Tbpl2 (TATA box binding protein-like 2) - Rat Genome Database

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Gene: Tbpl2 (TATA box binding protein-like 2) Rattus norvegicus
Analyze
Symbol: Tbpl2
Name: TATA box binding protein-like 2
RGD ID: 1596837
Description: Predicted to enable DNA binding activity and RNA polymerase II general transcription initiation factor activity. Predicted to be involved in DNA-templated transcription initiation. Predicted to be located in cytoplasm and female germ cell nucleus. Orthologous to human TBPL2 (TATA-box binding protein like 2); PARTICIPATES IN Huntington's disease pathway; INTERACTS WITH bisphenol A; cadmium dichloride; 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC680050; similar to TBP-related factor 3; TATA box-binding protein-like 2; TATA box-binding protein-like protein 2; TATA box-binding protein-related factor 3; TBP-like 2; TBP-like protein 2; TBP-related factor 3
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
GRCr8327,170,209 - 27,191,665 (-)NCBIGRCr8
mRatBN7.236,771,825 - 6,793,281 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl36,772,419 - 6,793,231 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx39,866,546 - 9,887,327 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0318,452,785 - 18,473,566 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0316,642,588 - 16,663,369 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.031,095,883 - 1,116,677 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl31,095,883 - 1,116,677 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.031,087,370 - 1,108,164 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.432,253,775 - 2,274,569 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera31,610,514 - 1,631,308 (-)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IEA,ISO)
female germ cell nucleus  (IEA,ISO)
nucleus  (IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14634207   PMID:17109819   PMID:17570761   PMID:17641088  


Genomics

Comparative Map Data
Tbpl2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8327,170,209 - 27,191,665 (-)NCBIGRCr8
mRatBN7.236,771,825 - 6,793,281 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl36,772,419 - 6,793,231 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx39,866,546 - 9,887,327 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0318,452,785 - 18,473,566 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0316,642,588 - 16,663,369 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.031,095,883 - 1,116,677 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl31,095,883 - 1,116,677 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.031,087,370 - 1,108,164 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.432,253,775 - 2,274,569 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera31,610,514 - 1,631,308 (-)NCBICelera
Cytogenetic Map3p13NCBI
TBPL2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381455,414,210 - 55,440,616 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1455,414,210 - 55,456,726 (-)EnsemblGRCh38hg38GRCh38
GRCh371455,880,928 - 55,907,334 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361454,950,681 - 54,977,016 (-)NCBINCBI36Build 36hg18NCBI36
Build 341454,950,684 - 54,977,016NCBI
Celera1435,930,314 - 35,956,646 (-)NCBICelera
Cytogenetic Map14q22.3NCBI
HuRef1436,044,117 - 36,070,458 (-)NCBIHuRef
CHM1_11455,819,427 - 55,845,666 (-)NCBICHM1_1
T2T-CHM13v2.01449,619,941 - 49,646,349 (-)NCBIT2T-CHM13v2.0
Tbpl2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39223,961,378 - 23,986,607 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl223,961,733 - 23,986,607 (-)EnsemblGRCm39 Ensembl
GRCm38224,071,366 - 24,096,595 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl224,071,721 - 24,096,595 (-)EnsemblGRCm38mm10GRCm38
MGSCv37223,927,241 - 23,952,115 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36223,893,730 - 23,918,604 (-)NCBIMGSCv36mm8
Celera223,801,598 - 23,826,565 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map216.14NCBI
Tbpl2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546613,871,562 - 13,897,302 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495546613,869,429 - 13,897,302 (+)NCBIChiLan1.0ChiLan1.0
TBPL2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21556,535,651 - 56,563,640 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11455,752,165 - 55,780,154 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01436,001,021 - 36,027,796 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11454,274,367 - 54,301,003 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1454,274,367 - 54,301,003 (-)Ensemblpanpan1.1panPan2
TBPL2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1831,235,996 - 31,269,777 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl831,236,285 - 31,260,936 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha831,002,723 - 31,027,391 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0831,495,114 - 31,518,043 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl831,495,067 - 31,524,831 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1831,097,962 - 31,122,802 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0831,174,633 - 31,199,174 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0831,540,208 - 31,565,673 (-)NCBIUU_Cfam_GSD_1.0
Tbpl2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864073,971,972 - 73,994,012 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936495197,687 - 219,477 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936495197,687 - 219,727 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TBPL2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1184,745,799 - 184,792,502 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11184,745,719 - 184,772,051 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21205,296,071 - 205,384,145 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TBPL2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12432,607,375 - 32,633,190 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605320,828,867 - 20,854,033 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tbpl2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624884222,198 - 256,319 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624884221,409 - 256,396 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tbpl2
7 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:35
Count of miRNA genes:32
Interacting mature miRNAs:34
Transcripts:ENSRNOT00000050371
Prediction methods:Microtar, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat


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

endocrine system exocrine system hepatobiliary system nervous system reproductive system
High
Medium
Low 4
Below cutoff 1 1 1 3 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000050371   ⟹   ENSRNOP00000039739
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl36,772,419 - 6,793,231 (-)Ensembl
Rnor_6.0 Ensembl31,095,883 - 1,116,677 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112982   ⟹   ENSRNOP00000082291
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl36,772,419 - 6,792,021 (-)Ensembl
RefSeq Acc Id: NM_001099361   ⟹   NP_001092831
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8327,170,209 - 27,191,665 (-)NCBI
mRatBN7.236,771,825 - 6,793,281 (-)NCBI
Rnor_6.031,095,883 - 1,116,677 (-)NCBI
Rnor_5.031,087,370 - 1,108,164 (-)NCBI
RGSC_v3.432,253,775 - 2,274,569 (-)RGD
Celera31,610,514 - 1,631,308 (-)RGD
Sequence:
RefSeq Acc Id: XM_063284539   ⟹   XP_063140609
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8327,170,803 - 27,191,609 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001092831 (Get FASTA)   NCBI Sequence Viewer  
  XP_063140609 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A6H909 (Get FASTA)   NCBI Sequence Viewer  
  DAA06034 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000039739
  ENSRNOP00000039739.4
  ENSRNOP00000082291.1
Reference Protein Sequences
RefSeq Acc Id: NP_001092831   ⟸   NM_001099361
- UniProtKB: A6H909 (UniProtKB/Swiss-Prot),   A0A8L2QJQ0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000039739   ⟸   ENSRNOT00000050371
RefSeq Acc Id: ENSRNOP00000082291   ⟸   ENSRNOT00000112982
RefSeq Acc Id: XP_063140609   ⟸   XM_063284539
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A6H909-F1-model_v2 AlphaFold A6H909 1-344 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1596837 AgrOrtholog
BioCyc Gene G2FUF-50524 BioCyc
Ensembl Genes ENSRNOG00000033682 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000050371 ENTREZGENE
  ENSRNOT00000050371.4 UniProtKB/TrEMBL
  ENSRNOT00000112982.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.310.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro TBP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TBP_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TBP_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TBP_eukaryotic UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:680050 UniProtKB/Swiss-Prot
NCBI Gene 680050 ENTREZGENE
PANTHER PTHR10126 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TATA BOX-BINDING PROTEIN-LIKE 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TBP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tbpl2 PhenoGen
PRINTS TIFACTORIID UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TFIID UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000033682 RatGTEx
Superfamily-SCOP TATA-box binding protein-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5ZXM7_RAT UniProtKB/TrEMBL
  A0A8L2QJQ0 ENTREZGENE, UniProtKB/TrEMBL
  A6H909 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Tbpl2  TATA box binding protein-like 2  LOC680050  similar to TBP-related factor 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC680050  similar to TBP-related factor 3      Symbol and Name status set to provisional 70820 PROVISIONAL