Bcan (brevican) - Rat Genome Database
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Gene: Bcan (brevican) Rattus norvegicus
Analyze
Symbol: Bcan
Name: brevican
RGD ID: 2194
Description: Predicted to have calcium ion binding activity; carbohydrate binding activity; and hyaluronic acid binding activity. Involved in cell-matrix adhesion; nervous system development; and regulation of neuronal synaptic plasticity. Localizes to several cellular components, including GABA-ergic synapse; main axon; and perineuronal net. Used to study high grade glioma. Biomarker of high grade glioma and middle cerebral artery infarction. Orthologous to human BCAN (brevican); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: ALPBRE; BEHAB; brain-enriched hyaluronan-binding protein; Brevican (brain specific proteoglycan in the aggrecan family); brevican core 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
mRatBN7.22173,454,479 - 173,467,717 (-)NCBI
Rnor_6.0 Ensembl2187,359,677 - 187,372,657 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02187,359,674 - 187,373,133 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02206,762,691 - 206,776,016 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42180,067,864 - 180,080,942 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12180,022,993 - 180,030,847 (-)NCBI
Celera2167,401,907 - 167,414,841 (-)NCBICelera
Cytogenetic Map2q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Ajmo JM, etal., J Neurochem. 2010 May;113(3):784-95. doi: 10.1111/j.1471-4159.2010.06647.x. Epub 2010 Feb 17.
2. Aya-ay J, etal., Exp Neurol. 2005 May;193(1):149-62. doi: 10.1016/j.expneurol.2004.11.021.
3. Carmichael ST, etal., Exp Neurol. 2005 Jun;193(2):291-311.
4. Davies JE, etal., Eur J Neurosci. 2004 Mar;19(5):1226-42.
5. Deepa SS, etal., J Biol Chem. 2006 Jun 30;281(26):17789-800. Epub 2006 Apr 27.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Hagihara K, etal., J Comp Neurol. 1999 Jul 26;410(2):256-64.
8. Hamel MG, etal., J Neurochem. 2005 Jun;93(6):1533-41.
9. Hedstrom KL, etal., J Cell Biol. 2007 Aug 27;178(5):875-86. doi: 10.1083/jcb.200705119. Epub 2007 Aug 20.
10. Jaworski DM, etal., J Cell Biol 1994 Apr;125(2):495-509.
11. Jaworski DM, etal., J Neurosci. 1995 Feb;15(2):1352-62.
12. John N, etal., Mol Cell Neurosci. 2006 Apr;31(4):774-84. doi: 10.1016/j.mcn.2006.01.011. Epub 2006 Feb 28.
13. Lu R, etal., BMC Cancer. 2012 Dec 19;12:607. doi: 10.1186/1471-2407-12-607.
14. MGD data from the GO Consortium
15. Miura R, etal., J Neurochem. 2001 Jan;76(2):413-24.
16. Morales DM, etal., Mol Cell Proteomics. 2011 Dec 20.
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. Nutt CL, etal., Cancer Res. 2001 Oct 1;61(19):7056-9.
