Ophn1 (oligophrenin 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Ophn1 (oligophrenin 1) Rattus norvegicus
Analyze
Symbol: Ophn1
Name: oligophrenin 1
RGD ID: 1563435
Description: Enables ionotropic glutamate receptor binding activity. Involved in maintenance of postsynaptic specialization structure. Is active in glutamatergic synapse. Human ortholog(s) of this gene implicated in X-linked mental retardation with cerebellar hypoplasia and distinctive facial appearance. Orthologous to human OPHN1 (oligophrenin 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC688676; LOC688676; Oligophrenin-1; Opn1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X63,599,746 - 63,976,678 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX63,603,042 - 63,976,633 (-)Ensembl
Rnor_6.0X68,185,865 - 68,579,518 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX68,189,161 - 68,563,137 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X69,060,378 - 69,453,851 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X86,519,900 - 86,801,421 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX64,002,740 - 64,359,348 (-)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. Novel intragenic deletion in OPHN1 in a family causing XLMR with cerebellar hypoplasia and distinctive facial appearance. Al-Owain M, etal., Clin Genet. 2011 Apr;79(4):363-70. doi: 10.1111/j.1399-0004.2010.01462.x.
2. Oligophrenin 1 (OPHN1) gene mutation causes syndromic X-linked mental retardation with epilepsy, rostral ventricular enlargement and cerebellar hypoplasia. Bergmann C, etal., Brain. 2003 Jul;126(Pt 7):1537-44. Epub 2003 May 21.
3. Delineation of the clinical phenotype associated with OPHN1 mutations based on the clinical and neuropsychological evaluation of three families. Chabrol B, etal., Am J Med Genet A. 2005 Nov 1;138(4):314-7.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. The X-linked mental retardation protein oligophrenin-1 is required for dendritic spine morphogenesis. Govek EE, etal., Nat Neurosci. 2004 Apr;7(4):364-72. Epub 2004 Mar 14.
6. Deletion of the OPHN1 gene detected by aCGH. Madrigal I, etal., J Intellect Disabil Res. 2008 Mar;52(Pt 3):190-4. doi: 10.1111/j.1365-2788.2007.00997.x.
7. The Rho-linked mental retardation protein oligophrenin-1 controls synapse maturation and plasticity by stabilizing AMPA receptors. Nadif Kasri N, etal., Genes Dev. 2009 Jun 1;23(11):1289-302.
8. The X-linked mental retardation protein OPHN1 interacts with Homer1b/c to control spine endocytic zone positioning and expression of synaptic potentiation. Nakano-Kobayashi A, etal., J Neurosci. 2014 Jun 25;34(26):8665-71. doi: 10.1523/JNEUROSCI.0894-14.2014.
9. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
10. Mutations in the oligophrenin-1 gene (OPHN1) cause X linked congenital cerebellar hypoplasia. Philip N, etal., J Med Genet. 2003 Jun;40(6):441-6.
11. Insertion of 16 amino acids in the BAR domain of the oligophrenin 1 protein causes mental retardation and cerebellar hypoplasia in an Italian family. Pirozzi F, etal., Hum Mutat. 2011 Nov;32(11):E2294-307. doi: 10.1002/humu.21567. Epub 2011 Sep 14.
12. GOA pipeline RGD automated data pipeline
13. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
15. A novel in-frame deletion affecting the BAR domain of OPHN1 in a family with intellectual disability and hippocampal alterations. Santos-Rebou├žas CB, etal., Eur J Hum Genet. 2014 May;22(5):644-51. doi: 10.1038/ejhg.2013.216. Epub 2013 Oct 9.
16. A circadian clock in hippocampus is regulated by interaction between oligophrenin-1 and Rev-erbalpha. Valnegri P, etal., Nat Neurosci. 2011 Aug 28;14(10):1293-301. doi: 10.1038/nn.2911.
Additional References at PubMed
PMID:12932438   PMID:15026118   PMID:18954304   PMID:19481455   PMID:22891260   PMID:27160703  


Genomics

Comparative Map Data
Ophn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X63,599,746 - 63,976,678 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX63,603,042 - 63,976,633 (-)Ensembl
Rnor_6.0X68,185,865 - 68,579,518 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX68,189,161 - 68,563,137 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X69,060,378 - 69,453,851 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X86,519,900 - 86,801,421 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX64,002,740 - 64,359,348 (-)NCBICelera
Cytogenetic MapXq22NCBI
OPHN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X68,042,344 - 68,433,841 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 EnsemblX67,949,349 - 68,433,913 (-)EnsemblGRCh38hg38GRCh38
GRCh37X67,262,186 - 67,653,337 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X67,179,440 - 67,570,372 (-)NCBINCBI36hg18NCBI36
Build 34X67,045,735 - 67,436,668NCBI
CeleraX67,613,664 - 68,004,666 (-)NCBI
Cytogenetic MapXq12NCBI
HuRefX61,092,466 - 61,481,527 (-)NCBIHuRef
CHM1_1X67,154,622 - 67,546,029 (-)NCBICHM1_1
T2T-CHM13v2.0X66,475,136 - 66,866,981 (-)NCBI
Ophn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X97,597,886 - 97,934,691 (-)NCBIGRCm39mm39
GRCm39 EnsemblX97,597,883 - 97,934,631 (-)Ensembl
GRCm38X98,554,280 - 98,891,082 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX98,554,277 - 98,891,025 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X95,752,854 - 96,086,324 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X94,760,234 - 95,093,704 (-)NCBImm8
CeleraX85,501,536 - 85,832,824 (-)NCBICelera
Cytogenetic MapXC3NCBI
Ophn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554757,581,675 - 8,018,139 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554757,576,629 - 8,019,132 (-)NCBIChiLan1.0ChiLan1.0
OPHN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X67,354,364 - 67,740,003 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX67,359,364 - 67,739,114 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X57,288,297 - 57,674,685 (-)NCBIMhudiblu_PPA_v0panPan3
OPHN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X52,418,390 - 52,983,155 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX52,455,373 - 52,982,244 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX43,271,709 - 43,797,820 (-)NCBI
ROS_Cfam_1.0X53,420,053 - 53,943,003 (-)NCBI
ROS_Cfam_1.0 EnsemblX53,423,094 - 53,942,104 (-)Ensembl
UMICH_Zoey_3.1X51,391,501 - 51,917,738 (-)NCBI
UNSW_CanFamBas_1.0X52,722,901 - 53,243,080 (-)NCBI
UU_Cfam_GSD_1.0X52,643,831 - 53,170,125 (-)NCBI
Ophn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X49,111,728 - 49,477,619 (+)NCBI
SpeTri2.0NW_0049366356,966 - 243,209 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OPHN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX53,884,012 - 54,616,960 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X54,056,504 - 54,617,045 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X60,818,920 - 61,106,085 (-)NCBISscrofa10.2Sscrofa10.2susScr3
OPHN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X57,906,868 - 58,291,358 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 EnsemblX57,911,555 - 58,290,900 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660835,360,305 - 5,607,870 (-)NCBIVero_WHO_p1.0
Ophn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248911,908,044 - 2,425,144 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046248911,907,233 - 2,429,714 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
DXRat31  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X63,958,410 - 63,958,542 (+)MAPPERmRatBN7.2
Rnor_6.0X68,544,586 - 68,544,715NCBIRnor6.0
Rnor_5.0X69,418,921 - 69,419,050UniSTSRnor5.0
RGSC_v3.4X86,886,522 - 86,886,652RGDRGSC3.4
RGSC_v3.4X86,886,523 - 86,886,652UniSTSRGSC3.4
RGSC_v3.1X86,959,573 - 86,960,070RGD
CeleraX64,342,523 - 64,342,652UniSTS
RH 2.0 Map2115.6RGD
FHH x ACI MapX23.52RGD
Cytogenetic MapXq31UniSTS
PMC169877P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X63,886,820 - 63,887,358 (+)MAPPERmRatBN7.2
mRatBN7.2323,603,189 - 23,603,720 (+)MAPPERmRatBN7.2
Rnor_6.0324,171,597 - 24,172,127NCBIRnor6.0
Rnor_6.0X68,471,397 - 68,471,934NCBIRnor6.0
Rnor_5.0329,388,989 - 29,389,519UniSTSRnor5.0
Rnor_5.0X69,346,132 - 69,346,669UniSTSRnor5.0
RGSC_v3.4X86,814,796 - 86,815,333UniSTSRGSC3.4
RGSC_v3.4319,691,805 - 19,692,335UniSTSRGSC3.4
Celera322,015,742 - 22,016,272UniSTS
CeleraX64,275,723 - 64,276,260UniSTS
Cytogenetic Map3q22UniSTS
Cytogenetic MapXq31UniSTS
BE106637  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X63,603,196 - 63,603,360 (+)MAPPERmRatBN7.2
Rnor_6.0X68,189,316 - 68,189,479NCBIRnor6.0
Rnor_5.0X69,063,829 - 69,063,992UniSTSRnor5.0
RGSC_v3.4X86,520,055 - 86,520,218UniSTSRGSC3.4
CeleraX64,002,895 - 64,003,058UniSTS
Cytogenetic MapXq31UniSTS
AA998661  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X63,610,306 - 63,610,423 (+)MAPPERmRatBN7.2
Rnor_6.0X68,196,426 - 68,196,542NCBIRnor6.0
Rnor_5.0X69,070,939 - 69,071,055UniSTSRnor5.0
RGSC_v3.4X86,527,165 - 86,527,281UniSTSRGSC3.4
CeleraX64,010,005 - 64,010,121UniSTS
Cytogenetic MapXq31UniSTS
PMC305603P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X63,885,649 - 63,885,862 (+)MAPPERmRatBN7.2
mRatBN7.2357,847,231 - 57,847,443 (+)MAPPERmRatBN7.2
Rnor_6.0359,679,764 - 59,679,975NCBIRnor6.0
Rnor_6.0X68,470,226 - 68,470,438NCBIRnor6.0
Rnor_5.0366,153,408 - 66,153,619UniSTSRnor5.0
Rnor_5.0X69,344,961 - 69,345,173UniSTSRnor5.0
RGSC_v3.4X86,813,625 - 86,813,837UniSTSRGSC3.4
RGSC_v3.4355,476,205 - 55,476,416UniSTSRGSC3.4
Celera357,386,085 - 57,386,296UniSTS
CeleraX64,274,552 - 64,274,764UniSTS
Cytogenetic Map3q22UniSTS
Cytogenetic MapXq31UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
70221Bp56Blood pressure QTL 564.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X5704214165612192Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:302
Count of miRNA genes:193
Interacting mature miRNAs:221
Transcripts:ENSRNOT00000034772
Prediction methods:Microtar, Miranda, Pita
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 renal system reproductive system respiratory system appendage
High
Medium 38 3 2 1 1 68 13 22 11 1
Low 3 5 52 39 17 39 7 10 6 22 19 7
Below cutoff 2 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000034772   ⟹   ENSRNOP00000035867
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX63,603,042 - 63,976,633 (-)Ensembl
Rnor_6.0 EnsemblX68,189,161 - 68,563,137 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076193   ⟹   ENSRNOP00000068017
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX63,603,128 - 63,975,868 (-)Ensembl
Rnor_6.0 EnsemblX68,189,195 - 68,562,873 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076551
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX68,347,515 - 68,355,247 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076720   ⟹   ENSRNOP00000067984
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX68,561,685 - 68,562,301 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106069   ⟹   ENSRNOP00000096923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX63,609,699 - 63,976,633 (-)Ensembl
RefSeq Acc Id: NM_001107848   ⟹   NP_001101318
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X63,603,042 - 63,976,633 (-)NCBI
Rnor_6.0X68,189,161 - 68,563,137 (-)NCBI
Rnor_5.0X69,060,378 - 69,453,851 (-)NCBI
RGSC_v3.4X86,519,900 - 86,801,421 (-)RGD
CeleraX64,002,740 - 64,359,348 (-)RGD
Sequence:
RefSeq Acc Id: XM_006257072   ⟹   XP_006257134
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X63,603,076 - 63,976,678 (-)NCBI
Rnor_6.0X68,185,865 - 68,563,373 (-)NCBI
Rnor_5.0X69,060,378 - 69,453,851 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099689   ⟹   XP_038955617
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X63,599,746 - 63,771,763 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001101318 (Get FASTA)   NCBI Sequence Viewer  
  XP_006257134 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955617 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL95953 (Get FASTA)   NCBI Sequence Viewer  
  EDL95954 (Get FASTA)   NCBI Sequence Viewer  
  P0CAX5 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101318   ⟸   NM_001107848
- UniProtKB: P0CAX5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006257134   ⟸   XM_006257072
- Peptide Label: isoform X1
- UniProtKB: P0CAX5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000035867   ⟸   ENSRNOT00000034772
RefSeq Acc Id: ENSRNOP00000068017   ⟸   ENSRNOT00000076193
RefSeq Acc Id: ENSRNOP00000067984   ⟸   ENSRNOT00000076720
RefSeq Acc Id: XP_038955617   ⟸   XM_039099689
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000096923   ⟸   ENSRNOT00000106069
Protein Domains
PH   Rho-GAP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P0CAX5-F1-model_v2 AlphaFold P0CAX5 1-802 view protein structure

Transcriptome

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

Promoters
RGD ID:13701855
Promoter ID:EPDNEW_R12379
Type:single initiation site
Name:Ophn1_1
Description:oligophrenin 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X68,563,101 - 68,563,161EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 68475542 68475543 C T snv SBH/Ygl (RGD), SBH/Ygl (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563435 AgrOrtholog
BioCyc Gene G2FUF-2165 BioCyc
Ensembl Genes ENSRNOG00000026573 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000035867 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000096923.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034772 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000106069.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.555.10 UniProtKB/Swiss-Prot
  1.20.1270.60 UniProtKB/Swiss-Prot
  2.30.29.30 UniProtKB/Swiss-Prot
InterPro AH/BAR_dom_sf UniProtKB/Swiss-Prot
  PH-like_dom_sf UniProtKB/Swiss-Prot
  PH_domain UniProtKB/Swiss-Prot
  Rho_GTPase_activation_prot UniProtKB/Swiss-Prot
  RhoGAP_dom UniProtKB/Swiss-Prot
KEGG Report rno:312108 UniProtKB/Swiss-Prot
NCBI Gene 312108 ENTREZGENE
Pfam PF00169 UniProtKB/Swiss-Prot
  RhoGAP UniProtKB/Swiss-Prot
PhenoGen Ophn1 PhenoGen
PROSITE PH_DOMAIN UniProtKB/Swiss-Prot
  RHOGAP UniProtKB/Swiss-Prot
SMART RhoGAP UniProtKB/Swiss-Prot
  SM00233 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF103657 UniProtKB/Swiss-Prot
  SSF48350 UniProtKB/Swiss-Prot
UniProt A0A8I6AVR8_RAT UniProtKB/TrEMBL
  OPHN1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Ophn1  oligophrenin 1  LOC688676  hypothetical protein LOC688676  Data Merged 737654 PROVISIONAL
2008-04-30 Ophn1  oligophrenin 1   Ophn1_predicted  oligophrenin 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-11-19 LOC688676  hypothetical protein LOC688676      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-07 Ophn1_predicted  oligophrenin 1 (predicted)  Ophn1  oligophrenin 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 Ophn1  oligophrenin 1      Symbol and Name status set to provisional 70820 PROVISIONAL