Gtf2h4 (general transcription factor 2H subunit 4) - Rat Genome Database

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Gene: Gtf2h4 (general transcription factor 2H subunit 4) Rattus norvegicus
Analyze
Symbol: Gtf2h4
Name: general transcription factor 2H subunit 4
RGD ID: 1303309
Description: Predicted to enable RNA polymerase II general transcription initiation factor activity and double-stranded DNA binding activity. Predicted to be involved in nucleotide-excision repair and transcription by RNA polymerase II. Predicted to be located in nuclear speck. Predicted to be part of core TFIIH complex portion of holo TFIIH complex and transcription factor TFIID complex. Orthologous to human GTF2H4 (general transcription factor IIH subunit 4); PARTICIPATES IN RNA polymerase II transcription initiation pathway; nucleotide excision repair pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A.
Type: protein-coding (Ensembl: pseudogene)
RefSeq Status: VALIDATED
Previously known as: general transcription factor II H, polypeptide 4; general transcription factor IIH subunit 4; MGC156549; TFIIH transcription/DNA repair factor p52 subunit
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
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,076,110 - 3,081,805 (+)NCBIGRCr8
mRatBN7.2203,071,328 - 3,076,990 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,071,328 - 3,076,984 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx203,122,767 - 3,128,327 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,127,740 - 3,133,300 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0203,154,062 - 3,159,622 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0203,582,688 - 3,588,373 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,582,742 - 3,588,375 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,679,682 - 5,685,358 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,222,265 - 3,227,921 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1203,222,534 - 3,228,142 (+)NCBI
Celera20497,038 - 502,694 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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. A history of TFIIH: two decades of molecular biology on a pivotal transcription/repair factor. Egly JM and Coin F, DNA Repair (Amst). 2011 Jul 15;10(7):714-21. doi: 10.1016/j.dnarep.2011.04.021. Epub 2011 May 17.
2. 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.
3. Cloning and characterization of p52, the fifth subunit of the core of the transcription/DNA repair factor TFIIH. Marinoni JC, etal., EMBO J 1997 Mar 3;16(5):1093-102.
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9852112   PMID:12477932   PMID:27193682  


Genomics

Comparative Map Data
Gtf2h4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,076,110 - 3,081,805 (+)NCBIGRCr8
mRatBN7.2203,071,328 - 3,076,990 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,071,328 - 3,076,984 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx203,122,767 - 3,128,327 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,127,740 - 3,133,300 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0203,154,062 - 3,159,622 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0203,582,688 - 3,588,373 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,582,742 - 3,588,375 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,679,682 - 5,685,358 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,222,265 - 3,227,921 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1203,222,534 - 3,228,142 (+)NCBI
Celera20497,038 - 502,694 (+)NCBICelera
Cytogenetic Map20p12NCBI
GTF2H4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38630,908,207 - 30,914,106 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl630,908,207 - 30,914,106 (+)EnsemblGRCh38hg38GRCh38
GRCh37630,875,984 - 30,881,883 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36630,983,956 - 30,989,859 (+)NCBINCBI36Build 36hg18NCBI36
Build 34630,983,955 - 30,989,858NCBI
Celera632,474,080 - 32,479,983 (+)NCBICelera
Cytogenetic Map6p21.33NCBI
HuRef630,676,064 - 30,681,967 (+)NCBIHuRef
CHM1_1630,878,163 - 30,884,066 (+)NCBICHM1_1
T2T-CHM13v2.0630,772,873 - 30,778,772 (+)NCBIT2T-CHM13v2.0
Gtf2h4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,978,624 - 35,984,607 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1735,978,622 - 35,984,631 (-)EnsemblGRCm39 Ensembl
GRCm381735,667,728 - 35,673,750 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,667,730 - 35,673,739 (-)EnsemblGRCm38mm10GRCm38
MGSCv371735,804,684 - 35,810,627 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361734,755,012 - 34,760,955 (-)NCBIMGSCv36mm8
MGSCv361735,275,792 - 35,281,735 (-)NCBIMGSCv36mm8
Celera1739,186,270 - 39,188,696 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.7NCBI
Gtf2h4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955583842,287 - 847,960 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955583842,750 - 847,575 (+)NCBIChiLan1.0ChiLan1.0
GTF2H4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2545,469,178 - 45,475,112 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1641,432,007 - 41,437,941 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0630,653,398 - 30,659,316 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1631,521,501 - 31,527,456 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl631,521,501 - 31,527,456 (+)Ensemblpanpan1.1panPan2
GTF2H4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.112675,960 - 681,504 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl12675,983 - 681,425 (+)EnsemblCanFam3.1canFam3CanFam3.1
Gtf2h4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494634,181,287 - 34,187,427 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936837546,509 - 552,754 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936837546,561 - 552,686 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GTF2H4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl723,398,445 - 23,404,524 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1723,398,414 - 23,404,268 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2727,120,669 - 27,126,509 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GTF2H4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11741,550,167 - 41,556,538 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1741,550,287 - 41,556,054 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604430,609,173 - 30,615,125 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gtf2h4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475424,871,008 - 24,877,436 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475424,871,006 - 24,876,957 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gtf2h4
102 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:155
Count of miRNA genes:131
Interacting mature miRNAs:142
Transcripts:ENSRNOT00000001103
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
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2013624629Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
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
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2026463954597031Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2026463954597031Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat

Markers in Region
MARC_6551-6552:992007295:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0203,586,140 - 3,586,762NCBIRnor6.0
Rnor_5.0205,683,125 - 5,683,747UniSTSRnor5.0
RGSC_v3.4203,225,690 - 3,226,312UniSTSRGSC3.4
Celera20500,463 - 501,085UniSTS
Cytogenetic Map20p12UniSTS


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 2 26 24 20 7 20 66 21 32 3
Low 1 17 33 21 12 21 8 11 8 14 9 8 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000001103   ⟹   ENSRNOP00000001103
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,071,328 - 3,076,984 (+)Ensembl
Rnor_6.0 Ensembl203,582,743 - 3,588,371 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000083556
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,582,742 - 3,588,375 (+)Ensembl
RefSeq Acc Id: NM_212501   ⟹   NP_997666
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,076,110 - 3,081,766 (+)NCBI
mRatBN7.2203,071,328 - 3,076,990 (+)NCBI
Rnor_6.0203,582,715 - 3,588,371 (+)NCBI
Rnor_5.0205,679,682 - 5,685,358 (+)NCBI
RGSC_v3.4203,222,265 - 3,227,921 (+)RGD
Celera20497,038 - 502,694 (+)RGD
Sequence:
RefSeq Acc Id: XM_063278998   ⟹   XP_063135068
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,078,254 - 3,081,805 (+)NCBI
RefSeq Acc Id: XM_063278999   ⟹   XP_063135069
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,078,597 - 3,081,805 (+)NCBI
RefSeq Acc Id: XR_010060632
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,077,027 - 3,079,878 (+)NCBI
Protein Sequences
Protein RefSeqs NP_997666 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135068 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135069 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI27470 (Get FASTA)   NCBI Sequence Viewer  
  CAE84027 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_997666   ⟸   NM_212501
- UniProtKB: Q6MG20 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001103   ⟸   ENSRNOT00000001103
RefSeq Acc Id: XP_063135068   ⟸   XM_063278998
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063135069   ⟸   XM_063278999
- Peptide Label: isoform X1
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6MG20-F1-model_v2 AlphaFold Q6MG20 1-463 view protein structure

Transcriptome

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

Promoters
RGD ID:13701312
Promoter ID:EPDNEW_R11830
Type:multiple initiation site
Name:Gtf2h4_1
Description:general transcription factor 2H subunit 4
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_6.0203,582,725 - 3,582,785EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303309 AgrOrtholog
BioCyc Gene G2FUF-4765 BioCyc
Ensembl Genes ENSRNOG00000000831 Ensembl
Gene3D-CATH 3.30.70.2610 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7190127 IMAGE-MGC_LOAD
  IMAGE:7324889 IMAGE-MGC_LOAD
InterPro Tfb2 UniProtKB/TrEMBL
  Tfb2_C UniProtKB/TrEMBL
KEGG Report rno:294236 UniProtKB/TrEMBL
MGC_CLONE MGC:156549 IMAGE-MGC_LOAD
  MGC:94582 IMAGE-MGC_LOAD
NCBI Gene 294236 ENTREZGENE
PANTHER GENERAL TRANSCRIPTION FACTOR IIH SUBUNIT 4 UniProtKB/TrEMBL
  Tfb2 UniProtKB/TrEMBL
Pfam Tfb2 UniProtKB/TrEMBL
  Tfb2_C UniProtKB/TrEMBL
PhenoGen Gtf2h4 PhenoGen
RatGTEx ENSRNOG00000000831 RatGTEx
UniProt Q6MG20 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-18 Gtf2h4  general transcription factor 2H subunit 4  Gtf2h4  general transcription factor II H, polypeptide 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-02-14 Gtf2h4  general transcription factor II H, polypeptide 4      Symbol and Name status set to provisional 70820 PROVISIONAL