Opn4 (opsin 4) - Rat Genome Database

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Gene: Opn4 (opsin 4) Rattus norvegicus
Analyze
Symbol: Opn4
Name: opsin 4
RGD ID: 621701
Description: Exhibits G protein-coupled photoreceptor activity. Involved in phototransduction. Predicted to localize to integral component of plasma membrane and sperm head plasma membrane. Orthologous to human OPN4 (opsin 4); INTERACTS WITH ammonium chloride; bisphenol A; furan.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: melanopsin; opsin 4 (melanopsin); opsin-4
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
mRatBN7.2169,920,408 - 9,929,580 (-)NCBI
Rnor_6.0 Ensembl1610,943,341 - 10,952,549 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01610,943,353 - 10,966,602 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0169,268,356 - 9,277,528 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41610,249,756 - 10,258,923 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11610,249,757 - 10,258,921 (-)NCBI
Celera165,287,559 - 5,296,704 (+)NCBICelera
Cytogenetic Map16p15NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12808468   PMID:12904470   PMID:14500998   PMID:15073514   PMID:15509757   PMID:15674244   PMID:16186625   PMID:16687290   PMID:17652756   PMID:18001324   PMID:18512147   PMID:19793992  
PMID:20339872   PMID:22101014   PMID:23187103   PMID:23541830   PMID:25378407   PMID:26176868   PMID:26320947   PMID:26572076  


Genomics

Comparative Map Data
Opn4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2169,920,408 - 9,929,580 (-)NCBI
Rnor_6.0 Ensembl1610,943,341 - 10,952,549 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01610,943,353 - 10,966,602 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0169,268,356 - 9,277,528 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41610,249,756 - 10,258,923 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11610,249,757 - 10,258,921 (-)NCBI
Celera165,287,559 - 5,296,704 (+)NCBICelera
Cytogenetic Map16p15NCBI
OPN4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1086,654,547 - 86,666,848 (+)EnsemblGRCh38hg38GRCh38
GRCh381086,653,495 - 86,666,460 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371088,414,304 - 88,426,217 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361088,404,294 - 88,416,197 (+)NCBINCBI36hg18NCBI36
Build 341088,404,377 - 88,416,192NCBI
Celera1082,417,087 - 82,428,990 (+)NCBI
Cytogenetic Map10q23.2NCBI
HuRef1082,268,556 - 82,280,460 (+)NCBIHuRef
CHM1_11088,695,970 - 88,707,871 (+)NCBICHM1_1
Opn4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391434,312,575 - 34,322,099 (-)NCBIGRCm39mm39
GRCm39 Ensembl1434,312,575 - 34,322,099 (-)Ensembl
GRCm381434,590,618 - 34,600,142 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1434,590,618 - 34,600,142 (-)EnsemblGRCm38mm10GRCm38
MGSCv371435,403,804 - 35,413,328 (-)NCBIGRCm37mm9NCBIm37
MGSCv361433,421,454 - 33,429,234 (-)NCBImm8
Celera1430,856,294 - 30,865,818 (-)NCBICelera
Cytogenetic Map14BNCBI
Opn4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555105,724,120 - 5,736,135 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555105,723,804 - 5,736,070 (+)NCBIChiLan1.0ChiLan1.0
OPN4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Mhudiblu_PPA_v01083,082,351 - 83,095,161 (+)NCBIMhudiblu_PPA_v0panPan3
OPN4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1434,350,058 - 34,365,410 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl434,355,128 - 34,365,215 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha434,341,511 - 34,356,871 (+)NCBI
ROS_Cfam_1.0434,709,962 - 34,725,323 (+)NCBI
UMICH_Zoey_3.1434,555,991 - 34,571,338 (+)NCBI
UNSW_CanFamBas_1.0434,725,234 - 34,740,584 (+)NCBI
UU_Cfam_GSD_1.0435,230,251 - 35,245,607 (+)NCBI
Opn4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721344,151,328 - 44,162,304 (-)NCBI
SpeTri2.0NW_004936804261,210 - 272,449 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OPN4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1487,644,240 - 87,722,245 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11487,645,563 - 87,660,820 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21494,902,249 - 94,913,351 (+)NCBISscrofa10.2Sscrofa10.2susScr3
OPN4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1945,199,897 - 45,212,193 (-)NCBI
ChlSab1.1 Ensembl945,200,707 - 45,211,636 (-)Ensembl
Opn4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624841472,053 - 483,623 (-)NCBI

