Tbpl1 (TATA-box binding protein like 1) - Rat Genome Database

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Gene: Tbpl1 (TATA-box binding protein like 1) Rattus norvegicus
Analyze
Symbol: Tbpl1
Name: TATA-box binding protein like 1
RGD ID: 1597456
Description: Predicted to have RNA polymerase II core promoter sequence-specific DNA binding activity and RNA polymerase II general transcription initiation factor activity. Predicted to be involved in nucleobase-containing compound biosynthetic process and spermatid development. Predicted to localize to cytoplasm and transcription factor TFIIA complex. Orthologous to human TBPL1 (TATA-box binding protein like 1); PARTICIPATES IN Huntington's disease pathway; INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC292173; LOC689030; similar to TATA box-binding protein-like protein 1 (TBP-like protein 1) (TATA box-binding protein-related factor 2) (TBP-related factor 2) (21-kDa TBP-like protein); TATA box binding protein-like 1; TATA box-binding protein-like 1; TATA box-binding protein-like protein 1; TBP-like 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2122,777,892 - 22,803,305 (+)NCBI
Rnor_6.0 Ensembl123,977,688 - 24,002,506 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0123,977,154 - 24,002,512 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0125,441,466 - 25,466,751 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4123,295,515 - 23,320,298 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1123,298,484 - 23,322,895 (+)NCBI
Celera121,506,025 - 21,530,791 (+)NCBICelera
Cytogenetic Map1p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8889548   PMID:11861477   PMID:12947022   PMID:15767669   PMID:15927180   PMID:16765935   PMID:18418073   PMID:23374846   PMID:25943107  


Genomics

Comparative Map Data
Tbpl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2122,777,892 - 22,803,305 (+)NCBI
Rnor_6.0 Ensembl123,977,688 - 24,002,506 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0123,977,154 - 24,002,512 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0125,441,466 - 25,466,751 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4123,295,515 - 23,320,298 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1123,298,484 - 23,322,895 (+)NCBI
Celera121,506,025 - 21,530,791 (+)NCBICelera
Cytogenetic Map1p12NCBI
TBPL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6133,952,170 - 133,990,432 (+)EnsemblGRCh38hg38GRCh38
GRCh386133,952,174 - 133,990,432 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376134,273,312 - 134,311,570 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366134,315,994 - 134,350,322 (+)NCBINCBI36hg18NCBI36
Build 346134,315,993 - 134,350,322NCBI
Celera6135,015,381 - 135,049,709 (+)NCBI
Cytogenetic Map6q23.2NCBI
HuRef6131,841,901 - 131,877,571 (+)NCBIHuRef
CHM1_16134,535,432 - 134,570,879 (+)NCBICHM1_1
Tbpl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391022,579,776 - 22,607,890 (-)NCBIGRCm39mm39
GRCm39 Ensembl1022,579,778 - 22,607,837 (-)Ensembl
GRCm381022,703,877 - 22,732,666 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1022,703,879 - 22,731,938 (-)EnsemblGRCm38mm10GRCm38
MGSCv371022,423,683 - 22,451,253 (-)NCBIGRCm37mm9NCBIm37
MGSCv361022,393,295 - 22,420,794 (-)NCBImm8
Celera1023,650,605 - 23,678,195 (-)NCBICelera
Cytogenetic Map10A3NCBI
Tbpl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554392,539,486 - 2,563,720 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554392,539,465 - 2,548,351 (-)NCBIChiLan1.0ChiLan1.0
TBPL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16135,817,603 - 135,852,876 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6135,817,613 - 135,852,876 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06131,719,606 - 131,754,960 (+)NCBIMhudiblu_PPA_v0panPan3
TBPL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1126,898,344 - 26,938,452 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl126,899,859 - 26,936,995 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha127,781,262 - 27,818,400 (+)NCBI
ROS_Cfam_1.0127,056,795 - 27,097,278 (+)NCBI
UMICH_Zoey_3.1126,942,064 - 26,979,193 (+)NCBI
UNSW_CanFamBas_1.0126,822,118 - 26,859,272 (+)NCBI
UU_Cfam_GSD_1.0127,131,596 - 27,168,730 (+)NCBI
Tbpl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946122,018,007 - 122,050,977 (+)NCBI
SpeTri2.0NW_0049365601,797,791 - 1,830,199 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TBPL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl129,899,957 - 29,936,718 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1129,899,956 - 29,936,773 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2133,403,547 - 33,440,366 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TBPL1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11339,487,007 - 39,523,752 (-)NCBI
ChlSab1.1 Ensembl1339,483,880 - 39,522,115 (-)Ensembl
Tbpl1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624942819,099 - 848,240 (-)NCBI

