Gtf2f1 (general transcription factor IIF subunit 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Gtf2f1 (general transcription factor IIF subunit 1) Rattus norvegicus
Analyze
Symbol: Gtf2f1
Name: general transcription factor IIF subunit 1
RGD ID: 1359646
Description: Predicted to enable several functions, including RNA polymerase II general transcription initiation factor activity; TFIIF-class transcription factor complex binding activity; and promoter-specific chromatin binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in cell junction and nucleoplasm. Predicted to be part of transcription factor TFIID complex and transcription factor TFIIF complex. Orthologous to human GTF2F1 (general transcription factor IIF subunit 1); PARTICIPATES IN RNA polymerase II transcription elongation pathway; RNA polymerase II transcription initiation pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: general transcription factor IIF, polypeptide 1; general transcription factor IIF, polypeptide 1, 74kDa; MGC94148; TFIIF-alpha; transcription initiation factor IIF subunit alpha
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
GRCr891,931,033 - 1,940,197 (-)NCBIGRCr8
mRatBN7.291,844,027 - 1,853,455 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,843,901 - 1,853,423 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx92,277,798 - 2,286,963 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.097,627,157 - 7,636,322 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.096,583,019 - 6,592,184 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,032,806 - 10,042,392 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,033,011 - 10,042,418 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,033,464 - 9,043,042 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera96,664,214 - 6,673,260 (+)NCBICelera
Cytogenetic Map9q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. A cDNA encoding RAP74, a general initiation factor for transcription by RNA polymerase II. Finkelstein A, etal., Nature 1992 Jan 30;355(6359):464-7.
2. The carboxyl terminus of RAP30 is similar in sequence to region 4 of bacterial sigma factors and is required for function. Garrett KP, etal., J Biol Chem 1992 Nov 25;267(33):23942-9.
3. 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.
4. Structural insights into transcription initiation by RNA polymerase II. Grunberg S and Hahn S, Trends Biochem Sci. 2013 Dec;38(12):603-11. doi: 10.1016/j.tibs.2013.09.002. Epub 2013 Oct 11.
5. Control of transcriptional elongation. Kwak H and Lis JT, Annu Rev Genet. 2013;47:483-508. doi: 10.1146/annurev-genet-110711-155440. Epub 2013 Sep 11.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Comprehensive gene review and curation RGD comprehensive gene curation
11. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
12. Tissue and cell distribution of a mammalian proteasomal ATPase, MSS1, and its complex formation with the basal transcription factors. Yanagi S, etal., Biochem Biophys Res Commun. 2000 Dec 20;279(2):568-73.
Additional References at PubMed
PMID:8625415   PMID:8662660   PMID:9265625   PMID:12721286   PMID:12732728   PMID:15489334   PMID:15723517   PMID:16548883   PMID:16854843   PMID:22658674   PMID:22681889   PMID:24441171  
PMID:27193682  


Genomics

Comparative Map Data
Gtf2f1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr891,931,033 - 1,940,197 (-)NCBIGRCr8
mRatBN7.291,844,027 - 1,853,455 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,843,901 - 1,853,423 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx92,277,798 - 2,286,963 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.097,627,157 - 7,636,322 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.096,583,019 - 6,592,184 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,032,806 - 10,042,392 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,033,011 - 10,042,418 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,033,464 - 9,043,042 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera96,664,214 - 6,673,260 (+)NCBICelera
Cytogenetic Map9q11NCBI
GTF2F1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38196,379,572 - 6,393,164 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl196,379,572 - 6,393,981 (-)EnsemblGRCh38hg38GRCh38
GRCh37196,379,583 - 6,393,175 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36196,330,580 - 6,344,291 (-)NCBINCBI36Build 36hg18NCBI36
Build 34196,330,580 - 6,344,184NCBI
Celera196,318,367 - 6,332,078 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef196,139,725 - 6,153,437 (-)NCBIHuRef
CHM1_1196,379,205 - 6,392,915 (-)NCBICHM1_1
T2T-CHM13v2.0196,368,474 - 6,382,065 (-)NCBIT2T-CHM13v2.0
Gtf2f1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391757,310,402 - 57,318,398 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1757,310,405 - 57,318,288 (-)EnsemblGRCm39 Ensembl
GRCm381757,003,401 - 57,011,394 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1757,003,405 - 57,011,288 (-)EnsemblGRCm38mm10GRCm38
MGSCv371757,142,825 - 57,150,711 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361756,688,526 - 56,696,417 (-)NCBIMGSCv36mm8
Celera1761,351,328 - 61,359,214 (-)NCBICelera
Cytogenetic Map17DNCBI
cM Map1729.62NCBI
Gtf2f1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554953,208,733 - 3,217,163 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554953,208,334 - 3,217,460 (+)NCBIChiLan1.0ChiLan1.0
GTF2F1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22010,780,235 - 10,794,718 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11910,006,147 - 10,020,634 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0195,401,090 - 5,414,142 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1196,323,259 - 6,336,812 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl196,323,780 - 6,336,215 (-)Ensemblpanpan1.1panPan2
GTF2F1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12053,771,201 - 53,780,646 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2053,771,325 - 53,780,644 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2053,518,020 - 53,527,557 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02054,425,381 - 54,434,910 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2054,425,568 - 54,434,910 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12053,491,833 - 53,501,378 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02053,940,180 - 53,949,728 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02054,169,704 - 54,179,458 (+)NCBIUU_Cfam_GSD_1.0
Gtf2f1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118214,084,208 - 214,095,837 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365883,742,921 - 3,750,196 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365883,742,880 - 3,750,400 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GTF2F1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl272,687,790 - 72,698,270 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1272,687,612 - 72,698,274 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2273,200,976 - 73,211,779 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GTF2F1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.165,996,585 - 6,006,893 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660812,012,088 - 2,027,210 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gtf2f1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248283,513,027 - 3,521,650 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248283,512,990 - 3,521,848 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gtf2f1
25 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:64
Count of miRNA genes:58
Interacting mature miRNAs:62
Transcripts:ENSRNOT00000073683
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat

Markers in Region
RH126039  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.291,844,038 - 1,844,255 (-)MAPPERmRatBN7.2
Rnor_6.0910,042,164 - 10,042,380NCBIRnor6.0
Rnor_5.099,042,814 - 9,043,030UniSTSRnor5.0
Celera96,673,034 - 6,673,250UniSTS
Cytogenetic Map9q11UniSTS


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 42 49 33 19 33 2 4 74 35 41 11 2
Low 1 8 8 8 6 7 6
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000073683   ⟹   ENSRNOP00000064830
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,843,901 - 1,853,346 (-)Ensembl
Rnor_6.0 Ensembl910,033,011 - 10,042,418 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000100918   ⟹   ENSRNOP00000076645
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,844,031 - 1,852,076 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101330   ⟹   ENSRNOP00000084850
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,843,901 - 1,853,423 (-)Ensembl
RefSeq Acc Id: NM_001007711   ⟹   NP_001007712
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,931,033 - 1,940,197 (-)NCBI
mRatBN7.291,844,029 - 1,853,195 (-)NCBI
Rnor_6.0910,033,028 - 10,042,390 (+)NCBI
Rnor_5.099,033,464 - 9,043,042 (+)NCBI
Celera96,664,214 - 6,673,260 (+)RGD
Sequence:
RefSeq Acc Id: NP_001007712   ⟸   NM_001007711
- UniProtKB: Q6AY96 (UniProtKB/Swiss-Prot),   A0A8I5Y917 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064830   ⟸   ENSRNOT00000073683
RefSeq Acc Id: ENSRNOP00000084850   ⟸   ENSRNOT00000101330
RefSeq Acc Id: ENSRNOP00000076645   ⟸   ENSRNOT00000100918

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6AY96-F1-model_v2 AlphaFold Q6AY96 1-508 view protein structure

Transcriptome

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

Promoters
RGD ID:13696443
Promoter ID:EPDNEW_R6968
Type:initiation region
Name:Gtf2f1_1
Description:general transcription factor IIF subunit 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_6.0910,033,000 - 10,033,060EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359646 AgrOrtholog
BioCyc Gene G2FUF-28497 BioCyc
Ensembl Genes ENSRNOG00000047134 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055014363 UniProtKB/Swiss-Prot
  ENSRNOG00060022091 UniProtKB/Swiss-Prot
  ENSRNOG00065013423 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000073683.3 UniProtKB/Swiss-Prot
  ENSRNOT00000100918 ENTREZGENE
  ENSRNOT00000100918.1 UniProtKB/TrEMBL
  ENSRNOT00000101330.1 UniProtKB/TrEMBL
  ENSRNOT00055024681 UniProtKB/Swiss-Prot
  ENSRNOT00060038526 UniProtKB/Swiss-Prot
  ENSRNOT00065022113 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7127699 IMAGE-MGC_LOAD
InterPro TFIIF-alpha UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIF_interaction UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:316123 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94148 IMAGE-MGC_LOAD
NCBI Gene 316123 ENTREZGENE
PANTHER GENERAL TRANSCRIPTION FACTOR IIF SUBUNIT 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR13011 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TFIIF_alpha UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gtf2f1 PhenoGen
RatGTEx ENSRNOG00000047134 RatGTEx
  ENSRNOG00055014363 RatGTEx
  ENSRNOG00060022091 RatGTEx
  ENSRNOG00065013423 RatGTEx
Superfamily-SCOP SSF46785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50916 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5Y917 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A212_RAT UniProtKB/TrEMBL
  A6KQT3_RAT UniProtKB/TrEMBL
  A6KQT4_RAT UniProtKB/TrEMBL
  Q6AY96 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-25 Gtf2f1  general transcription factor IIF subunit 1  Gtf2f1  general transcription factor IIF, polypeptide 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Gtf2f1  general transcription factor IIF, polypeptide 1    general transcription factor IIF, polypeptide 1, 74kDa  Name updated 1299863 APPROVED
2005-07-29 Gtf2f1  general transcription factor IIF, polypeptide 1, 74kDa      Symbol and Name status set to provisional 70820 PROVISIONAL