Tubb5 (tubulin, beta 5 class I) - Rat Genome Database

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Gene: Tubb5 (tubulin, beta 5 class I) Rattus norvegicus
Analyze
Symbol: Tubb5
Name: tubulin, beta 5 class I
RGD ID: 628596
Description: Enables GTPase activating protein binding activity and protein domain specific binding activity. Predicted to be involved in microtubule cytoskeleton organization; mitotic cell cycle; and regulation of synapse organization. Predicted to act upstream of or within spindle assembly. Located in membrane raft. Part of protein-containing complex. Human ortholog(s) of this gene implicated in complex cortical dysplasia with other brain malformations 6 and congenital symmetric circumferential skin creases 1. Orthologous to human TUBB (tubulin beta class I); PARTICIPATES IN phagocytosis pathway; INTERACTS WITH (S)-colchicine; 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Tubb; tubulin beta-5 chain; tubulin, beta; tubulin, beta 5
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
mRatBN7.2202,912,779 - 2,916,928 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl202,912,778 - 2,916,940 (+)Ensembl
Rnor_6.0203,422,448 - 3,426,420 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,422,461 - 3,426,371 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,519,551 - 5,523,476 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,060,224 - 3,090,776 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1203,060,491 - 3,065,012 (+)NCBI
Celera20338,700 - 342,843 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
(S)-colchicine  (EXP)
(S)-nicotine  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP,ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrotoluene  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP)
2,4-dinitrotoluene  (EXP)
2-acetamidofluorene  (EXP)
2-hydroxypropanoic acid  (ISO)
2-methylcholine  (ISO)
2-nitrofluorene  (EXP)
3,4-dihydrocoumarin  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (EXP,ISO)
aflatoxin B1  (EXP)
ammonium chloride  (EXP)
aniline  (ISO)
antirheumatic drug  (ISO)
apigenin  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
azathioprine  (ISO)
beauvericin  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (EXP)
beta-naphthoflavone  (ISO)
biochanin A  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (EXP)
Calpeptin  (EXP)
carbon nanotube  (ISO)
carmustine  (ISO)
chloropicrin  (ISO)
choline  (EXP)
chromium(6+)  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
corticosterone  (EXP)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dexamethasone  (EXP,ISO)
dibenz[a,h]anthracene  (EXP)
dibenzo[a,l]pyrene  (EXP)
dibutyl phthalate  (ISO)
dichlorvos  (EXP)
diethylstilbestrol  (EXP)
dopamine  (EXP,ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
enniatin  (EXP,ISO)
Enterolactone  (ISO)
enzyme inhibitor  (ISO)
ethanol  (EXP,ISO)
fenoldopam  (EXP)
fluoranthene  (EXP)
flutamide  (EXP)
folic acid  (EXP,ISO)
fumonisin B1  (ISO)
furan  (EXP)
genistein  (ISO)
gentamycin  (EXP)
gold atom  (ISO)
gold(0)  (ISO)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP)
indometacin  (ISO)
isoflavones  (ISO)
isoprenaline  (ISO)
ivermectin  (ISO)
L-methionine  (EXP)
lead(II) chloride  (ISO)
leflunomide  (EXP,ISO)
levofloxacin  (EXP)
lovastatin  (ISO)
maneb  (ISO)
melatonin  (ISO)
methamphetamine  (EXP)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
miconazole  (ISO)
Monobutylphthalate  (ISO)
N-acetyl-beta-D-glucosamine  (ISO)
N-acetyl-D-glucosamine  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
nicotine  (ISO)
ochratoxin A  (EXP)
oxaliplatin  (EXP)
oxycodone  (EXP)
paclitaxel  (ISO)
palbociclib  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
pinosylvin  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (ISO)
propiconazole  (ISO)
Propiverine  (EXP)
prostaglandin A1  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
rotenone  (EXP,ISO)
Salinomycin  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