19. RGD automated data pipeline
20. RGD automated import pipeline for gene-chemical interactions
21. Seidenbecher CI, etal., J Biol Chem 1995 Nov 10;270(45):27206-12.
22. Tanaka S, etal., Hiroshima Daigaku Shigaku Zasshi 1975;8(2):168-75.
23. Tang X, etal., J Neurosci Res 2003 Feb 1;71(3):427-44.
24. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
25. Viapiano MS, etal., Cancer Res. 2005 Aug 1;65(15):6726-33. doi: 10.1158/0008-5472.CAN-05-0585.
26. Viapiano MS, etal., J Biol Chem. 2003 Aug 29;278(35):33239-47. doi: 10.1074/jbc.M303480200. Epub 2003 Jun 10.
27. Wohl SG, etal., Nat Commun. 2017 Nov 17;8(1):1603. doi: 10.1038/s41467-017-01624-y.
28. Yamada H, etal., Biochem Biophys Res Commun 1995 Nov 22;216(3):957-63.
Additional References at PubMed
PMID:8889548   PMID:9294172   PMID:12370289   PMID:12379262   PMID:12477932   PMID:17972319   PMID:19141078   PMID:25052349   PMID:28712654   PMID:29476059  


Genomics

Comparative Map Data
Bcan
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22173,454,479 - 173,467,717 (-)NCBI
Rnor_6.0 Ensembl2187,359,677 - 187,372,657 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02187,359,674 - 187,373,133 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02206,762,691 - 206,776,016 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42180,067,864 - 180,080,942 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12180,022,993 - 180,030,847 (-)NCBI
Celera2167,401,907 - 167,414,841 (-)NCBICelera
Cytogenetic Map2q34NCBI
BCAN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1156,641,390 - 156,659,532 (+)EnsemblGRCh38hg38GRCh38
GRCh381156,642,117 - 156,659,528 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371156,611,909 - 156,629,320 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361154,878,364 - 154,895,944 (+)NCBINCBI36hg18NCBI36
Build 341153,424,812 - 153,442,391NCBI
Celera1129,682,549 - 129,700,133 (+)NCBI
Cytogenetic Map1q23.1NCBI
HuRef1127,969,333 - 127,986,922 (+)NCBIHuRef
CHM1_11158,007,947 - 158,025,532 (+)NCBICHM1_1
Bcan
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39387,894,838 - 87,911,134 (-)NCBIGRCm39mm39
GRCm39 Ensembl387,894,838 - 87,907,537 (-)Ensembl
GRCm38387,987,531 - 88,002,175 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl387,987,531 - 88,000,230 (-)EnsemblGRCm38mm10GRCm38
MGSCv37387,791,453 - 87,804,278 (-)NCBIGRCm37mm9NCBIm37
MGSCv36388,073,458 - 88,086,157 (-)NCBImm8
Celera388,024,909 - 88,037,731 (-)NCBICelera
Cytogenetic Map3F1NCBI
cM Map338.78NCBI
Bcan
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555452,723,780 - 2,739,450 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555452,723,780 - 2,739,334 (+)NCBIChiLan1.0ChiLan1.0
BCAN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11135,808,783 - 135,826,344 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1135,808,783 - 135,826,344 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01131,985,310 - 132,003,068 (+)NCBIMhudiblu_PPA_v0panPan3
BCAN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl741,313,579 - 41,330,178 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1741,313,578 - 41,330,178 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Bcan
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365805,816,196 - 5,828,531 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BCAN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl493,432,335 - 93,450,827 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1493,432,331 - 93,450,895 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24102,095,832 - 102,114,192 (-)NCBISscrofa10.2Sscrofa10.2susScr3
BCAN
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1207,203,546 - 7,221,108 (-)NCBI
ChlSab1.1 Ensembl207,203,378 - 7,220,973 (-)Ensembl
Bcan
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248851,816,591 - 1,829,971 (+)NCBI

Position Markers
RH138503  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02187,359,772 - 187,359,898NCBIRnor6.0
Rnor_6.02184,915,756 - 184,915,882NCBIRnor6.0
Rnor_5.02206,762,789 - 206,762,915UniSTSRnor5.0
Rnor_5.02204,306,829 - 204,306,955UniSTSRnor5.0
RGSC_v3.42180,067,962 - 180,068,088UniSTSRGSC3.4
Celera2167,402,005 - 167,402,131UniSTS
RH 3.4 Map21130.0UniSTS
Cytogenetic Map2q34UniSTS
UniSTS:224394  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02187,359,693 - 187,359,855NCBIRnor6.0
Rnor_6.02184,915,677 - 184,915,839NCBIRnor6.0
Rnor_5.02206,762,710 - 206,762,872UniSTSRnor5.0
Rnor_5.02204,306,750 - 204,306,912UniSTSRnor5.0
RGSC_v3.42180,067,883 - 180,068,045UniSTSRGSC3.4
Celera2167,401,926 - 167,402,088UniSTS
Cytogenetic Map2q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242776916195645082Rat
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)2157914311204022555Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2140566078217498545Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2147522550217498710Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246537589217498710Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243133606217498545Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243133606217498545Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2184730446229730446Rat
61473Bp19Blood pressure QTL 196.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2186611811189857032Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2184730446229730446Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2149114878225501939Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2181990297240020001Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256244671217498710Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141583337217498710Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828049217498710Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147122993240020001Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2147122993240020001Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2183984665228984665Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2142053350204585731Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2157914409217498545Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2116075644228737869Rat
631522Bp74Blood pressure QTL 740.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2186611811198704485Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2169852800217498545Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557254121739Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557237742948Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2161745602206745602Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2181522444226522444Rat
2301415Cm67Cardiac mass QTL 670.003heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2172795683189857032Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2116075644228737869Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2175403337239166203Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2118446646227707979Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2138901276217498710Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243149788198704485Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)275687495221880419Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2158159186217498710Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283819608239166203Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828236243550655Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283819608243901375Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2158159186217498710Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2142053350228984665Rat
1549833Bp257Blood pressure QTL 2570.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2181987080199696953Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2118446793228582621Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2177680772243901375Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2118446646200453484Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2118446646200453484Rat
1359032Hrtrt18Heart rate QTL 18heart pumping trait (VT:2000009)heart rate (CMO:0000002)2169852670207612467Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)278321410217498710Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2159585731204585731Rat
6903312Bw112Body weight QTL 1123.20.0013body mass (VT:0001259)body weight (CMO:0000012)2149614623198704357Rat
7488904Bp363Blood pressure QTL 3630.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2186889035189857032Rat
6907363Bp357Blood pressure QTL 3574.10.002arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2143447078188447078Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2174160958219160958Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2177339806222339806Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2169852670243026643Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)283754907237610852Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2149614466205573168Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2149614466205573168Rat
12879846Cm90Cardiac mass QTL 900.011heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)2172795683189857032Rat
12879836Kidm61Kidney mass QTL 610.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2172795683199696953Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat
12879839Cm85Cardiac mass QTL 850.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2172795683199696953Rat
11565181Bw176Body weight QTL 1760.002body mass (VT:0001259)body weight (CMO:0000012)2172795683189857032Rat
12879838Cm86Cardiac mass QTL 860.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2172795683199696953Rat
12879840Bw179Body weight QTL 1790.005body mass (VT:0001259)body weight (CMO:0000012)2172795683199696953Rat
12879845Cm89Cardiac mass QTL 890.008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2172795683189857032Rat
11565180Kidm56Kidney mass QTL 560.003kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2172795683189857032Rat
12879837Am2Aortic mass QTL 20.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2172795683199696953Rat
12879847Am4Aortic mass QTL 40.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2172795683189857032Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:50
Count of miRNA genes:43
Interacting mature miRNAs:49
Transcripts:ENSRNOT00000025496
Prediction methods: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 1 54
Low 5 9 2 10 11 7
Below cutoff 2 23 23 17 16 17 8 8 4 4 18 4 8

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001033665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_012916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101784 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101785 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101786 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101788 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101789 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101790 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005500246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005500247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AI535159 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC094307 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB577797 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB784255 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB810773 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473976 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U37142 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X79881 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X86406 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Z28366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000025496   ⟹   ENSRNOP00000025496
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2187,359,677 - 187,372,652 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000083116   ⟹   ENSRNOP00000070660
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2187,366,297 - 187,372,657 (-)Ensembl
RefSeq Acc Id: NM_001033665   ⟹   NP_001028837
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22173,454,479 - 173,467,460 (-)NCBI
Rnor_6.02187,359,674 - 187,372,652 (-)NCBI
Rnor_5.02206,762,691 - 206,776,016 (-)NCBI
RGSC_v3.42180,067,864 - 180,080,942 (-)RGD
Celera2167,401,907 - 167,414,841 (-)RGD
Sequence:
RefSeq Acc Id: NM_012916   ⟹   NP_037048
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22173,459,486 - 173,467,460 (-)NCBI
Rnor_6.02187,364,678 - 187,372,652 (-)NCBI
Rnor_5.02206,762,691 - 206,776,016 (-)NCBI
RGSC_v3.42180,067,864 - 180,080,942 (-)RGD
Celera2167,406,914 - 167,414,841 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006232596   ⟹   XP_006232658
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02187,359,674 - 187,371,870 (-)NCBI
Rnor_5.02206,762,691 - 206,776,016 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006232597   ⟹   XP_006232659
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02187,359,674 - 187,373,131 (-)NCBI
Rnor_5.02206,762,691 - 206,776,016 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590643   ⟹   XP_017446132
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02187,359,674 - 187,371,966 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590645   ⟹   XP_017446134
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02187,359,674 - 187,373,131 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039101784   ⟹   XP_038957712
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22173,454,479 - 173,465,898 (-)NCBI
RefSeq Acc Id: XM_039101785   ⟹   XP_038957713
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22173,454,479 - 173,465,898 (-)NCBI
RefSeq Acc Id: XM_039101786   ⟹   XP_038957714
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22173,454,479 - 173,465,898 (-)NCBI
RefSeq Acc Id: XM_039101787   ⟹   XP_038957715
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22173,454,479 - 173,467,717 (-)NCBI
RefSeq Acc Id: XM_039101788   ⟹   XP_038957716
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22173,454,479 - 173,467,717 (-)NCBI
RefSeq Acc Id: XM_039101789   ⟹   XP_038957717
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22173,454,479 - 173,465,813 (-)NCBI
RefSeq Acc Id: XM_039101790   ⟹   XP_038957718
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22173,454,479 - 173,466,774 (-)NCBI
RefSeq Acc Id: XR_001836420
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02187,359,674 - 187,373,133 (-)NCBI
Sequence:
RefSeq Acc Id: XR_005500246
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22173,454,479 - 173,465,898 (-)NCBI
RefSeq Acc Id: XR_005500247
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22173,454,795 - 173,465,898 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001028837   ⟸   NM_001033665
- Peptide Label: isoform 1 precursor
- UniProtKB: P55068 (UniProtKB/Swiss-Prot),   G3V8G4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_037048   ⟸   NM_012916
- Peptide Label: isoform 2 precursor
- UniProtKB: P55068 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006232659   ⟸   XM_006232597
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006232658   ⟸   XM_006232596
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017446134   ⟸   XM_017590645
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017446132   ⟸   XM_017590643
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000070660   ⟸   ENSRNOT00000083116
RefSeq Acc Id: ENSRNOP00000025496   ⟸   ENSRNOT00000025496
RefSeq Acc Id: XP_038957715   ⟸   XM_039101787
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957716   ⟸   XM_039101788
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957718   ⟸   XM_039101790
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957713   ⟸   XM_039101785
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038957714   ⟸   XM_039101786
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038957712   ⟸   XM_039101784
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957717   ⟸   XM_039101789
- Peptide Label: isoform X1
Protein Domains
C-type lectin   EGF-like   Ig-like   Ig-like V-type   Link   Sushi

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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 206768534 206768535 C T snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), KFRS3B/Kyo (KyushuU), F344/Jcl (KyushuU), F344/Stm (KyushuU), IS-Tlk/Kyo (KyushuU), F344/NSlc (KyushuU), F344/DuCrlCrlj (KyushuU), BUF/MNa (KyushuU), SBH/Ygl (MCW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), SBH/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), M520/N (KNAW), IS/Kyo (KyushuU)
2 206770943 206770944 C T snv RCS/Kyo (KyushuU), ZF (KyushuU), SR/JrHsd (KNAW), LL/MavRrrc (KNAW), LH/MavRrrc (KNAW), SR/JrHsd (MCW), GK/Ox (KNAW), ZFDM (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 187365517 187365518 C T snv ACI/EurMcwi (MCW), WKY/NHsd (RGD), SBH/Ygl (MCW), COP/CrCrl (MCW & UW), WKY/Gcrc (RGD), WKY/NCrl (RGD), WAG/Rij (RGD), SHRSP/Gcrc (RGD), CDR, CDS, ACI/N (MCW), F344/NRrrc (MCW), M520/N (MCW), WKY/N (MCW), ACI/EurMcwi (RGD), F344/NCrl (RGD), SBH/Ygl (RGD), SHR/NHsd (RGD)
2 187367926 187367927 C T snv SR/JrHsd (RGD), LL/MavRrrc (RGD), LH/MavRrrc (RGD), GK/Ox (RGD), SR/JrHsd (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 180073416 180073417 C A snv SS/JrHsdMcwi (MCW)
2 180073419 180073420 G A snv SS/JrHsdMcwi (MCW)
2 180073710 180073711 C T snv ACI/N (KNAW), F344/NRrrc (KNAW), M520/N (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), ACI/EurMcwi (MCW), F344/NHsd (ICAHN), SHR/OlaIpcv (ICL), SHRSP/Gcrc (MDC), LCR/2Mco (UMich), HCR/2Mco (UMich), LCR/1Mco (UMich), HCR/1Mco (UMich), COP/CrCrl (MCW & UW), ACI/EurMcwi (ICL), F344/NCrl (ICL), SBH/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WAG/Rij (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL)
2 180076119 180076120 C T snv GK/Ox (ICL), SR/JrHsd (ICL), LL/MavRrrc (ICL), LH/MavRrrc (ICL), SR/JrHsd (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2194 AgrOrtholog
Ensembl Genes ENSRNOG00000018798 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000025496 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070660 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025496 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000083116 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.10.100.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro C-type_lectin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-type_lectin-like/link_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-type_lectin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CTDL_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_Ca-bd_dom UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig/MHC_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Link_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sushi/SCR/CCP_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sushi_SCR_CCP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25393 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 25393 ENTREZGENE
Pfam EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lectin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sushi UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Xlink UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Bcan PhenoGen
PRINTS LINKMODULE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE C_TYPE_LECTIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C_TYPE_LECTIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_MHC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LINK_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LINK_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SUSHI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CCP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CLECT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  IGv UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LINK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56436 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57535 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC218890
UniProt A0A0G2JYH8_RAT UniProtKB/TrEMBL
  G3V8G4 ENTREZGENE, UniProtKB/TrEMBL
  P55068 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q62860 UniProtKB/Swiss-Prot
  Q63040 UniProtKB/Swiss-Prot
  Q63513 UniProtKB/Swiss-Prot


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