Position Markers
RH136694  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2169,920,505 - 9,920,661 (+)MAPPER
Rnor_6.01610,943,475 - 10,943,630NCBIRnor6.0
Rnor_5.0169,268,454 - 9,268,609UniSTSRnor5.0
RGSC_v3.41610,249,849 - 10,250,004UniSTSRGSC3.4
Celera165,296,478 - 5,296,633UniSTS
RH 3.4 Map1698.3UniSTS
Cytogenetic Map16p15UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16124228366Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16127556253Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16127556253Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16127556253Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16131816439Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16133160624Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16134465490Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16141240937Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16141240937Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16141240957Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)1624459345244593Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16134074146340741Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)16155018749247447Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)16155018763210301Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16155018763210301Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)16155018763210301Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)16155018763210301Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16172829746728297Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)16329668817464293Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16413635523105837Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16413635545905331Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380218360147Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16501380245905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380245905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16501380245905331Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380250013802Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16501380250169318Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16501380252144919Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380264012784Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16509870419398181Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:215
Count of miRNA genes:137
Interacting mature miRNAs:148
Transcripts:ENSRNOT00000015642
Prediction methods:Microtar, 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 renal system reproductive system respiratory system appendage
High
Medium
Low 14 3 4 3 1
Below cutoff 2 29 13 2 9 2 8 8 56 22 32 10 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000089041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1610,947,474 - 10,948,851 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091315   ⟹   ENSRNOP00000069548
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1610,943,341 - 10,952,549 (-)Ensembl
RefSeq Acc Id: NM_138860   ⟹   NP_620215
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,920,408 - 9,929,580 (-)NCBI
Rnor_6.01610,943,377 - 10,952,549 (-)NCBI
Rnor_5.0169,268,356 - 9,277,528 (-)NCBI
RGSC_v3.41610,249,756 - 10,258,923 (-)RGD
Celera165,287,559 - 5,296,704 (+)RGD
Sequence:
RefSeq Acc Id: XM_017599985   ⟹   XP_017455474
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,943,353 - 10,958,156 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599986   ⟹   XP_017455475
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,943,353 - 10,958,156 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599987   ⟹   XP_017455476
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,943,353 - 10,966,602 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599988   ⟹   XP_017455477
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,943,353 - 10,966,599 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599989   ⟹   XP_017455478
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,943,353 - 10,957,216 (-)NCBI
Sequence:
RefSeq Acc Id: XR_001841532
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,947,474 - 10,958,156 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_620215 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAL61854 (Get FASTA)   NCBI Sequence Viewer  
  EDL88866 (Get FASTA)   NCBI Sequence Viewer  
  EDL88867 (Get FASTA)   NCBI Sequence Viewer  
  Q8R456 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_620215   ⟸   NM_138860
- UniProtKB: Q8R456 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017455476   ⟸   XM_017599987
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017455477   ⟸   XM_017599988
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017455475   ⟸   XM_017599986
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017455474   ⟸   XM_017599985
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017455478   ⟸   XM_017599989
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000069548   ⟸   ENSRNOT00000091315

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)
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:621701 AgrOrtholog
Ensembl Genes ENSRNOG00000053893 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000069548 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000091315 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro GPCR_Rhodpsn UniProtKB/Swiss-Prot
  GPCR_Rhodpsn_7TM UniProtKB/Swiss-Prot
  Opsin UniProtKB/Swiss-Prot
  Retinal_BS UniProtKB/Swiss-Prot
KEGG Report rno:192223 UniProtKB/Swiss-Prot
NCBI Gene 192223 ENTREZGENE
Pfam 7tm_1 UniProtKB/Swiss-Prot
PhenoGen Opn4 PhenoGen
PRINTS GPCRRHODOPSN UniProtKB/Swiss-Prot
  OPSIN UniProtKB/Swiss-Prot
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/Swiss-Prot
  G_PROTEIN_RECEP_F1_2 UniProtKB/Swiss-Prot
  OPSIN UniProtKB/Swiss-Prot
SMART 7TM_GPCR_Srsx UniProtKB/Swiss-Prot
UniProt OPN4_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-25 Opn4  opsin 4  Opn4  opsin 4 (melanopsin)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Opn4  opsin 4 (melanopsin)      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Opn4  opsin 4 (melanopsin)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in cell bodies, dendrites, and proximal axonal segments of a subset of rat retinal ganglion cells 633348