Position Markers
BF401688  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2122,798,098 - 22,798,291 (+)MAPPER
Rnor_6.0123,997,307 - 23,997,499NCBIRnor6.0
Rnor_5.0125,461,537 - 25,461,729UniSTSRnor5.0
RGSC_v3.4123,315,093 - 23,315,285UniSTSRGSC3.4
Celera121,525,638 - 21,525,830UniSTS
RH 3.4 Map1235.2UniSTS
Cytogenetic Map1p12UniSTS
RH144371  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2122,803,396 - 22,803,656 (+)MAPPER
Rnor_6.0124,002,604 - 24,002,863NCBIRnor6.0
Rnor_5.0125,466,834 - 25,467,093UniSTSRnor5.0
RGSC_v3.4123,320,390 - 23,320,649UniSTSRGSC3.4
Celera121,530,883 - 21,531,142UniSTS
RH 3.4 Map1231.8UniSTS
Cytogenetic Map1p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124368159Rat
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128468970Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1134993530Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1134993530Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)1134993530Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1164407321Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)125439343579402Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)125439343579402Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)125439343579402Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)125439386904217Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1186804543724576Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1457869349578693Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1565577285706974Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11131448975844121Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11131448983657083Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11131448983657083Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11131448983657083Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11131448983657083Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)11131465834993348Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)11249343957493439Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11362925158629251Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)11614314349547474Rat
5684999Bss102Bone structure and strength QTL 1025.50.00000072tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)11614314349547474Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)12034156058000154Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12107930566079305Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12130082249454378Rat
1558642Prcr2Prostate cancer resistance QTL 24.3prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)12181262344409802Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12340642849547474Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)12340642849547474Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12340642868406428Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:79
Count of miRNA genes:56
Interacting mature miRNAs:78
Transcripts:ENSRNOT00000014805
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 56 40 19 40 8 10 74 35 41 11 8
Low 1 1 1 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001127201 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006227721 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006227722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017589742 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091288 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091290 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091312 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091315 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091317 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AW434020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF414163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CF109177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213058 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213420 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220549 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234587 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000014805   ⟹   ENSRNOP00000014805
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl123,977,688 - 24,002,506 (+)Ensembl
RefSeq Acc Id: NM_001127201   ⟹   NP_001120673
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2122,778,481 - 22,803,305 (+)NCBI
Rnor_6.0123,977,688 - 24,002,512 (+)NCBI
Rnor_5.0125,441,466 - 25,466,751 (+)NCBI
RGSC_v3.4123,295,515 - 23,320,298 (+)RGD
Celera121,506,025 - 21,530,791 (+)RGD
Sequence:
RefSeq Acc Id: XM_006227721   ⟹   XP_006227783
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2122,778,346 - 22,803,305 (+)NCBI
Rnor_6.0123,977,655 - 24,002,512 (+)NCBI
Rnor_5.0125,441,466 - 25,466,751 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006227722   ⟹   XP_006227784
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2122,777,894 - 22,803,305 (+)NCBI
Rnor_6.0123,977,154 - 24,002,512 (+)NCBI
Rnor_5.0125,441,466 - 25,466,751 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589742   ⟹   XP_017445231
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2122,791,340 - 22,803,305 (+)NCBI
Rnor_6.0123,990,549 - 24,002,512 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039091288   ⟹   XP_038947216
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2122,778,325 - 22,803,305 (+)NCBI
RefSeq Acc Id: XM_039091290   ⟹   XP_038947218
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2122,777,892 - 22,803,305 (+)NCBI
RefSeq Acc Id: XM_039091312   ⟹   XP_038947240
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2122,778,350 - 22,803,305 (+)NCBI
RefSeq Acc Id: XM_039091315   ⟹   XP_038947243
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2122,780,321 - 22,803,305 (+)NCBI
RefSeq Acc Id: XM_039091317   ⟹   XP_038947245
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2122,777,892 - 22,803,305 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001120673   ⟸   NM_001127201
- UniProtKB: D4A898 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006227784   ⟸   XM_006227722
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006227783   ⟸   XM_006227721
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017445231   ⟸   XM_017589742
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000014805   ⟸   ENSRNOT00000014805
RefSeq Acc Id: XP_038947218   ⟸   XM_039091290
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038947245   ⟸   XM_039091317
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038947216   ⟸   XM_039091288
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947240   ⟸   XM_039091312
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038947243   ⟸   XM_039091315
- Peptide Label: isoform X4

Transcriptome

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

Promoters
RGD ID:13689536
Promoter ID:EPDNEW_R60
Type:initiation region
Name:Tbpl1_1
Description:TATA-box binding protein like 1
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_6.0123,977,694 - 23,977,754EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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/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 (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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1597456 AgrOrtholog
Ensembl Genes ENSRNOG00000011114 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000014805 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014805 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.310.10 UniProtKB/TrEMBL
InterPro TBP UniProtKB/TrEMBL
  TBP-like UniProtKB/TrEMBL
  TBP_dom_sf UniProtKB/TrEMBL
KEGG Report rno:689030 UniProtKB/TrEMBL
NCBI Gene 689030 ENTREZGENE
PANTHER TBP UniProtKB/TrEMBL
Pfam TBP UniProtKB/TrEMBL
PhenoGen Tbpl1 PhenoGen
PRINTS TIFACTORIID UniProtKB/TrEMBL
UniProt D4A898 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-02 Tbpl1  TATA-box binding protein like 1  Tbpl1  TBP-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-03-07 Tbpl1  TBP-like 1  Tbpl1  TATA box binding protein-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-06 Tbpl1  TATA box binding protein-like 1  Tbpl1_predicted  TATA box binding protein-like 1 (predicted)  Data Merged 737654 APPROVED
2008-03-06 Tbpl1  TATA box binding protein-like 1  LOC689030  similar to TATA box-binding protein-like protein 1 (TBP-like protein 1) (TATA box-binding protein-related factor 2) (TBP-related factor 2) (21-kDa TBP-like protein)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC689030  similar to TATA box-binding protein-like protein 1 (TBP-like protein 1) (TATA box-binding protein-related factor 2) (TBP-related factor 2) (21-kDa TBP-like protein)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-12 Tbpl1_predicted  TATA box binding protein-like 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED