Tnrc6b (trinucleotide repeat containing adaptor 6B) - Rat Genome Database

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Gene: Tnrc6b (trinucleotide repeat containing adaptor 6B) Rattus norvegicus
Analyze
Symbol: Tnrc6b
Name: trinucleotide repeat containing adaptor 6B
RGD ID: 621428
Description: Predicted to enable nucleic acid binding activity. Predicted to be involved in regulation of gene expression. Predicted to be located in cytosol. Predicted to be active in P-body and nucleoplasm. Human ortholog(s) of this gene implicated in subserous uterine fibroid and uterine fibroid. Orthologous to human TNRC6B (trinucleotide repeat containing adaptor 6B); PARTICIPATES IN microRNA pathway; INTERACTS WITH 2,6-dinitrotoluene; aconitine; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: androgen receptor-related apoptosis-associated protein CBL27; Cbl27; trinucleotide repeat containing 6B; trinucleotide repeat-containing gene 6B protein
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
mRatBN7.27112,252,351 - 112,469,829 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7112,252,359 - 112,461,790 (+)Ensembl
Rnor_6.07121,930,610 - 122,147,934 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7121,930,615 - 122,147,934 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07121,922,421 - 122,139,717 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47118,993,653 - 119,212,958 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17119,193,462 - 119,235,531 (+)NCBI
Celera7108,576,591 - 108,793,423 (+)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12477932   PMID:19716330   PMID:22658674  


Genomics

Comparative Map Data
Tnrc6b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27112,252,351 - 112,469,829 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7112,252,359 - 112,461,790 (+)Ensembl
Rnor_6.07121,930,610 - 122,147,934 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7121,930,615 - 122,147,934 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07121,922,421 - 122,139,717 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47118,993,653 - 119,212,958 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17119,193,462 - 119,235,531 (+)NCBI
Celera7108,576,591 - 108,793,423 (+)NCBICelera
Cytogenetic Map7q34NCBI
TNRC6B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2240,044,817 - 40,335,808 (+)EnsemblGRCh38hg38GRCh38
GRCh382240,044,834 - 40,335,808 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372240,440,838 - 40,731,812 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362238,770,767 - 39,061,758 (+)NCBINCBI36hg18NCBI36
Build 342238,898,445 - 39,043,860NCBI
Celera2224,242,863 - 24,533,872 (+)NCBI
Cytogenetic Map22q13.1NCBI
HuRef2223,404,077 - 23,694,839 (+)NCBIHuRef
CHM1_12240,400,124 - 40,690,692 (+)NCBICHM1_1
Tnrc6b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391580,595,514 - 80,825,287 (+)NCBIGRCm39mm39
GRCm39 Ensembl1580,595,514 - 80,825,286 (+)Ensembl
GRCm381580,711,313 - 80,941,086 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1580,711,313 - 80,941,085 (+)EnsemblGRCm38mm10GRCm38
MGSCv371580,541,743 - 80,771,516 (+)NCBIGRCm37mm9NCBIm37
MGSCv361580,538,568 - 80,768,341 (+)NCBImm8
Celera1582,831,358 - 83,061,497 (+)NCBICelera
Cytogenetic Map15E1NCBI
Tnrc6b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541325,886,077 - 26,048,546 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541325,820,428 - 26,060,681 (+)NCBIChiLan1.0ChiLan1.0
TNRC6B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12238,969,663 - 39,058,432 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2238,850,107 - 39,045,914 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02221,149,646 - 21,240,006 (+)NCBIMhudiblu_PPA_v0panPan3
TNRC6B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11024,852,168 - 25,094,400 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1024,813,854 - 25,094,393 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1024,787,185 - 25,030,572 (-)NCBI
ROS_Cfam_1.01025,602,650 - 25,846,409 (-)NCBI
UMICH_Zoey_3.11025,314,565 - 25,558,084 (-)NCBI
UNSW_CanFamBas_1.01025,637,095 - 25,880,678 (-)NCBI
UU_Cfam_GSD_1.01025,811,506 - 26,055,123 (-)NCBI
Tnrc6b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049458,451,252 - 8,687,007 (-)NCBI
SpeTri2.0NW_0049364921,461,572 - 1,697,500 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNRC6B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl58,060,979 - 8,311,418 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.158,052,434 - 8,311,811 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.255,418,164 - 5,430,080 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TNRC6B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11922,823,447 - 22,907,942 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1922,823,937 - 22,898,476 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666045102,681,707 - 102,976,263 (-)NCBIVero_WHO_p1.0
Tnrc6b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247528,125,472 - 8,394,809 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D7Mit13  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27112,308,254 - 112,308,525 (+)MAPPERmRatBN7.2
Rnor_6.07121,986,439 - 121,986,709NCBIRnor6.0
Rnor_5.07121,978,222 - 121,978,492UniSTSRnor5.0
RGSC_v3.47119,049,926 - 119,050,195RGDRGSC3.4
RGSC_v3.47119,049,927 - 119,050,197UniSTSRGSC3.4
RGSC_v3.17119,084,157 - 119,084,427RGD
RH 3.4 Map7877.2UniSTS
RH 3.4 Map7877.2RGD
RH 2.0 Map7663.3RGD
Cytogenetic Map7q34UniSTS
D7Rat129  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27112,419,298 - 112,419,498 (+)MAPPERmRatBN7.2
Rnor_6.07122,097,408 - 122,097,607NCBIRnor6.0
Rnor_5.07122,089,191 - 122,089,390UniSTSRnor5.0
RGSC_v3.47119,161,518 - 119,161,718RGDRGSC3.4
RGSC_v3.47119,161,519 - 119,161,718UniSTSRGSC3.4
RGSC_v3.17119,195,749 - 119,195,948RGD
Celera7108,743,264 - 108,743,463UniSTS
RH 3.4 Map7877.0RGD
RH 3.4 Map7877.0UniSTS
RH 2.0 Map7661.5RGD
SHRSP x BN Map764.65RGD
Cytogenetic Map7q34UniSTS
AI848765  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27112,469,540 - 112,469,677 (+)MAPPERmRatBN7.2
Rnor_6.07122,147,646 - 122,147,782NCBIRnor6.0
Rnor_5.07122,139,429 - 122,139,565UniSTSRnor5.0
RGSC_v3.47119,212,670 - 119,212,806UniSTSRGSC3.4
Celera7108,793,135 - 108,793,271UniSTS
Cytogenetic Map7q34UniSTS
STS-R92764  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27112,341,689 - 112,341,813 (+)MAPPERmRatBN7.2
Rnor_6.07122,019,873 - 122,019,996NCBIRnor6.0
Rnor_5.07122,011,656 - 122,011,779UniSTSRnor5.0
RGSC_v3.47119,083,984 - 119,084,107UniSTSRGSC3.4
Celera7108,665,371 - 108,665,494UniSTS
Cytogenetic Map7q34UniSTS
RH140722  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27112,460,468 - 112,460,677 (+)MAPPERmRatBN7.2
Rnor_6.07122,138,573 - 122,138,781NCBIRnor6.0
Rnor_5.07122,130,356 - 122,130,564UniSTSRnor5.0
RGSC_v3.47119,203,597 - 119,203,805UniSTSRGSC3.4
Celera7108,784,062 - 108,784,270UniSTS
RH 3.4 Map7876.7UniSTS
Cytogenetic Map7q34UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)768938720113886318Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)768938720113886318Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)768938720113886318Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)769736226117455174Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)769736356112729554Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)780221299112308525Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)780221299125221299Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)781737938126737938Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)794811085116738842Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)794811326116294265Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7103146217116738842Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1549
Count of miRNA genes:364
Interacting mature miRNAs:563
Transcripts:ENSRNOT00000033975
Prediction methods:Miranda, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 32 44 28 19 28 8 8 74 30 36 11 8
Low 11 13 13 13 3 5 5
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_138845 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242061 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594645 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594646 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594647 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594648 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594649 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594650 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594651 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078365 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078369 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF275151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC061751 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473950 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212411 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216989 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226824 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232468 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000186 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000033975   ⟹   ENSRNOP00000036077
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7112,252,359 - 112,458,166 (+)Ensembl
Rnor_6.0 Ensembl7121,930,638 - 122,147,934 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091270   ⟹   ENSRNOP00000073908
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7112,252,359 - 112,458,166 (+)Ensembl
Rnor_6.0 Ensembl7121,930,615 - 122,140,091 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000102287   ⟹   ENSRNOP00000079479
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7112,326,723 - 112,461,790 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106327   ⟹   ENSRNOP00000080619
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7112,326,723 - 112,458,166 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108883   ⟹   ENSRNOP00000092295
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7112,339,468 - 112,458,166 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114032   ⟹   ENSRNOP00000085877
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7112,444,239 - 112,458,581 (+)Ensembl
RefSeq Acc Id: NM_138845   ⟹   NP_620200
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27112,252,392 - 112,469,829 (+)NCBI
Rnor_6.07121,930,638 - 122,147,934 (+)NCBI
Rnor_5.07121,922,421 - 122,139,717 (+)NCBI
RGSC_v3.47118,993,653 - 119,212,958 (+)RGD
Celera7108,576,591 - 108,793,423 (+)RGD
Sequence:
RefSeq Acc Id: XM_006242061   ⟹   XP_006242123
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27112,339,452 - 112,469,829 (+)NCBI
Rnor_6.07122,017,593 - 122,147,934 (+)NCBI
Rnor_5.07121,922,421 - 122,139,717 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594645   ⟹   XP_017450134
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27112,252,351 - 112,469,829 (+)NCBI
Rnor_6.07121,930,611 - 122,147,934 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594647   ⟹   XP_017450136
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27112,252,351 - 112,469,829 (+)NCBI
Rnor_6.07121,930,610 - 122,147,934 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039078361   ⟹   XP_038934289
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27112,306,143 - 112,469,829 (+)NCBI
RefSeq Acc Id: XM_039078362   ⟹   XP_038934290
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27112,306,143 - 112,469,829 (+)NCBI
RefSeq Acc Id: XM_039078363   ⟹   XP_038934291
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27112,288,699 - 112,469,829 (+)NCBI
RefSeq Acc Id: XM_039078364   ⟹   XP_038934292
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27112,252,351 - 112,469,829 (+)NCBI
RefSeq Acc Id: XM_039078365   ⟹   XP_038934293
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27112,252,351 - 112,469,829 (+)NCBI
RefSeq Acc Id: XM_039078366   ⟹   XP_038934294
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27112,306,143 - 112,469,829 (+)NCBI
RefSeq Acc Id: XM_039078367   ⟹   XP_038934295
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27112,288,700 - 112,469,829 (+)NCBI
RefSeq Acc Id: XM_039078368   ⟹   XP_038934296
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27112,252,351 - 112,469,829 (+)NCBI
RefSeq Acc Id: XM_039078369   ⟹   XP_038934297
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27112,402,528 - 112,469,829 (+)NCBI
RefSeq Acc Id: XM_039078371   ⟹   XP_038934299
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27112,306,143 - 112,469,829 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_620200   ⟸   NM_138845
- UniProtKB: F1LV37 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242123   ⟸   XM_006242061
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017450136   ⟸   XM_017594647
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017450134   ⟸   XM_017594645
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000036077   ⟸   ENSRNOT00000033975
RefSeq Acc Id: ENSRNOP00000073908   ⟸   ENSRNOT00000091270
RefSeq Acc Id: XP_038934293   ⟸   XM_039078365
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038934292   ⟸   XM_039078364
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934296   ⟸   XM_039078368
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038934291   ⟸   XM_039078363
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934295   ⟸   XM_039078367
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038934294   ⟸   XM_039078366
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038934290   ⟸   XM_039078362
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038934289   ⟸   XM_039078361
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934299   ⟸   XM_039078371
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038934297   ⟸   XM_039078369
- Peptide Label: isoform X6
RefSeq Acc Id: ENSRNOP00000079479   ⟸   ENSRNOT00000102287
RefSeq Acc Id: ENSRNOP00000080619   ⟸   ENSRNOT00000106327
RefSeq Acc Id: ENSRNOP00000092295   ⟸   ENSRNOT00000108883
RefSeq Acc Id: ENSRNOP00000085877   ⟸   ENSRNOT00000114032
Protein Domains
Ago_hook   TNRC6-PABC_bdg

Transcriptome

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

Promoters
RGD ID:13695499
Promoter ID:EPDNEW_R6024
Type:multiple initiation site
Name:Tnrc6b_1
Description:trinucleotide repeat containing 6B
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_6.07121,930,668 - 121,930,728EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621428 AgrOrtholog
Ensembl Genes ENSRNOG00000024907 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000036077 UniProtKB/TrEMBL
  ENSRNOP00000073908 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000033975 UniProtKB/TrEMBL
  ENSRNOT00000091270 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
InterPro Argonaute_hook_dom UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  TNRC6_PABC-bd UniProtKB/TrEMBL
  TNRC6B UniProtKB/TrEMBL
  TNRC6B_RRM UniProtKB/TrEMBL
KEGG Report rno:192178 UniProtKB/TrEMBL
NCBI Gene 192178 ENTREZGENE
PANTHER PTHR13020:SF32 UniProtKB/TrEMBL
Pfam Ago_hook UniProtKB/TrEMBL
  TNRC6-PABC_bdg UniProtKB/TrEMBL
PhenoGen Tnrc6b PhenoGen
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt A0A0G2K6R0_RAT UniProtKB/TrEMBL
  F1LV37 ENTREZGENE, UniProtKB/TrEMBL
  Q6P7B1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-02 Tnrc6b  trinucleotide repeat containing adaptor 6B  Tnrc6b  trinucleotide repeat containing 6B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-22 Tnrc6b  trinucleotide repeat containing 6B  Cbl27  androgen receptor-related apoptosis-associated protein CBL27  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Cbl27  androgen receptor-related apoptosis-associated protein CBL27      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Cbl27  androgen receptor-related apoptosis-associated protein CBL27      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the spleen 634611