sulfasalazine  (ISO)
sunitinib  (ISO)
T-2 toxin  (EXP)
tamoxifen  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trans-pinosylvin  (ISO)
Tributyltin oxide  (ISO)
trimellitic anhydride  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
trovafloxacin  (EXP)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vincaleukoblastine  (EXP)
vinclozolin  (EXP)
vincristine  (EXP,ISO)
vitamin E  (ISO)
warfarin  (ISO)
withaferin A  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11120798   PMID:11870213   PMID:12519789   PMID:15060004   PMID:15121885   PMID:15121898   PMID:15489334   PMID:16418269   PMID:16854843   PMID:18480465   PMID:19567321   PMID:19961433  
PMID:20387083   PMID:21362503   PMID:21525035   PMID:21630459   PMID:21753002   PMID:22082260   PMID:22309793   PMID:22871113   PMID:23178297   PMID:23533145   PMID:23979707   PMID:24833723  
PMID:25763846   PMID:25931508   PMID:26316108   PMID:29476059  


Genomics

Candidate Gene Status
Tubb5 is a candidate Gene for QTL Pur27
Tubb5 is a candidate Gene for QTL Pur30
Comparative Map Data
Tubb5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2202,912,779 - 2,916,928 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl202,912,778 - 2,916,940 (+)Ensembl
Rnor_6.0203,422,448 - 3,426,420 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,422,461 - 3,426,371 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,519,551 - 5,523,476 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,060,224 - 3,090,776 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1203,060,491 - 3,065,012 (+)NCBI
Celera20338,700 - 342,843 (+)NCBICelera
Cytogenetic Map20p12NCBI
TUBB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl630,717,435 - 30,725,538 (+)EnsemblGRCh38hg38GRCh38
GRCh38630,720,352 - 30,725,422 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37630,688,129 - 30,693,199 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36630,796,136 - 30,801,178 (+)NCBINCBI36hg18NCBI36
Celera632,286,289 - 32,291,331 (+)NCBI
Cytogenetic Map6p21.33NCBI
HuRef630,488,105 - 30,493,147 (+)NCBIHuRef
CHM1_1630,690,286 - 30,695,330 (+)NCBICHM1_1
Tubb5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391736,144,812 - 36,149,193 (-)NCBIGRCm39mm39
GRCm39 Ensembl1736,144,813 - 36,149,198 (-)Ensembl
GRCm381735,833,920 - 35,838,301 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,833,921 - 35,838,306 (-)EnsemblGRCm38mm10GRCm38
MGSCv371735,970,865 - 35,975,246 (-)NCBIGRCm37mm9NCBIm37
MGSCv361735,442,858 - 35,446,260 (-)NCBImm8
Celera1739,343,980 - 39,348,363 (-)NCBICelera
Cytogenetic Map17B1NCBI
Tubb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955583704,750 - 718,649 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955583704,811 - 715,742 (+)NCBIChiLan1.0ChiLan1.0
TUBB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1631,333,985 - 31,339,739 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0630,465,367 - 30,470,451 (+)NCBIMhudiblu_PPA_v0panPan3
TUBB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.112512,738 - 517,154 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha12650,056 - 654,417 (+)NCBI
ROS_Cfam_1.012655,875 - 660,238 (+)NCBI
UMICH_Zoey_3.112513,860 - 518,216 (+)NCBI
UNSW_CanFamBas_1.012582,704 - 587,060 (+)NCBI
UU_Cfam_GSD_1.012651,287 - 655,647 (+)NCBI
Tubb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494634,015,619 - 34,019,493 (+)NCBI
SpeTri2.0NW_004936837380,880 - 384,752 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TUBB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl723,245,743 - 23,294,218 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1723,247,827 - 23,252,240 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2726,969,793 - 26,974,207 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TUBB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11741,728,103 - 41,733,206 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1741,729,143 - 41,733,243 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604430,417,844 - 30,423,077 (+)NCBIVero_WHO_p1.0
Tubb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475425,001,555 - 25,005,459 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH127649  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,915,964 - 2,916,146 (+)MAPPERmRatBN7.2
Rnor_6.0203,425,634 - 3,425,815NCBIRnor6.0
Rnor_5.0205,522,737 - 5,522,918UniSTSRnor5.0
RGSC_v3.4203,063,883 - 3,064,064UniSTSRGSC3.4
Celera20341,885 - 342,066UniSTS
RH 3.4 Map2052.12UniSTS
Cytogenetic Map20p12UniSTS
RH128120  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera20342,552 - 342,756UniSTS
RH 3.4 Map2052.52UniSTS
Cytogenetic Map20p12UniSTS
BI273785  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,915,964 - 2,916,138 (+)MAPPERmRatBN7.2
Rnor_6.0203,425,634 - 3,425,807NCBIRnor6.0
Rnor_5.0205,522,737 - 5,522,910UniSTSRnor5.0
RGSC_v3.4203,063,883 - 3,064,056UniSTSRGSC3.4
Celera20341,885 - 342,058UniSTS
RH 3.4 Map2053.33UniSTS
Cytogenetic Map20p12UniSTS
UniSTS:267009  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,915,857 - 2,916,059 (+)MAPPERmRatBN7.2
Rnor_6.0203,425,527 - 3,425,728NCBIRnor6.0
Rnor_5.0205,522,630 - 5,522,831UniSTSRnor5.0
RGSC_v3.4203,063,776 - 3,063,977UniSTSRGSC3.4
Celera20341,778 - 341,979UniSTS
Cytogenetic Map20p12UniSTS
PMC26660P4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,915,579 - 2,915,897 (+)MAPPERmRatBN7.2
Rnor_6.0203,425,249 - 3,425,566NCBIRnor6.0
Rnor_5.0205,522,352 - 5,522,669UniSTSRnor5.0
RGSC_v3.4203,063,498 - 3,063,815UniSTSRGSC3.4
Celera20341,500 - 341,817UniSTS
Cytogenetic Map20p12UniSTS
Tubb5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X33,327,476 - 33,327,680 (+)MAPPERmRatBN7.2
mRatBN7.2202,915,929 - 2,916,130 (+)MAPPERmRatBN7.2
Rnor_6.0X35,110,833 - 35,111,036NCBIRnor6.0
Rnor_6.0203,425,599 - 3,425,799NCBIRnor6.0
Rnor_5.0205,522,702 - 5,522,902UniSTSRnor5.0
Rnor_5.0X35,446,990 - 35,447,193UniSTSRnor5.0
Celera20341,850 - 342,050UniSTS
CeleraX33,613,160 - 33,613,363UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2013624629Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2026463954597031Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2026463954597031Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:55
Count of miRNA genes:52
Interacting mature miRNAs:54
Transcripts:ENSRNOT00000001095
Prediction methods:Miranda, Rnahybrid
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 24 18 14 4 14 55 16 24
Medium 3 19 39 27 15 27 8 11 19 19 17 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000079854   ⟹   ENSRNOP00000075269
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,912,778 - 2,916,940 (+)Ensembl
Rnor_6.0 Ensembl203,422,489 - 3,426,371 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084917   ⟹   ENSRNOP00000072090
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,912,795 - 2,916,940 (+)Ensembl
Rnor_6.0 Ensembl203,422,461 - 3,425,901 (+)Ensembl
RefSeq Acc Id: NM_173102   ⟹   NP_775125
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2202,912,779 - 2,916,928 (+)NCBI
Rnor_6.0203,422,448 - 3,426,420 (+)NCBI
Rnor_5.0205,519,551 - 5,523,476 (+)NCBI
RGSC_v3.4203,060,224 - 3,090,776 (+)RGD
Celera20338,700 - 342,843 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_775125 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH60540 (Get FASTA)   NCBI Sequence Viewer  
  BAA32736 (Get FASTA)   NCBI Sequence Viewer  
  CAE84031 (Get FASTA)   NCBI Sequence Viewer  
  EDL86739 (Get FASTA)   NCBI Sequence Viewer  
  P69897 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_775125   ⟸   NM_173102
- UniProtKB: P69897 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075269   ⟸   ENSRNOT00000079854
RefSeq Acc Id: ENSRNOP00000072090   ⟸   ENSRNOT00000084917

Transcriptome

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

Promoters
RGD ID:13701304
Promoter ID:EPDNEW_R11824
Type:initiation region
Name:Tubb5_1
Description:tubulin, beta 5 class I
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_6.0203,422,464 - 3,422,524EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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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)
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
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/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)
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
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
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)
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
MNS/Gib (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
MR/N (2020)
Visual CSV TAB Printer
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)
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
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)
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
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: 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)
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/OlalpcvMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
SR/JrHsd (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: 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)
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/JrHsdMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
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)
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/RijCrl (2020)
Visual CSV TAB Printer
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)
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
WKY/N (2020)
Visual CSV TAB Printer
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)
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
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:628596 AgrOrtholog
Ensembl Genes ENSRNOG00000061216 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000072090 UniProtKB/Swiss-Prot
  ENSRNOP00000075269 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000079854 UniProtKB/Swiss-Prot
  ENSRNOT00000084917 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.287.600 UniProtKB/Swiss-Prot
  3.30.1330.20 UniProtKB/Swiss-Prot
  3.40.50.1440 UniProtKB/Swiss-Prot
InterPro Beta-tubulin_BS UniProtKB/Swiss-Prot
  Beta_tubulin UniProtKB/Swiss-Prot
  Tub_FtsZ_C UniProtKB/Swiss-Prot
  Tubulin UniProtKB/Swiss-Prot
  Tubulin/FtsZ_2-layer-sand-dom UniProtKB/Swiss-Prot
  Tubulin/FtsZ_C_sf UniProtKB/Swiss-Prot
  Tubulin/FtsZ_GTPase_sf UniProtKB/Swiss-Prot
  Tubulin_C UniProtKB/Swiss-Prot
  Tubulin_CS UniProtKB/Swiss-Prot
  Tubulin_FtsZ_GTPase UniProtKB/Swiss-Prot
KEGG Report rno:29214 UniProtKB/Swiss-Prot
NCBI Gene 29214 ENTREZGENE
PANTHER PTHR11588 UniProtKB/Swiss-Prot
Pfam Tubulin UniProtKB/Swiss-Prot
  Tubulin_C UniProtKB/Swiss-Prot
PharmGKB TUBB RGD
PhenoGen Tubb5 PhenoGen
PRINTS BETATUBULIN UniProtKB/Swiss-Prot
  TUBULIN UniProtKB/Swiss-Prot
PROSITE TUBULIN UniProtKB/Swiss-Prot
  TUBULIN_B_AUTOREG UniProtKB/Swiss-Prot
SMART Tubulin UniProtKB/Swiss-Prot
  Tubulin_C UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52490 UniProtKB/Swiss-Prot
  SSF55307 UniProtKB/Swiss-Prot
UniProt P69897 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary P05218 UniProtKB/Swiss-Prot
  Q6P9X8 UniProtKB/Swiss-Prot
  Q8WUC1 UniProtKB/Swiss-Prot
  Q9CY33 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-10-19 Tubb5  tubulin, beta 5 class I  Tubb  tubulin, beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-10-12 Tubb  tubulin, beta  Tubb5  tubulin, beta 5 class I  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-10-10 Tubb5  tubulin, beta 5 class I  Tubb5  tubulin, beta 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Tubb5  tubulin, beta 5      Symbol and Name status set to approved 1299863 APPROVED
2003-02-27 Tubb5  tubulin, beta 5      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA downregulated during brain development 727284