Ttf1 (transcription termination factor 1) - Rat Genome Database

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Gene: Ttf1 (transcription termination factor 1) Rattus norvegicus
Analyze
Symbol: Ttf1
Name: transcription termination factor 1
RGD ID: 1565673
Description: Predicted to enable DNA binding activity and chromatin binding activity. Predicted to be involved in termination of RNA polymerase I transcription. Predicted to act upstream of or within chromatin remodeling and transcription initiation at RNA polymerase I promoter. Predicted to be located in nucleoplasm. Predicted to be active in nucleolus. Orthologous to human TTF1 (transcription termination factor 1); PARTICIPATES IN RNA polymerase I transcription pathway; INTERACTS WITH 6-propyl-2-thiouracil; all-trans-retinoic acid; amitrole.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC499766; RGD1565673; similar to RNA polymerase I transcription termination factor 1; transcription termination factor, RNA polymerase I
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8332,782,544 - 32,807,202 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl332,782,308 - 32,807,201 (+)EnsemblGRCr8
mRatBN7.2312,384,626 - 12,409,257 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl312,384,655 - 12,409,257 (+)EnsemblmRatBN7.2
Rnor_6.037,635,630 - 7,660,153 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl37,635,933 - 7,660,673 (+)Ensemblrn6Rnor6.0
Rnor_5.0312,984,215 - 13,008,867 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.438,067,017 - 8,086,185 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera37,163,853 - 7,188,383 (+)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
fibrillar center  (IEA,ISO)
nucleolus  (IBA,IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IEA,ISO)

Molecular Function
chromatin binding  (IBA,IEA,ISO)
DNA binding  (IEA,ISO)
protein binding  (ISO)

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. RNA polymerase I termination: Where is the end? Nemeth A, etal., Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):306-17. doi: 10.1016/j.bbagrm.2012.10.007. Epub 2012 Oct 23.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:7720715   PMID:9049305   PMID:19285000   PMID:22174936   PMID:22370158   PMID:29305861   PMID:33622350  


Genomics

Comparative Map Data
Ttf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8332,782,544 - 32,807,202 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl332,782,308 - 32,807,201 (+)EnsemblGRCr8
mRatBN7.2312,384,626 - 12,409,257 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl312,384,655 - 12,409,257 (+)EnsemblmRatBN7.2
Rnor_6.037,635,630 - 7,660,153 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl37,635,933 - 7,660,673 (+)Ensemblrn6Rnor6.0
Rnor_5.0312,984,215 - 13,008,867 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.438,067,017 - 8,086,185 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera37,163,853 - 7,188,383 (+)NCBICelera
Cytogenetic Map3p12NCBI
TTF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389132,375,548 - 132,406,840 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9132,375,548 - 132,406,851 (-)Ensemblhg38GRCh38
GRCh379135,250,935 - 135,282,227 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369134,240,756 - 134,272,042 (-)NCBIBuild 36Build 36hg18NCBI36
Build 349132,280,492 - 132,311,775NCBI
Celera9105,792,754 - 105,824,048 (-)NCBICelera
Cytogenetic Map9q34.13NCBI
HuRef9104,744,257 - 104,775,555 (-)NCBIHuRef
CHM1_19135,400,954 - 135,432,252 (-)NCBICHM1_1
T2T-CHM13v2.09144,590,014 - 144,621,286 (-)NCBIT2T-CHM13v2.0
Ttf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39228,950,211 - 28,977,668 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl228,950,274 - 28,977,668 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38229,060,199 - 29,087,656 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl229,060,262 - 29,087,656 (+)Ensemblmm10GRCm38
MGSCv37228,915,783 - 28,943,170 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36228,882,286 - 28,909,115 (+)NCBIMGSCv36mm8
Celera228,766,271 - 28,793,645 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map219.38NCBI
Ttf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555131,807,010 - 1,823,376 (-)Ensembl
ChiLan1.0NW_0049555131,804,690 - 1,829,705 (-)NCBIChiLan1.0ChiLan1.0
TTF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2116,950,839 - 6,980,899 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan196,953,176 - 6,983,236 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09103,495,737 - 103,525,775 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19132,129,318 - 132,158,660 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9132,129,318 - 132,158,660 (-)EnsemblpanPan2panpan1.1
TTF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1951,855,565 - 51,881,000 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl951,855,559 - 51,878,459 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha951,120,246 - 51,145,642 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0952,748,649 - 52,774,067 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl952,746,666 - 52,772,199 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1951,528,526 - 51,553,908 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0951,852,982 - 51,876,680 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0951,939,290 - 51,964,688 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ttf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947199,188,472 - 199,215,336 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648718,956,899 - 18,983,888 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493648718,956,364 - 18,983,850 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TTF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1272,180,498 - 272,212,478 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11272,180,488 - 272,212,504 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21306,231,749 - 306,244,296 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TTF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1125,734,136 - 5,763,768 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl125,738,166 - 5,764,533 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660799,856,700 - 9,886,986 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ttf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247603,893,665 - 3,918,237 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Ttf1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v157,598,132 - 7,620,283 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ttf1
69 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:31
Count of miRNA genes:30
Interacting mature miRNAs:31
Transcripts:ENSRNOT00000061029
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32905627547904329Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10450811Scl73Serum cholesterol level QTL 734.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat
10450808Scl72Serum cholesterol level QTL 724.40.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
10450806Scl71Serum cholesterol level QTL 715.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)32862533967641995Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)3612543751125437Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)33083238444921701Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3136721849Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3655634751556347Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)31527234860272348Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)32905627547904329Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat

Markers in Region
BF406161  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2312,401,780 - 12,401,950 (+)MAPPERmRatBN7.2
Rnor_6.037,652,772 - 7,652,941NCBIRnor6.0
Rnor_5.0313,001,335 - 13,001,504UniSTSRnor5.0
RGSC_v3.438,079,996 - 8,080,165UniSTSRGSC3.4
Celera37,181,000 - 7,181,169UniSTS
RH 3.4 Map321.9UniSTS
Cytogenetic Map3p12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000061029   ⟹   ENSRNOP00000057745
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl332,782,308 - 32,807,201 (+)Ensembl
mRatBN7.2 Ensembl312,385,040 - 12,409,257 (+)Ensembl
Rnor_6.0 Ensembl37,635,933 - 7,660,673 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000099128   ⟹   ENSRNOP00000097927
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl312,385,040 - 12,407,208 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000113662   ⟹   ENSRNOP00000088164
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl332,784,311 - 32,807,201 (+)Ensembl
mRatBN7.2 Ensembl312,384,655 - 12,409,257 (+)Ensembl
RefSeq Acc Id: NM_001427196   ⟹   NP_001414125
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,782,647 - 32,807,198 (+)NCBI
RefSeq Acc Id: XM_006233882   ⟹   XP_006233944
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,782,544 - 32,807,202 (+)NCBI
mRatBN7.2312,384,626 - 12,409,257 (+)NCBI
Rnor_6.037,635,630 - 7,660,153 (+)NCBI
Rnor_5.0312,984,215 - 13,008,867 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039106155   ⟹   XP_038962083
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,782,544 - 32,791,932 (+)NCBI
mRatBN7.2312,384,626 - 12,393,976 (+)NCBI
RefSeq Acc Id: XM_039106156   ⟹   XP_038962084
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,782,544 - 32,789,503 (+)NCBI
mRatBN7.2312,384,626 - 12,391,558 (+)NCBI
RefSeq Acc Id: XM_063284344   ⟹   XP_063140414
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,785,562 - 32,807,202 (+)NCBI
RefSeq Acc Id: XR_352207
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,782,544 - 32,801,357 (+)NCBI
mRatBN7.2312,384,626 - 12,406,749 (+)NCBI
Rnor_6.037,635,630 - 7,657,740 (+)NCBI
Rnor_5.0312,984,215 - 13,008,867 (+)NCBI
Sequence:
RefSeq Acc Id: XP_006233944   ⟸   XM_006233882
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AA77 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000057745   ⟸   ENSRNOT00000061029
RefSeq Acc Id: XP_038962083   ⟸   XM_039106155
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038962084   ⟸   XM_039106156
- Peptide Label: isoform X4
Ensembl Acc Id: ENSRNOP00000088164   ⟸   ENSRNOT00000113662
Ensembl Acc Id: ENSRNOP00000097927   ⟸   ENSRNOT00000099128
RefSeq Acc Id: NP_001414125   ⟸   NM_001427196
- UniProtKB: A6JTQ6 (UniProtKB/TrEMBL),   D4A1Z7 (UniProtKB/TrEMBL),   A0A8I6B6I4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140414   ⟸   XM_063284344
- Peptide Label: isoform X2
- UniProtKB: A0A8I6B6I4 (UniProtKB/TrEMBL)
Protein Domains
Myb-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A1Z7-F1-model_v2 AlphaFold D4A1Z7 1-857 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:1565673 AgrOrtholog
BioCyc Gene G2FUF-50264 BioCyc
Ensembl Genes ENSRNOG00000039777 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061029 ENTREZGENE
  ENSRNOT00000061029.6 UniProtKB/TrEMBL
  ENSRNOT00000113662.2 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeodomain-like UniProtKB/TrEMBL
  SANT_DNA-bd UniProtKB/TrEMBL
  TTF1-like UniProtKB/TrEMBL
NCBI Gene 499766 ENTREZGENE
PANTHER TRANSCRIPTION TERMINATION FACTOR 1 UniProtKB/TrEMBL
  TRANSCRIPTION TERMINATION FACTOR 1 UniProtKB/TrEMBL
Pfam Myb_DNA-bind_6 UniProtKB/TrEMBL
PhenoGen Ttf1 PhenoGen
PROSITE MYB_LIKE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000039777 RatGTEx
SMART SANT UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A0A8I6AA77 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6B6I4 ENTREZGENE
  A6JTQ6 ENTREZGENE, UniProtKB/TrEMBL
  D4A1Z7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-03 Ttf1  transcription termination factor 1  Ttf1  transcription termination factor, RNA polymerase I  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Ttf1  transcription termination factor, RNA polymerase I  RGD1565673_predicted  similar to RNA polymerase I transcription termination factor 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565673_predicted  similar to RNA polymerase I transcription termination factor 1 (predicted)  LOC499766  similar to RNA polymerase I transcription termination factor 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499766  similar to RNA polymerase I transcription termination factor 1      Symbol and Name status set to provisional 70820 PROVISIONAL