Tfe3 (transcription factor binding to IGHM enhancer 3) - Rat Genome Database

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Gene: Tfe3 (transcription factor binding to IGHM enhancer 3) Rattus norvegicus
Analyze
Symbol: Tfe3
Name: transcription factor binding to IGHM enhancer 3
RGD ID: 1559642
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and protein heterodimerization activity. Predicted to be involved in several processes, including negative regulation of cold-induced thermogenesis; positive regulation of brown fat cell differentiation; and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of transcription, DNA-templated and regulation of osteoclast differentiation. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in renal cell carcinoma. Orthologous to human TFE3 (transcription factor binding to IGHM enhancer 3); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC317376; RGD1559642; similar to Tcfe3 protein; Tcfe3; transcription factor E3
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
mRatBN7.2X14,729,547 - 14,742,830 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX14,729,550 - 14,742,571 (-)Ensembl
Rnor_6.0X15,574,579 - 15,587,826 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,575,934 - 15,587,419 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X16,355,812 - 16,369,002 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,768,875 - 26,781,006 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX14,814,215 - 14,827,305 (-)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetylsalicylic acid  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aristolochic acid  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (ISO)
bisphenol F  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
chloroacetaldehyde  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (EXP,ISO)
cylindrospermopsin  (ISO)
cytarabine  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenofibrate  (EXP,ISO)
fenvalerate  (EXP)
fingolimod hydrochloride  (ISO)
flutamide  (EXP)
fonofos  (ISO)
glycochenodeoxycholic acid  (ISO)
ibuprofen  (EXP,ISO)
indometacin  (ISO)
ketamine  (EXP)
menadione  (ISO)
mercury dibromide  (ISO)
metformin  (EXP)
methimazole  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
N-acetyl-L-cysteine  (ISO)
N-acetylsphingosine  (ISO)
nefazodone  (EXP)
nickel sulfate  (ISO)
okadaic acid  (ISO)
p-chloromercuribenzoic acid  (ISO)
paracetamol  (ISO)
parathion  (ISO)
pirinixic acid  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
tetrachloromethane  (EXP)
torin 1  (ISO)
triptonide  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zebularine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cellular_component  (ND)
cytoplasm  (ISO,ISS)
cytosol  (ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,ISO,ISS)

References

Additional References at PubMed
PMID:11930005   PMID:15994295   PMID:16936731   PMID:21209915   PMID:22692423   PMID:26352760   PMID:27913603   PMID:29146937   PMID:32716134  


Genomics

Comparative Map Data
Tfe3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,729,547 - 14,742,830 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX14,729,550 - 14,742,571 (-)Ensembl
Rnor_6.0X15,574,579 - 15,587,826 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,575,934 - 15,587,419 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X16,355,812 - 16,369,002 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,768,875 - 26,781,006 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX14,814,215 - 14,827,305 (-)NCBICelera
Cytogenetic MapXq12NCBI
TFE3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX49,028,726 - 49,043,410 (-)EnsemblGRCh38hg38GRCh38
GRCh38X49,028,726 - 49,043,357 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X48,886,237 - 48,900,883 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X48,771,186 - 48,787,934 (-)NCBINCBI36hg18NCBI36
Build 34X48,642,489 - 48,657,239NCBI
CeleraX52,763,508 - 52,778,256 (+)NCBI
Cytogenetic MapXp11.23NCBI
HuRefX46,544,091 - 46,558,358 (-)NCBIHuRef
CHM1_1X48,917,574 - 48,932,321 (-)NCBICHM1_1
Tfe3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X7,628,769 - 7,641,441 (+)NCBIGRCm39mm39
GRCm39 EnsemblX7,628,799 - 7,641,441 (+)Ensembl
GRCm38X7,762,530 - 7,775,202 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX7,762,560 - 7,775,202 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X7,339,787 - 7,352,328 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X6,919,676 - 6,932,158 (+)NCBImm8
CeleraX3,695,480 - 3,708,004 (-)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX3.5NCBI
Tfe3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955543547,037 - 561,073 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955543547,037 - 561,073 (-)NCBIChiLan1.0ChiLan1.0
TFE3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X49,182,795 - 49,197,194 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX49,182,795 - 49,197,194 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X41,326,802 - 41,341,574 (-)NCBIMhudiblu_PPA_v0panPan3
TFE3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X42,181,639 - 42,192,709 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX42,183,037 - 42,193,892 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX16,557,254 - 16,568,302 (-)NCBI
ROS_Cfam_1.0X42,317,881 - 42,328,931 (-)NCBI
UMICH_Zoey_3.1X42,304,191 - 42,315,238 (-)NCBI
UNSW_CanFamBas_1.0X42,291,847 - 42,302,895 (-)NCBI
UU_Cfam_GSD_1.0X42,386,591 - 42,397,641 (-)NCBI
Tfe3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X34,693,183 - 34,705,282 (-)NCBI
SpeTri2.0NW_004936721933,572 - 945,717 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TFE3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX43,100,005 - 43,116,227 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X43,100,375 - 43,116,377 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X47,948,307 - 47,964,209 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TFE3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X46,141,377 - 46,155,445 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 EnsemblX46,140,543 - 46,155,372 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607611,655,554 - 11,669,637 (-)NCBIVero_WHO_p1.0
Tfe3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624893803,717 - 817,700 (-)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:140
Count of miRNA genes:74
Interacting mature miRNAs:79
Transcripts:ENSRNOT00000012829, ENSRNOT00000029776
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 26 15 7 11 7 2 66 30 34 11
Low 1 17 42 34 8 34 8 9 8 5 7 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001271227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256721 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099775 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099776 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099778 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099779 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005497983 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005497984 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC130624 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000012829   ⟹   ENSRNOP00000012830
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX14,729,552 - 14,742,571 (-)Ensembl
Rnor_6.0 EnsemblX15,575,934 - 15,587,419 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100614   ⟹   ENSRNOP00000080433
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX14,729,550 - 14,741,456 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104339   ⟹   ENSRNOP00000080987
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX14,729,552 - 14,742,571 (-)Ensembl
RefSeq Acc Id: NM_001271227   ⟹   NP_001258156
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,729,547 - 14,742,769 (-)NCBI
Rnor_6.0X15,574,579 - 15,587,698 (-)NCBI
Rnor_5.0X16,355,812 - 16,369,002 (-)NCBI
CeleraX14,814,215 - 14,827,305 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256721   ⟹   XP_006256783
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,729,549 - 14,741,430 (-)NCBI
Rnor_6.0X15,574,579 - 15,586,379 (-)NCBI
Rnor_5.0X16,355,812 - 16,369,002 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256722   ⟹   XP_006256784
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,729,549 - 14,742,764 (-)NCBI
Rnor_6.0X15,574,579 - 15,587,700 (-)NCBI
Rnor_5.0X16,355,812 - 16,369,002 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256723   ⟹   XP_006256785
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,729,549 - 14,742,757 (-)NCBI
Rnor_6.0X15,574,579 - 15,587,699 (-)NCBI
Rnor_5.0X16,355,812 - 16,369,002 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256727   ⟹   XP_006256789
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,729,549 - 14,741,641 (-)NCBI
Rnor_6.0X15,574,579 - 15,586,797 (-)NCBI
Rnor_5.0X16,355,812 - 16,369,002 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256728   ⟹   XP_006256790
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,729,549 - 14,742,830 (-)NCBI
Rnor_6.0X15,574,579 - 15,587,826 (-)NCBI
Rnor_5.0X16,355,812 - 16,369,002 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256729   ⟹   XP_006256791
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,729,549 - 14,742,473 (-)NCBI
Rnor_6.0X15,574,579 - 15,587,296 (-)NCBI
Rnor_5.0X16,355,812 - 16,369,002 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602063   ⟹   XP_017457552
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,729,549 - 14,741,472 (-)NCBI
Rnor_6.0X15,574,579 - 15,587,150 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099775   ⟹   XP_038955703
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,729,549 - 14,742,249 (-)NCBI
RefSeq Acc Id: XM_039099776   ⟹   XP_038955704
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,729,549 - 14,741,447 (-)NCBI
RefSeq Acc Id: XM_039099777   ⟹   XP_038955705
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,729,549 - 14,741,415 (-)NCBI
RefSeq Acc Id: XM_039099778   ⟹   XP_038955706
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,735,087 - 14,742,764 (-)NCBI
RefSeq Acc Id: XM_039099779   ⟹   XP_038955707
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,735,085 - 14,742,764 (-)NCBI
RefSeq Acc Id: XR_005497983
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,729,549 - 14,742,764 (-)NCBI
RefSeq Acc Id: XR_005497984
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,729,549 - 14,742,764 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001258156   ⟸   NM_001271227
- UniProtKB: D3ZAW6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256790   ⟸   XM_006256728
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006256784   ⟸   XM_006256722
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006256785   ⟸   XM_006256723
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006256791   ⟸   XM_006256729
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006256789   ⟸   XM_006256727
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006256783   ⟸   XM_006256721
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457552   ⟸   XM_017602063
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000012830   ⟸   ENSRNOT00000012829
RefSeq Acc Id: XP_038955703   ⟸   XM_039099775
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955704   ⟸   XM_039099776
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955705   ⟸   XM_039099777
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955707   ⟸   XM_039099779
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038955706   ⟸   XM_039099778
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000080433   ⟸   ENSRNOT00000100614
RefSeq Acc Id: ENSRNOP00000080987   ⟸   ENSRNOT00000104339
Protein Domains
bHLH

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 (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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-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)
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
BN/NHsdMcwi (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
BN/SsN (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
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (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
BXH2/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
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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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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)
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
F344/DuCrl (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/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)
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
F344/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
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/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
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)
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
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)
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
HXB2/IpcvMcwi (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
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)
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
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)
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
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)
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
LEXF11/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
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)
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
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)
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
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)
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
PVG/Seac (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
SBH/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: 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)
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/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)
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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
X 16362179 16362180 T C snv DOB/Oda (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559642 AgrOrtholog
Ensembl Genes ENSRNOG00000009605 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012830 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012829 UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/TrEMBL
InterPro bHLH_ZIP_TF_MiT/TFE UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/TrEMBL
  HLH_dom UniProtKB/TrEMBL
  MiT/TFE_N UniProtKB/TrEMBL
  TFE3 UniProtKB/TrEMBL
KEGG Report rno:317376 UniProtKB/TrEMBL
NCBI Gene 317376 ENTREZGENE
PANTHER PTHR45776:SF3 UniProtKB/TrEMBL
Pfam DUF3371 UniProtKB/TrEMBL
  HLH UniProtKB/TrEMBL
  MITF_TFEB_C_3_N UniProtKB/TrEMBL
PhenoGen Tfe3 PhenoGen
PROSITE HLH UniProtKB/TrEMBL
SMART HLH UniProtKB/TrEMBL
Superfamily-SCOP HLH_basic UniProtKB/TrEMBL
UniProt D3ZAW6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Tcfe3  transcription factor E3   Tcfe3_predicted  transcription factor E3 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Tcfe3_predicted  transcription factor E3 (predicted)  RGD1559642_predicted  similar to Tcfe3 protein (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1559642_predicted  similar to Tcfe3 protein (predicted)  LOC317376  similar to Tcfe3 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317376  similar to Tcfe3 protein      Symbol and Name status set to provisional 70820 PROVISIONAL