Gphn (gephyrin) - Rat Genome Database
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Gene: Gphn (gephyrin) Rattus norvegicus
Analyze
Symbol: Gphn
Name: gephyrin
RGD ID: 69194
Description: Exhibits several functions, including identical protein binding activity; molybdopterin adenylyltransferase activity; and molybdopterin molybdotransferase activity. Involved in several processes, including Mo-molybdopterin cofactor biosynthetic process; neurotransmitter receptor localization to postsynaptic specialization membrane; and synapse assembly. Localizes to several cellular components, including extrinsic component of cytoplasmic side of plasma membrane; glycinergic synapse; and postsynaptic specialization, intracellular component. Human ortholog(s) of this gene implicated in inherited metabolic disorder and molybdenum cofactor deficiency type C. Orthologous to human GPHN (gephyrin); PARTICIPATES IN molybdenum cofactor biosynthetic pathway; Inhibitory synaptic transmission pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Geph; gephyrin isoform; putative glycine receptor-tubulin linker protein
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
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
Rnor_6.0 Ensembl6101,532,518 - 101,859,164 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06101,327,874 - 101,859,169 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06110,709,516 - 111,190,440 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.06111,210,069 - 111,237,661 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46100,833,004 - 101,302,957 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16100,836,459 - 101,306,408 (+)NCBI
Celera695,358,601 - 95,872,910 (+)NCBICelera
Cytogenetic Map6q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Allison DW, etal., J Neurosci. 2000 Jun 15;20(12):4545-54.
2. Belaidi AA and Schwarz G, Biochem J. 2013 Feb 15;450(1):149-57. doi: 10.1042/BJ20121078.
3. Colin I, etal., J Comp Neurol. 1998 Aug 31;398(3):359-72.
4. Danglot L, etal., Mol Cell Neurosci. 2003 Jun;23(2):264-78.
5. Fuhrmann JC, etal., J Neurosci 2002 Jul 1;22(13):5393-402.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Giesemann T, etal., J Neurosci. 2003 Sep 10;23(23):8330-9.
8. Harvey K, etal., J Neurosci. 2004 Jun 23;24(25):5816-26.
9. Hines RM, etal., J Neurosci. 2008 Jun 11;28(24):6055-67. doi: 10.1523/JNEUROSCI.0032-08.2008.
10. KEGG
11. Kins S, etal., Nat Neurosci 2000 Jan;3(1):22-9.
12. Kirsch J, etal., Nature. 1993 Dec 23-30;366(6457):745-8. doi: 10.1038/366745a0.
13. Levinson JN, etal., Neuroscience. 2010 Feb 3;165(3):782-93. doi: 10.1016/j.neuroscience.2009.11.016. Epub 2009 Nov 13.
14. Mendel RR and Bittner F, Biochim Biophys Acta. 2006 Jul;1763(7):621-35. Epub 2006 May 12.
15. MGD data from the GO Consortium
16. NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. OMIM Disease Annotation Pipeline
18. Poulopoulos A, etal., Neuron. 2009 Sep 10;63(5):628-42. doi: 10.1016/j.neuron.2009.08.023.
19. Prior P, etal., Neuron 1992 Jun;8(6):1161-70.
20. Rees MI, etal., J Biol Chem. 2003 Jul 4;278(27):24688-96. Epub 2003 Apr 8.
21. Reiss J and Johnson JL, Hum Mutat 2003 Jun;21(6):569-76.
22. Reiss J, etal., Am J Hum Genet 2001 Jan;68(1):208-13.
23. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
24. RGD automated import pipeline for gene-chemical interactions
25. Sassoe-Pognetto M and Wassle H, J Comp Neurol. 1997 May 5;381(2):158-74.
26. Sassoè-Pognetto M, etal., J Comp Neurol. 2000 May 15;420(4):481-98.
27. Schrader N, etal., J Biol Chem 2004 Apr 30;279(18):18733-41. Epub 2004 Feb 19.
28. Schwarz G, etal., J Mol Biol 2001 Sep14;312(2):405-18.
29. Smith KR, etal., Mol Cell Neurosci. 2010 Aug;44(4):330-41. doi: 10.1016/j.mcn.2010.04.004. Epub 2010 Apr 22.
30. Specht CG, etal., EMBO J. 2011 Aug 9;30(18):3842-53. doi: 10.1038/emboj.2011.276.
31. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
32. Tretter V, etal., J Biol Chem. 2011 Oct 28;286(43):37702-11. doi: 10.1074/jbc.M111.291336. Epub 2011 Aug 31.
33. Yang J, etal., EMBO J. 2011 Jan 5;30(1):165-80. doi: 10.1038/emboj.2010.286. Epub 2010 Nov 30.
Additional References at PubMed
PMID:9812897   PMID:9990024   PMID:10531433   PMID:10900017   PMID:11083919   PMID:11325967   PMID:14760703   PMID:14960612   PMID:15201864   PMID:15647495   PMID:16376568   PMID:16449194  
PMID:16511563   PMID:16616186   PMID:17001074   PMID:17145751   PMID:17698049   PMID:17916433   PMID:18199120   PMID:18204977   PMID:18231803   PMID:18366064   PMID:19105974   PMID:19660531  
PMID:19723286   PMID:19955355   PMID:20206270   PMID:20833253   PMID:21173228   PMID:21404332   PMID:21507951   PMID:22006921   PMID:22290869   PMID:22351777   PMID:22778260   PMID:23294024  
PMID:23408424   PMID:23889935   PMID:24100323   PMID:24297911   PMID:24554721   PMID:24613359   PMID:24894704   PMID:25093719   PMID:25535349   PMID:25663431   PMID:25755278   PMID:26093381  
PMID:26613940   PMID:27002143   PMID:27609886   PMID:27941024   PMID:28026001   PMID:29379879   PMID:29464196   PMID:30053369   PMID:30454851  


Genomics

Comparative Map Data
Gphn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
Rnor_6.0 Ensembl6101,532,518 - 101,859,164 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06101,327,874 - 101,859,169 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06110,709,516 - 111,190,440 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.06111,210,069 - 111,237,661 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46100,833,004 - 101,302,957 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16100,836,459 - 101,306,408 (+)NCBI
Celera695,358,601 - 95,872,910 (+)NCBICelera
Cytogenetic Map6q24NCBI
GPHN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1466,507,407 - 67,181,803 (+)EnsemblGRCh38hg38GRCh38
GRCh381466,507,934 - 67,181,805 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371466,974,865 - 67,648,520 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh371466,974,125 - 67,648,525 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361466,043,878 - 66,718,278 (+)NCBINCBI36hg18NCBI36
Build 341466,044,988 - 66,718,268NCBI
Celera1447,033,183 - 47,707,584 (+)NCBI
Cytogenetic Map14q23.3-q24.1NCBI
HuRef1447,144,073 - 47,817,837 (+)NCBIHuRef
CHM1_11466,912,247 - 67,587,111 (+)NCBICHM1_1
Gphn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391278,264,099 - 78,731,546 (+)NCBIGRCm39mm39
GRCm381278,217,325 - 78,684,772 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1278,226,379 - 78,684,772 (+)EnsemblGRCm38mm10GRCm38
MGSCv371279,327,642 - 79,785,759 (+)NCBIGRCm37mm9NCBIm37
MGSCv361279,145,574 - 79,603,578 (+)NCBImm8
Celera1279,690,472 - 80,148,022 (+)NCBICelera
Cytogenetic Map12C3NCBI
Gphn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554663,016,479 - 3,526,231 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554663,017,474 - 3,526,375 (-)NCBIChiLan1.0ChiLan1.0
GPHN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11465,963,473 - 66,634,550 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1466,137,166 - 66,634,550 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01447,081,527 - 47,755,182 (+)NCBIMhudiblu_PPA_v0panPan3
GPHN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl840,585,883 - 41,203,245 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1840,585,625 - 41,204,007 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Gphn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364959,970,683 - 10,565,467 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GPHN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl790,346,590 - 91,041,189 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1790,345,726 - 90,913,625 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2796,902,547 - 97,222,781 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GPHN
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12443,702,384 - 44,421,890 (+)NCBI
ChlSab1.1 Ensembl2443,880,344 - 44,422,276 (+)Ensembl
Gphn
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473433,871,664 - 34,483,770 (-)NCBI

Position Markers
D6Got126  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06101,667,852 - 101,668,021NCBIRnor6.0
Rnor_5.06111,044,885 - 111,045,054UniSTSRnor5.0
RGSC_v3.46101,086,290 - 101,086,459UniSTSRGSC3.4
RGSC_v3.46101,086,289 - 101,086,459RGDRGSC3.4
RGSC_v3.16101,089,746 - 101,089,915RGD
Celera695,681,117 - 95,681,286UniSTS
RH 3.4 Map6669.4RGD
RH 3.4 Map6669.4UniSTS
RH 2.0 Map6882.4RGD
Cytogenetic Map6q24UniSTS
D6Got125  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06101,412,420 - 101,412,605NCBIRnor6.0
Rnor_5.06110,794,508 - 110,794,693UniSTSRnor5.0
RGSC_v3.46100,910,815 - 100,911,001RGDRGSC3.4
RGSC_v3.46100,910,816 - 100,911,001UniSTSRGSC3.4
RGSC_v3.16100,914,272 - 100,914,457RGD
Celera695,433,732 - 95,433,917UniSTS
RH 3.4 Map6677.0UniSTS
RH 3.4 Map6677.0RGD
Cytogenetic Map6q24UniSTS
BE106545  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06101,640,586 - 101,640,748NCBIRnor6.0
Rnor_5.06111,017,619 - 111,017,781UniSTSRnor5.0
RGSC_v3.46101,057,182 - 101,057,344UniSTSRGSC3.4
Celera695,653,887 - 95,654,049UniSTS
RH 3.4 Map6688.9UniSTS
Cytogenetic Map6q24UniSTS
RH136931  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06101,858,877 - 101,859,070NCBIRnor6.0
Rnor_5.06111,237,369 - 111,237,562UniSTSRnor5.0
RGSC_v3.46101,302,665 - 101,302,858UniSTSRGSC3.4
Celera695,872,618 - 95,872,811UniSTS
Cytogenetic Map6q24UniSTS
MARC_1069-1070:991929832:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06101,858,208 - 101,858,375NCBIRnor6.0
Rnor_5.06111,236,700 - 111,236,867UniSTSRnor5.0
RGSC_v3.46101,301,996 - 101,302,163UniSTSRGSC3.4
Celera695,871,949 - 95,872,116UniSTS
Cytogenetic Map6q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)648432758108268790Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)660606431108154445Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)660606431108154445Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)662263348107263348Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)666129520111129520Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)671206251116206251Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)675449871120449871Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)675623277120276465Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)675623277120623277Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)676902247114203334Rat
2293837Kiddil1Kidney dilation QTL 13.7kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)684763275108464097Rat
2293842Kiddil3Kidney dilation QTL 34.3kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)684763275108464097Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)686422697115379601Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)687418448111129520Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)688507712133507712Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)689631358134631358Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)689631358134631358Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)691703409136703409Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)692879510137879510Rat
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)693706176111134673Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)697949772133849286Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)6101207574147991367Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:728
Count of miRNA genes:235
Interacting mature miRNAs:296
Transcripts:ENSRNOT00000030470, ENSRNOT00000068469, ENSRNOT00000075054
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 2 29 38 27 14 27 8 10 74 35 36 11 8
Low 1 14 19 14 5 14 1 5
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_022865 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112893 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112895 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112896 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112897 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112898 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112899 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112900 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112901 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112902 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112903 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112904 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112907 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112908 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112912 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112915 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC139976 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU735541 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X66366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000030470   ⟹   ENSRNOP00000036544
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6101,603,319 - 101,859,164 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000075054   ⟹   ENSRNOP00000064099
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6101,532,518 - 101,858,501 (+)Ensembl
RefSeq Acc Id: NM_022865   ⟹   NP_074056
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,573 - 97,483,617 (+)NCBI
Rnor_6.06101,327,874 - 101,859,169 (+)NCBI
Rnor_5.06110,709,516 - 111,190,440 (+)NCBI
Rnor_5.06111,210,069 - 111,237,661 (+)NCBI
RGSC_v3.46100,833,004 - 101,302,957 (+)RGD
Celera695,358,601 - 95,872,910 (+)RGD
Sequence:
RefSeq Acc Id: XM_039112893   ⟹   XP_038968821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112894   ⟹   XP_038968822
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,681 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112895   ⟹   XP_038968823
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112896   ⟹   XP_038968824
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112897   ⟹   XP_038968825
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112898   ⟹   XP_038968826
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112899   ⟹   XP_038968827
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112900   ⟹   XP_038968828
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112901   ⟹   XP_038968829
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112902   ⟹   XP_038968830
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112903   ⟹   XP_038968831
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112904   ⟹   XP_038968832
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112905   ⟹   XP_038968833
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112906   ⟹   XP_038968834
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112907   ⟹   XP_038968835
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112908   ⟹   XP_038968836
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112909   ⟹   XP_038968837
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112910   ⟹   XP_038968838
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112911   ⟹   XP_038968839
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112912   ⟹   XP_038968840
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112913   ⟹   XP_038968841
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112914   ⟹   XP_038968842
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,718 - 97,483,617 (+)NCBI
RefSeq Acc Id: XM_039112915   ⟹   XP_038968843
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2696,954,365 - 97,483,617 (+)NCBI
Protein Sequences
