Gtf3c5 (general transcription factor IIIC subunit 5) - Rat Genome Database

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Gene: Gtf3c5 (general transcription factor IIIC subunit 5) Rattus norvegicus
Analyze
Symbol: Gtf3c5
Name: general transcription factor IIIC subunit 5
RGD ID: 1305173
Description: Predicted to enable RNA polymerase III general transcription initiation factor activity. Predicted to contribute to RNA polymerase III type 1 promoter sequence-specific DNA binding activity and RNA polymerase III type 2 promoter sequence-specific DNA binding activity. Predicted to be involved in transcription initiation at RNA polymerase III promoter. Predicted to act upstream of or within skeletal muscle cell differentiation. Predicted to be located in nucleoplasm. Predicted to be part of transcription factor TFIIIC complex. Orthologous to human GTF3C5 (general transcription factor IIIC subunit 5); PARTICIPATES IN RNA polymerase III transcription pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: general transcription factor 3C polypeptide 5; general transcription factor IIIC, polypeptide 5; LOC362095
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
GRCr8332,291,851 - 32,312,188 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl332,291,859 - 32,312,164 (-)EnsemblGRCr8
mRatBN7.2311,893,867 - 11,914,187 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl311,893,875 - 11,914,180 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx314,966,142 - 14,986,494 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0323,551,097 - 23,571,449 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0321,805,549 - 21,825,903 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.037,144,354 - 7,164,678 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl37,144,250 - 7,164,654 (-)Ensemblrn6Rnor6.0
Rnor_5.0312,495,477 - 12,515,794 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.437,552,088 - 7,572,394 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera36,675,056 - 6,695,359 (-)NCBICelera
RGSC_v3.137,553,773 - 7,572,450 (-)NCBI
Cytogenetic Map3p12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (IEA,ISO)
transcription factor TFIIIC complex  (IBA,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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Comprehensive gene review and curation RGD comprehensive gene curation
4. A structural perspective on RNA polymerase I and RNA polymerase III transcription machineries. Vannini A Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):258-64. doi: 10.1016/j.bbagrm.2012.09.009. Epub 2012 Sep 29.
Additional References at PubMed
PMID:12477932   PMID:17409385   PMID:22147266  


Genomics

Comparative Map Data
Gtf3c5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8332,291,851 - 32,312,188 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl332,291,859 - 32,312,164 (-)EnsemblGRCr8
mRatBN7.2311,893,867 - 11,914,187 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl311,893,875 - 11,914,180 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx314,966,142 - 14,986,494 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0323,551,097 - 23,571,449 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0321,805,549 - 21,825,903 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.037,144,354 - 7,164,678 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl37,144,250 - 7,164,654 (-)Ensemblrn6Rnor6.0
Rnor_5.0312,495,477 - 12,515,794 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.437,552,088 - 7,572,394 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera36,675,056 - 6,695,359 (-)NCBICelera
RGSC_v3.137,553,773 - 7,572,450 (-)NCBI
Cytogenetic Map3p12NCBI
GTF3C5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389133,030,708 - 133,058,503 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9133,030,675 - 133,058,503 (+)Ensemblhg38GRCh38
GRCh379135,906,384 - 135,933,890 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369134,895,934 - 134,923,708 (+)NCBIBuild 36Build 36hg18NCBI36
Build 349132,935,666 - 132,963,440NCBI
Celera9106,447,792 - 106,475,620 (+)NCBICelera
Cytogenetic Map9q34.13NCBI
HuRef9105,399,764 - 105,427,593 (+)NCBIHuRef
CHM1_19136,056,638 - 136,084,466 (+)NCBICHM1_1
T2T-CHM13v2.09145,244,842 - 145,272,659 (+)NCBIT2T-CHM13v2.0
Gtf3c5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39228,456,257 - 28,473,291 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl228,456,323 - 28,473,763 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38228,566,245 - 28,583,279 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl228,566,311 - 28,583,751 (-)Ensemblmm10GRCm38
MGSCv37228,421,783 - 28,438,799 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36228,388,324 - 28,405,255 (-)NCBIMGSCv36mm8
Celera228,270,438 - 28,287,458 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map219.38NCBI
Gtf3c5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555132,304,133 - 2,321,597 (+)Ensembl
ChiLan1.0NW_0049555132,304,133 - 2,320,977 (+)NCBIChiLan1.0ChiLan1.0
GTF3C5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2116,298,205 - 6,328,578 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan196,300,540 - 6,330,906 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09104,150,392 - 104,178,242 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19132,779,664 - 132,807,518 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9132,779,664 - 132,807,518 (+)EnsemblpanPan2panpan1.1
GTF3C5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1951,347,273 - 51,362,621 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl951,337,187 - 51,362,422 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha950,610,478 - 50,625,850 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0952,240,488 - 52,255,871 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl952,230,540 - 52,255,656 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1951,019,025 - 51,034,403 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0951,343,551 - 51,358,924 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0951,422,937 - 51,438,315 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Gtf3c5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947199,671,711 - 199,686,697 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648719,440,222 - 19,458,552 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493648719,438,537 - 19,455,712 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GTF3C5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11272,743,527 - 272,760,055 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21306,729,971 - 306,935,093 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GTF3C5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1125,080,660 - 5,108,001 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl125,078,277 - 5,107,933 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366607910,544,454 - 10,572,056 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gtf3c5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247603,400,224 - 3,415,929 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247603,402,718 - 3,415,925 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Gtf3c5
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v158,090,661 - 8,110,251 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Gtf3c5
85 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:284
Count of miRNA genes:180
Interacting mature miRNAs:210
Transcripts:ENSRNOT00000015068
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 (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
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10450806Scl71Serum cholesterol level QTL 715.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
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
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)32905627547904329Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
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


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 67 161 91 90 59 92 59 6 356 192 11 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000015068   ⟹   ENSRNOP00000015068
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl332,291,859 - 32,312,164 (-)Ensembl
mRatBN7.2 Ensembl311,893,875 - 11,914,180 (-)Ensembl
Rnor_6.0 Ensembl37,144,250 - 7,164,654 (-)Ensembl
RefSeq Acc Id: NM_001079941   ⟹   NP_001073410
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,291,858 - 32,312,164 (-)NCBI
mRatBN7.2311,893,874 - 11,914,180 (-)NCBI
Rnor_6.037,144,361 - 7,164,667 (-)NCBI
Rnor_5.0312,495,477 - 12,515,794 (-)NCBI
RGSC_v3.437,552,088 - 7,572,394 (-)RGD
Celera36,675,056 - 6,695,359 (-)RGD
Sequence:
RefSeq Acc Id: XM_006233835   ⟹   XP_006233897
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,291,851 - 32,312,188 (-)NCBI
mRatBN7.2311,893,867 - 11,914,187 (-)NCBI
Rnor_6.037,144,354 - 7,164,678 (-)NCBI
Rnor_5.0312,495,477 - 12,515,794 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039105367   ⟹   XP_038961295
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,291,851 - 32,311,741 (-)NCBI
mRatBN7.2311,893,867 - 11,913,772 (-)NCBI
RefSeq Acc Id: NP_001073410   ⟸   NM_001079941
- UniProtKB: A1L1K6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233897   ⟸   XM_006233835
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000015068   ⟸   ENSRNOT00000015068
RefSeq Acc Id: XP_038961295   ⟸   XM_039105367
- Peptide Label: isoform X2
- UniProtKB: A6JTP2 (UniProtKB/TrEMBL)
Protein Domains
Transcription factor IIIC subunit 5 HTH   Transcription factor IIIC subunit Tfc1/Sfc1 triple

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A1L1K6-F1-model_v2 AlphaFold A1L1K6 1-515 view protein structure

Transcriptome

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

Promoters
RGD ID:13691935
Promoter ID:EPDNEW_R2460
Type:single initiation site
Name:Gtf3c5_1
Description:general transcription factor IIIC subunit 5
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_6.037,164,647 - 7,164,707EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305173 AgrOrtholog
BioCyc Gene G2FUF-50277 BioCyc
Ensembl Genes ENSRNOG00000010981 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015068 ENTREZGENE
  ENSRNOT00000015068.8 UniProtKB/TrEMBL
Gene3D-CATH 3.30.200.160 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7105121 IMAGE-MGC_LOAD
InterPro Tau95_N UniProtKB/TrEMBL
  TF_IIIC_su-5 UniProtKB/TrEMBL
  TF_IIIC_su-5 UniProtKB/TrEMBL
  TFIIIC_tauA_Sfc1 UniProtKB/TrEMBL
KEGG Report rno:362095 UniProtKB/TrEMBL
MGC_CLONE MGC:156738 IMAGE-MGC_LOAD
NCBI Gene 362095 ENTREZGENE
PANTHER GENERAL TRANSCRIPTION FACTOR 3C POLYPEPTIDE 5 UniProtKB/TrEMBL
  PTHR13230 UniProtKB/TrEMBL
Pfam Tau95 UniProtKB/TrEMBL
  Tau95_N UniProtKB/TrEMBL
PhenoGen Gtf3c5 PhenoGen
RatGTEx ENSRNOG00000010981 RatGTEx
UniProt A1L1K6 ENTREZGENE, UniProtKB/TrEMBL
  A6JTP2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-25 Gtf3c5  general transcription factor IIIC subunit 5  Gtf3c5  general transcription factor IIIC, polypeptide 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Gtf3c5  general transcription factor IIIC, polypeptide 5   Gtf3c5_predicted  general transcription factor IIIC, polypeptide 5 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Gtf3c5_predicted  general transcription factor IIIC, polypeptide 5 (predicted)      Symbol and Name status set to approved 70820 APPROVED