Gtf3c6 (general transcription factor 3C subunit 6) - Rat Genome Database

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Gene: Gtf3c6 (general transcription factor 3C subunit 6) Rattus norvegicus
Analyze
Symbol: Gtf3c6
Name: general transcription factor 3C subunit 6
RGD ID: 1307434
Description: Predicted to enable RNA polymerase III general transcription initiation factor activity. Predicted to contribute to DNA binding activity. Predicted to be involved in transcription by RNA polymerase III. Predicted to be located in nuclear body. Predicted to be part of transcription factor TFIIIC complex. Orthologous to human GTF3C6 (general transcription factor IIIC subunit 6); PARTICIPATES IN RNA polymerase III transcription pathway; INTERACTS WITH 2,2',5,5'-tetrachlorobiphenyl; bisphenol A; chlorpyrifos.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: general transcription factor 3C polypeptide 6; general transcription factor IIIC, polypeptide 6, alpha; LOC361858; RGD1307434; similar to RIKEN cDNA 2410016F19
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82045,210,906 - 45,222,888 (-)NCBIGRCr8
mRatBN7.22043,656,400 - 43,668,382 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2043,655,875 - 43,667,873 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2045,405,389 - 45,417,367 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02045,064,578 - 45,076,557 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02045,808,206 - 45,821,166 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02045,347,788 - 45,356,868 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2045,347,271 - 45,356,358 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02047,067,523 - 47,076,603 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42044,415,016 - 44,424,722 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12044,438,231 - 44,447,217 (-)NCBI
Celera2044,363,122 - 44,372,177 (-)NCBICelera
Cytogenetic Map20q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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  


Genomics

Comparative Map Data
Gtf3c6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82045,210,906 - 45,222,888 (-)NCBIGRCr8
mRatBN7.22043,656,400 - 43,668,382 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2043,655,875 - 43,667,873 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2045,405,389 - 45,417,367 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02045,064,578 - 45,076,557 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02045,808,206 - 45,821,166 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02045,347,788 - 45,356,868 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2045,347,271 - 45,356,358 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02047,067,523 - 47,076,603 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42044,415,016 - 44,424,722 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12044,438,231 - 44,447,217 (-)NCBI
Celera2044,363,122 - 44,372,177 (-)NCBICelera
Cytogenetic Map20q12NCBI
GTF3C6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386110,958,706 - 110,967,872 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6110,958,706 - 110,967,890 (+)EnsemblGRCh38hg38GRCh38
GRCh376111,279,909 - 111,289,075 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366111,386,456 - 111,395,775 (+)NCBINCBI36Build 36hg18NCBI36
Build 346111,386,455 - 111,395,772NCBI
Celera6112,026,336 - 112,035,665 (+)NCBICelera
Cytogenetic Map6q21NCBI
HuRef6108,850,927 - 108,860,248 (+)NCBIHuRef
CHM1_16111,542,813 - 111,552,141 (+)NCBICHM1_1
T2T-CHM13v2.06112,137,328 - 112,146,494 (+)NCBIT2T-CHM13v2.0
Gtf3c6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391040,123,697 - 40,133,708 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1040,123,699 - 40,134,104 (-)EnsemblGRCm39 Ensembl
GRCm381040,247,701 - 40,257,712 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1040,247,703 - 40,258,108 (-)EnsemblGRCm38mm10GRCm38
MGSCv371039,969,009 - 39,977,471 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361039,938,619 - 39,947,081 (-)NCBIMGSCv36mm8
Celera1041,135,997 - 41,144,459 (-)NCBICelera
Cytogenetic Map10B1NCBI
cM Map1021.79NCBI
Gtf3c6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495541135,609,772 - 35,619,448 (+)NCBIChiLan1.0ChiLan1.0
GTF3C6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25130,963,397 - 130,972,879 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16128,849,480 - 128,858,913 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06108,757,848 - 108,767,282 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16112,840,557 - 112,849,386 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6112,840,557 - 112,849,386 (+)Ensemblpanpan1.1panPan2
GTF3C6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11267,491,034 - 67,505,012 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1267,490,780 - 67,557,609 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1267,309,603 - 67,323,567 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01268,369,556 - 68,383,288 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1268,369,836 - 68,383,286 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11267,720,575 - 67,734,296 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01267,566,718 - 67,580,482 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01267,844,702 - 67,858,436 (+)NCBIUU_Cfam_GSD_1.0
Gtf3c6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946102,442,405 - 102,450,100 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365646,717,260 - 6,724,964 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365646,717,282 - 6,727,280 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GTF3C6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl176,896,756 - 76,909,749 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1176,896,761 - 76,909,758 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2186,353,216 - 86,366,183 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GTF3C6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11362,903,890 - 62,912,958 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1362,903,952 - 62,912,767 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604035,205,040 - 35,214,136 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gtf3c6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249161,916,619 - 1,925,260 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249161,916,483 - 1,925,334 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gtf3c6
136 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:300
Count of miRNA genes:204
Interacting mature miRNAs:237
Transcripts:ENSRNOT00000000716
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203161428444396023Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat

Markers in Region
RH129945  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22043,655,942 - 43,656,092 (+)MAPPERmRatBN7.2
Rnor_6.02045,347,331 - 45,347,480NCBIRnor6.0
Rnor_5.02047,067,066 - 47,067,215UniSTSRnor5.0
RGSC_v3.42044,414,559 - 44,414,708UniSTSRGSC3.4
Celera2044,362,665 - 44,362,814UniSTS
RH 3.4 Map20482.8UniSTS
Cytogenetic Map20q12UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000000716   ⟹   ENSRNOP00000000716
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2043,655,875 - 43,667,873 (-)Ensembl
Rnor_6.0 Ensembl2045,347,271 - 45,356,358 (-)Ensembl
RefSeq Acc Id: NM_001108537   ⟹   NP_001102007
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82045,210,906 - 45,222,888 (-)NCBI
mRatBN7.22043,656,400 - 43,668,382 (-)NCBI
Rnor_6.02045,347,788 - 45,356,868 (-)NCBI
Rnor_5.02047,067,523 - 47,076,603 (-)NCBI
RGSC_v3.42044,415,016 - 44,424,722 (-)RGD
Celera2044,363,122 - 44,372,177 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102007 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI59438 (Get FASTA)   NCBI Sequence Viewer  
  EDL87842 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000000716.5
RefSeq Acc Id: NP_001102007   ⟸   NM_001108537
- UniProtKB: B0K037 (UniProtKB/TrEMBL),   F7ENN0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000000716   ⟸   ENSRNOT00000000716
Protein Domains
Transcription factor TFIIIC triple barrel

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B0K037-F1-model_v2 AlphaFold B0K037 1-227 view protein structure

Transcriptome

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

Promoters
RGD ID:13701658
Promoter ID:EPDNEW_R12181
Type:multiple initiation site
Name:Gtf3c6_1
Description:general transcription factor 3C subunit 6
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_6.02045,356,362 - 45,356,422EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307434 AgrOrtholog
BioCyc Gene G2FUF-3435 BioCyc
Ensembl Genes ENSRNOG00000000586 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000716.7 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.4370 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9102105 IMAGE-MGC_LOAD
InterPro GTF3C6-like UniProtKB/TrEMBL
  TFIIIC_tau55-rel UniProtKB/TrEMBL
KEGG Report rno:361858 UniProtKB/TrEMBL
MGC_CLONE MGC:188773 IMAGE-MGC_LOAD
NCBI Gene 361858 ENTREZGENE
PANTHER GENERAL TRANSCRIPTION FACTOR 3C POLYPEPTIDE 6 UniProtKB/TrEMBL
  PTHR21860 UniProtKB/TrEMBL
Pfam TFIIIC_subunit UniProtKB/TrEMBL
PhenoGen Gtf3c6 PhenoGen
RatGTEx ENSRNOG00000000586 RatGTEx
UniProt B0K037 ENTREZGENE, UniProtKB/TrEMBL
  F7ENN0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-18 Gtf3c6  general transcription factor 3C subunit 6  Gtf3c6  general transcription factor IIIC, polypeptide 6, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Gtf3c6  general transcription factor IIIC, polypeptide 6, alpha  RGD1307434_predicted  similar to RIKEN cDNA 2410016F19 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1307434_predicted  similar to RIKEN cDNA 2410016F19 (predicted)  LOC361858_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC361858_predicted  similar to RIKEN cDNA 2410016F19 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL