Ophn1 (oligophrenin 1) - Rat Genome Database

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Gene: Ophn1 (oligophrenin 1) Rattus norvegicus
Analyze
Symbol: Ophn1
Name: oligophrenin 1
RGD ID: 1563435
Description: Exhibits ionotropic glutamate receptor binding activity. Involved in maintenance of postsynaptic specialization structure. Localizes to 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
Also 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X63,599,746 - 63,976,678 (-)NCBI
Rnor_6.0 EnsemblX68,189,161 - 68,563,137 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X68,185,865 - 68,579,518 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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

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 (-)NCBI
Rnor_6.0 EnsemblX68,189,161 - 68,563,137 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X68,185,865 - 68,579,518 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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
GRCh38.p13 EnsemblX67,949,349 - 68,433,913 (-)EnsemblGRCh38hg38GRCh38
GRCh38X68,042,344 - 68,433,841 (-)NCBIGRCh38GRCh38hg38GRCh38
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
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
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 (-)NCBI
ChlSab1.1 EnsemblX57,911,555 - 58,290,900 (-)Ensembl
Vero_WHO_p1.0NW_0236660835,360,305 - 5,607,870 (-)NCBI
Ophn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248911,907,233 - 2,429,714 (+)NCBI

Position Markers
DXRat31  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X63,958,410 - 63,958,542 (+)MAPPER
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 (+)MAPPER
mRatBN7.2323,603,189 - 23,603,720 (+)MAPPER
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 (+)MAPPER
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 (+)MAPPER
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 (+)MAPPER
mRatBN7.2357,847,231 - 57,847,443 (+)MAPPER
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 (Rnor_6.0)
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)X15688119127888215Rat
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)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
70221Bp56Blood pressure QTL 564.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X6139809770352120Rat

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
Rnor_6.0 EnsemblX68,189,161 - 68,563,137 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076193   ⟹   ENSRNOP00000068017
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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: 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_017602029   ⟹   XP_017457518
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X68,185,865 - 68,579,518 (-)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: XP_017457518   ⟸   XM_017602029
- Peptide Label: isoform X1
- 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
Protein Domains
PH   Rho-GAP

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 (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)
Visual CSV TAB Printer
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)
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
F344/NRrrc (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
FHH/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)
FHH/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
FHL/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)
FHL/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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
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:1563435 AgrOrtholog
Ensembl Genes ENSRNOG00000026573 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000035867 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000067984 UniProtKB/TrEMBL
  ENSRNOP00000068017 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000034772 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000076193 UniProtKB/Swiss-Prot
  ENSRNOT00000076720 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, UniProtKB/TrEMBL
  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, UniProtKB/TrEMBL
  SSF48350 UniProtKB/Swiss-Prot
UniProt A0A096MJ43_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