Protein RefSeqs NP_074056 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968821 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968822 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968823 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968824 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968825 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968826 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968827 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968828 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968829 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968830 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968831 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968832 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968833 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968834 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968835 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968836 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968837 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968838 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968839 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968840 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968841 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968842 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968843 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ACE06970 (Get FASTA)   NCBI Sequence Viewer  
  CAA47009 (Get FASTA)   NCBI Sequence Viewer  
  Q03555 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_074056   ⟸   NM_022865
- UniProtKB: Q03555 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064099   ⟸   ENSRNOT00000075054
RefSeq Acc Id: ENSRNOP00000036544   ⟸   ENSRNOT00000030470
RefSeq Acc Id: XP_038968821   ⟸   XM_039112893
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968825   ⟸   XM_039112897
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038968830   ⟸   XM_039112902
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038968824   ⟸   XM_039112896
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038968827   ⟸   XM_039112899
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038968832   ⟸   XM_039112904
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038968826   ⟸   XM_039112898
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038968828   ⟸   XM_039112900
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038968833   ⟸   XM_039112905
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038968836   ⟸   XM_039112908
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038968829   ⟸   XM_039112901
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038968834   ⟸   XM_039112906
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038968841   ⟸   XM_039112913
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038968823   ⟸   XM_039112895
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968838   ⟸   XM_039112910
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038968831   ⟸   XM_039112903
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038968839   ⟸   XM_039112911
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038968837   ⟸   XM_039112909
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038968840   ⟸   XM_039112912
- Peptide Label: isoform X20
RefSeq Acc Id: XP_038968835   ⟸   XM_039112907
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038968843   ⟸   XM_039112915
- Peptide Label: isoform X23
RefSeq Acc Id: XP_038968822   ⟸   XM_039112894
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038968842   ⟸   XM_039112914
- Peptide Label: isoform X22
Protein Domains
MoCF_biosynth

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)
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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 (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/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 (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)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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
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)
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
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)
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
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:69194 AgrOrtholog
BIND 134400
  134401
Ensembl Genes ENSRNOG00000028366 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000036544 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000064099 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030470 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000075054 UniProtKB/TrEMBL
Gene3D-CATH 2.40.340.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.980.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro MoaB/Mog-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MoaB/Mog_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MoCF_biosynth_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MoeA-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MoeA_C_domain_IV UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MoeA_C_domain_IV_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MoeA_linker/N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MoeA_linker/N_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:64845 UniProtKB/Swiss-Prot
NCBI Gene 64845 ENTREZGENE
PANTHER PTHR10192 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam MoCF_biosynth UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MoeA_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MoeA_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gphn PhenoGen
PROSITE MOCF_BIOSYNTHESIS_1 UniProtKB/Swiss-Prot
  MOCF_BIOSYNTHESIS_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART MoCF_biosynth UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53218 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF63867 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF63882 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC216665
TIGRFAMs molyb_syn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F1MA86_RAT UniProtKB/TrEMBL
  GEPH_RAT UniProtKB/Swiss-Prot
  M0R423_RAT UniProtKB/TrEMBL
  Q03555 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Gphn  gephyrin      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization membrane-associated protein 68677
gene_cellular_localization membrane-associated protein 69377
gene_disease mutation of the human homolog has been identified in a patient with molybdenum cofactor deficiency who does not have a mutation in MOCS1 or MOCS2 68677
gene_function catalyses the insertion of molybdenum into molybdopterin 68677
gene_function catalyses the insertion of molybdenum into molybdopterin 69377
gene_process essential for the postsynaptic localization of receptors for neurotransmitters 68677
gene_process essential for the postsynaptic localization of receptors for neurotransmitters 69377
gene_process plays a role in molybdenum cofactor biosynthesis 68677
gene_process plays a role in molybdenum cofactor biosynthesis 69377