Homer1 (homer scaffold protein 1) - Rat Genome Database

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Gene: Homer1 (homer scaffold protein 1) Rattus norvegicus
Analyze
Symbol: Homer1
Name: homer scaffold protein 1
RGD ID: 628725
Description: Enables several functions, including identical protein binding activity; scaffold protein binding activity; and type 5 metabotropic glutamate receptor binding activity. A structural constituent of postsynapse. Involved in several processes, including G protein-coupled glutamate receptor signaling pathway; protein tetramerization; and regulation of dendritic spine maintenance. Located in dendritic shaft; dendritic spine; and neuronal cell body. Is active in glutamatergic synapse and postsynaptic density. Colocalizes with excitatory synapse. Orthologous to human HOMER1 (homer scaffold protein 1); PARTICIPATES IN glutamate signaling pathway; INTERACTS WITH (+)-schisandrin B; 1,2,4-trimethylbenzene; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: homer homolog 1; homer homolog 1 (Drosophila); homer protein homolog 1; homer scaffolding protein 1; homer, neuronal immediate early gene, 1; HOMER1F; PSD-Zip45; scaffold protein; VASP/Ena-related gene up-regulated during seizure and LTP 1; Vesl-1
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
mRatBN7.2224,542,777 - 24,645,715 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl224,543,093 - 24,644,785 (+)Ensembl
Rnor_6.0222,909,550 - 23,012,303 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl222,909,569 - 23,009,678 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0242,106,531 - 42,208,187 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera220,619,882 - 20,720,929 (+)NCBICelera
Cytogenetic Map2q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(S)-amphetamine  (ISO)
(S)-nicotine  (ISO)
1,2,4-trimethylbenzene  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bexarotene  (EXP)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
caffeine  (EXP)
calcium atom  (EXP)
calcium(0)  (EXP)
carbon nanotube  (ISO)
chaetocin  (EXP)
chromium(6+)  (ISO)
cisplatin  (ISO)
clozapine  (EXP)
cocaine  (EXP,ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclic ADP-ribose  (EXP)
cyclosporin A  (ISO)
D-cycloserine  (EXP)
dantrolene  (ISO)
dexamethasone  (EXP)
diazinon  (EXP)
dibutyl phthalate  (EXP)
dioxygen  (EXP)
elemental selenium  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
fluoxetine  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
glycidol  (EXP)
haloperidol  (EXP)
halothane  (ISO)
hexachlorophene  (ISO)
hydrogen peroxide  (ISO)
isoprenaline  (EXP)
ivermectin  (ISO)
kainic acid  (EXP)
lead diacetate  (EXP)
lead(0)  (EXP)
lead(2+)  (EXP)
linalool  (EXP)
lipopolysaccharide  (EXP)
methamphetamine  (EXP)
methyl methanesulfonate  (ISO)
methylisothiazolinone  (ISO)
methylphenidate  (EXP)
morphine  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N1'-[2-[[5-[(dimethylamino)methyl]-2-furanyl]methylthio]ethyl]-N1-methyl-2-nitroethene-1,1-diamine  (EXP)
naphthalenes  (EXP)
nefazodone  (EXP)
nickel sulfate  (ISO)
nicotine  (ISO)
oxycodone  (EXP)
paracetamol  (ISO)
phencyclidine  (ISO)
phenobarbital  (ISO)
phenylephrine  (EXP)
pirinixic acid  (EXP)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
ranitidine  (EXP)
risperidone  (EXP)
rotenone  (ISO)
ryanodine  (ISO)
SCH 23390  (EXP)
scopolamine  (EXP)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (EXP)
Soman  (EXP)
testosterone  (EXP)
tetrachloromethane  (EXP)
tetradecane  (EXP)
toluene  (EXP)
undecane  (EXP)
valproic acid  (EXP,ISO)
vincaleukoblastine  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
apical part of cell  (IEA,ISO)
axon  (IEA,ISO)
costamere  (IEA,ISO)
cytoplasm  (IBA,ISO)
cytosol  (TAS)
dendrite  (IBA,IDA)
dendritic shaft  (IDA)
dendritic spine  (IDA)
excitatory synapse  (IDA)
glutamatergic synapse  (IDA,IEA,IMP,ISO)
membrane  (ISO)
neuron projection  (IDA,ISO)
neuron spine  (IDA)
neuronal cell body  (IDA)
plasma membrane  (IBA,IEA,ISO)
postsynapse  (ISO)
postsynaptic cytosol  (IEA,ISO)
postsynaptic density  (IBA,IDA,IEA,ISO)
synapse  (IDA)
Z disc  (IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Ageta H, etal., Brain Res Mol Brain Res 2001 Dec 30;97(2):186-9.
2. Berke JD, etal., J Neurosci 1998 Jul 15;18(14):5301-10.
3. Brakeman PR, etal., Nature 1997 Mar 20;386(6622):284-8.
4. Feng W, etal., J Biol Chem 2002 Nov 22;277(47):44722-30.
5. Fujiyama K, etal., Synapse 2003 Sep 1;49(3):143-9.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Ghasemzadeh MB, etal., Neuroscience. 2009 Mar 3;159(1):414-26. Epub 2008 Nov 1.
8. Ghasemzadeh MB, etal., Synapse. 2009 Jan;63(1):42-53.
9. GOA data from the GO Consortium
10. Hayashi MK, etal., Cell. 2009 Apr 3;137(1):159-71. doi: 10.1016/j.cell.2009.01.050.
11. Jung KM, etal., Mol Pharmacol. 2007 Sep;72(3):612-21. doi: 10.1124/mol.107.037796. Epub 2007 Jun 21.
12. Kane JK, etal., Eur J Neurosci. 2005 Mar;21(5):1145-54.
13. Kato A, etal., FEBS Lett 1997 Jul 21;412(1):183-9.
14. Kato A, etal., J Biol Chem 1998 Sep 11;273(37):23969-75.
15. Lu J, etal., Neuron. 2007 Sep 20;55(6):874-89.
16. Mao L, etal., J Neurosci. 2005 Mar 9;25(10):2741-52.
17. MGD data from the GO Consortium
18. Nelson SE, etal., Neurosci Lett. 2004 Aug 26;367(1):105-8.
19. Nielsen HS, etal., Brain Res Mol Brain Res 2002 Sep 30;105(1-2):79-85.
20. Orsetti M, etal., Eur J Neurosci. 2008 Apr;27(8):2156-64. Epub 2008 Mar 25.
21. Park JM, etal., Cell. 2013 Aug 1;154(3):637-50. doi: 10.1016/j.cell.2013.07.001.
22. Piard J, etal., Hum Mol Genet. 2018 Feb 15;27(4):589-600. doi: 10.1093/hmg/ddx426.
23. Pipeline to import KEGG annotations from KEGG into RGD
24. Polese D, etal., Neuropsychopharmacology 2002 Dec;27(6):906-13.
25. RGD automated import pipeline for gene-chemical interactions
26. Rong R, etal., Nat Neurosci 2003 Nov;6(11):1153-61. Epub 2003 Oct 5.
27. Roselli F, etal., PLoS One. 2009 Jun 23;4(6):e6011.
28. Sala C, etal., J Neurosci. 2003 Jul 16;23(15):6327-37.
29. Sandona D, etal., Biochem Biophys Res Commun 2000 Dec 20;279(2):348-53.
30. Sgambato-Faure V, etal., Biochem Biophys Res Commun. 2006 May 5;343(2):630-7. Epub 2006 Mar 15.
31. Stucchi R, etal., Cell Rep. 2018 Jul 17;24(3):685-700. doi: 10.1016/j.celrep.2018.06.071.
32. Sun J, etal., FEBS Lett 1998 Oct 23;437(3):304-8.
33. Tu JC, etal., Neuron 1998 Oct;21(4):717-26.
34. Tu JC, etal., Neuron. 1999 Jul;23(3):583-92.
35. Xiao B, etal., Neuron 1998 Oct;21(4):707-16.
Additional References at PubMed
PMID:9647694   PMID:10798399   PMID:10851183   PMID:11418862   PMID:12054806   PMID:12176012   PMID:12524440   PMID:12646135   PMID:12810060   PMID:12834253   PMID:12860966   PMID:12887973  
PMID:12911619   PMID:14505576   PMID:14559352   PMID:14698459   PMID:15033484   PMID:15294147   PMID:15574735   PMID:15579147   PMID:15632121   PMID:15673434   PMID:15691715   PMID:16002212  
PMID:16087291   PMID:17015857   PMID:17169339   PMID:17234898   PMID:17372981   PMID:17389377   PMID:17540011   PMID:17630046   PMID:17670980   PMID:18268005   PMID:18636533   PMID:18716215  
PMID:19118598   PMID:19201745   PMID:19243698   PMID:19419424   PMID:19443779   PMID:19709672   PMID:19923532   PMID:20147574   PMID:20181604   PMID:20304506   PMID:20738409   PMID:20886623  
PMID:21144999   PMID:21558424   PMID:21664258   PMID:21795692   PMID:22003220   PMID:22012123   PMID:22238580   PMID:22393587   PMID:22445886   PMID:22465321   PMID:22617701   PMID:22660975  
PMID:22732411   PMID:22814532   PMID:22871113   PMID:23523268   PMID:23587936   PMID:23733398   PMID:23791195   PMID:23800465   PMID:24036210   PMID:24377717   PMID:24530450   PMID:24554721  
PMID:24613359   PMID:24626340   PMID:24966368   PMID:25503822   PMID:25824461   PMID:26929812   PMID:27075036   PMID:27177972   PMID:27259299   PMID:28154077   PMID:28337539   PMID:28698564  
PMID:29238619   PMID:29476059   PMID:30265419   PMID:30335140   PMID:31369778   PMID:31404590   PMID:31505169   PMID:31891692   PMID:32013638   PMID:32756473  


Genomics

Comparative Map Data
Homer1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2224,542,777 - 24,645,715 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl224,543,093 - 24,644,785 (+)Ensembl
Rnor_6.0222,909,550 - 23,012,303 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl222,909,569 - 23,009,678 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0242,106,531 - 42,208,187 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera220,619,882 - 20,720,929 (+)NCBICelera
Cytogenetic Map2q12NCBI
HOMER1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl579,372,636 - 79,514,134 (-)EnsemblGRCh38hg38GRCh38
GRCh38579,372,636 - 79,514,134 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37578,668,459 - 78,809,957 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36578,705,542 - 78,845,456 (-)NCBINCBI36hg18NCBI36
Build 34578,705,542 - 78,845,456NCBI
Celera574,569,550 - 74,709,526 (-)NCBI
Cytogenetic Map5q14.1NCBI
HuRef573,877,773 - 74,017,416 (-)NCBIHuRef
CHM1_1578,102,358 - 78,242,362 (-)NCBICHM1_1
Homer1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391393,440,265 - 93,549,471 (+)NCBIGRCm39mm39
GRCm39 Ensembl1393,436,143 - 93,541,637 (+)Ensembl
GRCm381393,303,757 - 93,405,129 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1393,299,635 - 93,405,129 (+)EnsemblGRCm38mm10GRCm38
MGSCv371394,074,450 - 94,174,917 (+)NCBIGRCm37mm9NCBIm37
MGSCv361394,405,552 - 94,504,882 (+)NCBImm8
Celera1396,912,321 - 97,012,695 (+)NCBICelera
Cytogenetic Map13C3NCBI
Homer1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542521,644,571 - 21,775,735 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542521,644,577 - 21,774,843 (+)NCBIChiLan1.0ChiLan1.0
HOMER1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1536,065,045 - 36,205,928 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl536,064,665 - 36,205,928 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0535,794,627 - 35,936,111 (+)NCBIMhudiblu_PPA_v0panPan3
HOMER1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1327,395,337 - 27,525,822 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl327,400,839 - 27,523,320 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha328,635,060 - 28,765,722 (+)NCBI
ROS_Cfam_1.0327,314,347 - 27,445,373 (+)NCBI
UMICH_Zoey_3.1327,254,336 - 27,384,769 (+)NCBI
UNSW_CanFamBas_1.0327,231,171 - 27,362,707 (+)NCBI
UU_Cfam_GSD_1.0327,511,836 - 27,642,805 (+)NCBI
Homer1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213183,538,579 - 183,681,403 (+)NCBI
SpeTri2.0NW_0049365497,189,588 - 7,320,117 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOMER1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl288,122,877 - 88,255,281 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1288,116,664 - 88,253,843 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2289,846,977 - 89,904,301 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.2289,987,133 - 89,996,112 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HOMER1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1473,591,105 - 73,729,680 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl473,589,495 - 73,728,353 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604922,438,015 - 22,576,283 (-)NCBIVero_WHO_p1.0
Homer1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248693,878,646 - 4,012,211 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D2Rat190  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0222,988,221 - 22,988,322NCBIRnor6.0
Rnor_5.0242,184,052 - 42,184,206UniSTSRnor5.0
Celera220,697,451 - 20,697,590UniSTS
SHRSP x BN Map26.9998RGD
SHRSP x BN Map26.9998UniSTS
Cytogenetic Map2q12UniSTS
D2Rat309  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2224,590,228 - 24,590,426 (+)MAPPERmRatBN7.2
Rnor_6.0222,956,364 - 22,956,561NCBIRnor6.0
Rnor_5.0242,153,656 - 42,153,853UniSTSRnor5.0
Celera220,665,895 - 20,666,092UniSTS
SHRSP x BN Map26.9998RGD
SHRSP x BN Map26.9998UniSTS
Cytogenetic Map2q12UniSTS
D2Wox53  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map2q12UniSTS
D2Wox51  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2224,601,970 - 24,602,285 (+)MAPPERmRatBN7.2
Rnor_6.0222,968,106 - 22,968,420NCBIRnor6.0
Rnor_5.0242,165,398 - 42,165,712UniSTSRnor5.0
Celera220,677,481 - 20,677,795UniSTS
Cytogenetic Map2q12UniSTS
BE119015  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2224,603,046 - 24,603,236 (+)MAPPERmRatBN7.2
Rnor_6.0222,969,182 - 22,969,371NCBIRnor6.0
Rnor_5.0242,166,474 - 42,166,663UniSTSRnor5.0
Celera220,678,557 - 20,678,746UniSTS
Cytogenetic Map2q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1506
Count of miRNA genes:341
Interacting mature miRNAs:484
Transcripts:ENSRNOT00000071804, ENSRNOT00000073871
Prediction methods:Microtar, Miranda, 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 40 18 12 12 8 10 74 20 26 8
Low 3 3 39 29 19 29 1 15 15 11
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031707 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006231775 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760635 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102105 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB003726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB007688 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB017140 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF030088 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF093267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF093268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ276327 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ276328 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY189942 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY189943 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473955 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U92079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000071804   ⟹   ENSRNOP00000065989
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl224,543,604 - 24,644,785 (+)Ensembl
Rnor_6.0 Ensembl222,950,018 - 23,009,481 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000073871   ⟹   ENSRNOP00000066634
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl224,543,499 - 24,644,202 (+)Ensembl
Rnor_6.0 Ensembl222,909,569 - 23,009,678 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078266   ⟹   ENSRNOP00000070611
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl224,544,099 - 24,642,932 (+)Ensembl
Rnor_6.0 Ensembl222,910,236 - 23,009,522 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094656   ⟹   ENSRNOP00000094833
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl224,543,093 - 24,642,751 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095158   ⟹   ENSRNOP00000097408
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl224,544,294 - 24,644,785 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095790   ⟹   ENSRNOP00000086769
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl224,630,611 - 24,644,785 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104131   ⟹   ENSRNOP00000080883
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl224,543,604 - 24,644,785 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104734   ⟹   ENSRNOP00000079557
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl224,543,093 - 24,609,841 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118061   ⟹   ENSRNOP00000080673
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl224,629,849 - 24,644,785 (+)Ensembl
RefSeq Acc Id: NM_031707   ⟹   NP_113895
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2224,544,000 - 24,645,547 (+)NCBI
Rnor_6.0222,910,137 - 23,012,137 (+)NCBI
Rnor_5.0242,106,531 - 42,208,187 (+)NCBI
Celera220,619,882 - 20,720,929 (+)RGD
Sequence:
RefSeq Acc Id: XM_006231775   ⟹   XP_006231837
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2224,542,778 - 24,645,715 (+)NCBI
Rnor_6.0222,909,550 - 23,012,303 (+)NCBI
Rnor_5.0242,106,531 - 42,208,187 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039102105   ⟹   XP_038958033
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2224,542,777 - 24,619,216 (+)NCBI
Protein Sequences
Protein RefSeqs NP_113895 (Get FASTA)   NCBI Sequence Viewer  
  XP_006231837 (Get FASTA)   NCBI Sequence Viewer  
  XP_038958033 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC53113 (Get FASTA)   NCBI Sequence Viewer  
  AAC71031 (Get FASTA)   NCBI Sequence Viewer  
  AAC71032 (Get FASTA)   NCBI Sequence Viewer  
  AAO39002 (Get FASTA)   NCBI Sequence Viewer  
  AAO39003 (Get FASTA)   NCBI Sequence Viewer  
  BAA21671 (Get FASTA)   NCBI Sequence Viewer  
  BAA32477 (Get FASTA)   NCBI Sequence Viewer  
  BAA34311 (Get FASTA)   NCBI Sequence Viewer  
  CAB77249 (Get FASTA)   NCBI Sequence Viewer  
  CAB77250 (Get FASTA)   NCBI Sequence Viewer  
  EDM10038 (Get FASTA)   NCBI Sequence Viewer  
  EDM10039 (Get FASTA)   NCBI Sequence Viewer  
  EDM10040 (Get FASTA)   NCBI Sequence Viewer  
  EDM10041 (Get FASTA)   NCBI Sequence Viewer  
  EDM10042 (Get FASTA)   NCBI Sequence Viewer  
  EDM10043 (Get FASTA)   NCBI Sequence Viewer  
  EDM10044 (Get FASTA)   NCBI Sequence Viewer  
  EDM10045 (Get FASTA)   NCBI Sequence Viewer  
  EDM10046 (Get FASTA)   NCBI Sequence Viewer  
  EDM10047 (Get FASTA)   NCBI Sequence Viewer  
  EDM10048 (Get FASTA)   NCBI Sequence Viewer  
  EDM10049 (Get FASTA)   NCBI Sequence Viewer  
  EDM10050 (Get FASTA)   NCBI Sequence Viewer  
  EDM10051 (Get FASTA)   NCBI Sequence Viewer  
  EDM10052 (Get FASTA)   NCBI Sequence Viewer  
  EDM10053 (Get FASTA)   NCBI Sequence Viewer  
  EDM10054 (Get FASTA)   NCBI Sequence Viewer  
  Q9Z214 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_113895   ⟸   NM_031707
- UniProtKB: Q9Z214 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006231837   ⟸   XM_006231775
- Peptide Label: isoform X1
- UniProtKB: Q9Z214 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070611   ⟸   ENSRNOT00000078266
RefSeq Acc Id: ENSRNOP00000066634   ⟸   ENSRNOT00000073871
RefSeq Acc Id: ENSRNOP00000065989   ⟸   ENSRNOT00000071804
RefSeq Acc Id: XP_038958033   ⟸   XM_039102105
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000080883   ⟸   ENSRNOT00000104131
RefSeq Acc Id: ENSRNOP00000097408   ⟸   ENSRNOT00000095158
RefSeq Acc Id: ENSRNOP00000080673   ⟸   ENSRNOT00000118061
RefSeq Acc Id: ENSRNOP00000094833   ⟸   ENSRNOT00000094656
RefSeq Acc Id: ENSRNOP00000086769   ⟸   ENSRNOT00000095790
RefSeq Acc Id: ENSRNOP00000079557   ⟸   ENSRNOT00000104734
Protein Domains
WH1

Transcriptome

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

Promoters
RGD ID:13691066
Promoter ID:EPDNEW_R1591
Type:single initiation site
Name:Homer1_1
Description:homer scaffolding protein 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_6.0222,909,483 - 22,909,543EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
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/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)
ACI/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
