_006239833
- Peptide Label: isoform X6
- UniProtKB: Q9ERC5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008762757   ⟸   XM_008764535
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008762756   ⟸   XM_008764534
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017449876   ⟸   XM_017594387
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017449877   ⟸   XM_017594388
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000074490   ⟸   ENSRNOT00000091159
RefSeq Acc Id: ENSRNOP00000046997   ⟸   ENSRNOT00000044278
RefSeq Acc Id: XP_038968939   ⟸   XM_039113011
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038968933   ⟸   XM_039113005
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968934   ⟸   XM_039113006
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968936   ⟸   XM_039113008
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038968937   ⟸   XM_039113009
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968938   ⟸   XM_039113010
- Peptide Label: isoform X4
Protein Domains
C2

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620646 AgrOrtholog
Ensembl Genes ENSRNOG00000009967 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000046997 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000074490 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044278 UniProtKB/Swiss-Prot
  ENSRNOT00000091159 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro C2_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2A_Ferlin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2B_Ferlin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2C_Ferlin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2D_Ferlin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2E_Ferlin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2F_Ferlin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FerIin_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ferlin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ferlin_B-domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ferlin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Otoferlin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84573 UniProtKB/TrEMBL
NCBI Gene 84573 ENTREZGENE
PANTHER PTHR12546 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12546:SF32 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam FerB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FerI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ferlin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00168 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Otof PhenoGen
PRINTS C2DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PS50004 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART FerB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FerI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K867 ENTREZGENE, UniProtKB/TrEMBL
  OTOF_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Otof  otoferlin      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Otof  otoferlin      Symbol and Name status set to provisional 70820 PROVISIONAL