ACI/N (2020)
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Sequenced By: MCW
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
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/SsN (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
BUF/N (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
Buf/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
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)
DA/OlaHsd (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/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
F344/Stm (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
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
FXLE16/Stm (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
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/FarMcwi (2019)
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Sequenced By: MCW
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
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
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 (2019)
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Sequenced By: MCW
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
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
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/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/MavRrrcAek (2020)
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Sequenced By: MCW
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/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/MavRrrcAek (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
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
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 (2020)
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Sequenced By: MCW
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
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
MWF/Hsd (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
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)
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
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
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 (2020)
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Sequenced By: MCW
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
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 (2019)
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Sequenced By: MCW
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
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
WAG/RijCrl (2020)
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Sequenced By: MCW
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/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 (2020)
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Sequenced By: MCW
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/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 (2019)
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Sequenced By: MCW
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/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 (2020)
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Sequenced By: MCW
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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628725 AgrOrtholog
Ensembl Genes ENSRNOG00000047014 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065989 UniProtKB/TrEMBL
  ENSRNOP00000066634 UniProtKB/Swiss-Prot
  ENSRNOP00000070611 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071804 UniProtKB/TrEMBL
  ENSRNOT00000073871 UniProtKB/Swiss-Prot
  ENSRNOT00000078266 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Homer_EVH1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH1/EVH1_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29546 UniProtKB/Swiss-Prot
NCBI Gene 29546 ENTREZGENE
Pfam WH1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB HOMER1 RGD
PhenoGen Homer1 PhenoGen
PROSITE WH1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART WH1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JYD5_RAT UniProtKB/TrEMBL
  A0A0H2UI35_RAT UniProtKB/TrEMBL
  HOME1_RAT UniProtKB/Swiss-Prot
  Q811R0_RAT UniProtKB/TrEMBL
  Q811R1_RAT UniProtKB/TrEMBL
  Q9Z214 ENTREZGENE
UniProt Secondary O08567 UniProtKB/Swiss-Prot
  O88800 UniProtKB/Swiss-Prot
  Q9QUJ8 UniProtKB/Swiss-Prot
  Q9QWN5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-03-16 Homer1  homer scaffold protein 1  Homer1  homer scaffolding protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-02-25 Homer1  homer scaffolding protein 1  Homer1  homer homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Homer1  homer homolog 1 (Drosophila)    homer, neuronal immediate early gene, 1  Name updated 1299863 APPROVED
2003-02-27 Homer1  homer, neuronal immediate early gene, 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains a PDZ domain 633021