Gtf2a1l (general transcription factor 2A subunit 1 like) - Rat Genome Database

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Gene: Gtf2a1l (general transcription factor 2A subunit 1 like) Rattus norvegicus
Analyze
Symbol: Gtf2a1l
Name: general transcription factor 2A subunit 1 like
RGD ID: 1308625
Description: Predicted to be involved in cognition and transcription by RNA polymerase II. Predicted to be located in cytoplasm and male germ cell nucleus. Predicted to be part of transcription factor TFIIA complex. Orthologous to human GTF2A1L (general transcription factor IIA subunit 1 like); INTERACTS WITH bisphenol A; cadmium dichloride; methoxychlor.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: general transcription factor II A, 1-like factor; general transcription factor IIA, 1-like; Gtf2a1lf; LOC316711; TFIIA-alpha and beta-like factor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8611,506,362 - 11,591,622 (-)NCBIGRCr8
mRatBN7.265,752,814 - 5,834,797 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl65,752,823 - 5,836,472 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx66,041,628 - 6,090,322 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.066,351,009 - 6,399,699 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.065,878,176 - 5,926,867 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0612,412,198 - 12,468,613 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl612,415,805 - 12,468,596 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0622,367,835 - 22,431,365 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4612,527,076 - 12,583,946 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1612,527,075 - 12,583,945 (+)NCBI
Celera65,532,314 - 5,581,303 (-)NCBICelera
Cytogenetic Map6q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15927180   PMID:16646664   PMID:23227193  


Genomics

Comparative Map Data
Gtf2a1l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8611,506,362 - 11,591,622 (-)NCBIGRCr8
mRatBN7.265,752,814 - 5,834,797 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl65,752,823 - 5,836,472 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx66,041,628 - 6,090,322 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.066,351,009 - 6,399,699 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.065,878,176 - 5,926,867 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0612,412,198 - 12,468,613 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl612,415,805 - 12,468,596 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0622,367,835 - 22,431,365 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4612,527,076 - 12,583,946 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1612,527,075 - 12,583,945 (+)NCBI
Celera65,532,314 - 5,581,303 (-)NCBICelera
Cytogenetic Map6q12NCBI
GTF2A1L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38248,617,856 - 48,679,604 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl248,617,798 - 48,733,148 (+)EnsemblGRCh38hg38GRCh38
GRCh37248,844,995 - 48,906,743 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36248,698,452 - 48,813,791 (+)NCBINCBI36Build 36hg18NCBI36
Celera248,684,850 - 48,747,052 (+)NCBICelera
Cytogenetic Map2p16.3NCBI
HuRef248,578,316 - 48,640,115 (+)NCBIHuRef
CHM1_1248,775,674 - 48,837,484 (+)NCBICHM1_1
T2T-CHM13v2.0248,620,659 - 48,675,632 (+)NCBIT2T-CHM13v2.0
Gtf2a1l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391788,972,921 - 89,022,585 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1788,976,088 - 89,022,580 (+)EnsemblGRCm39 Ensembl
GRCm381788,665,493 - 88,715,157 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1788,668,660 - 88,715,152 (+)EnsemblGRCm38mm10GRCm38
MGSCv371789,068,000 - 89,114,490 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361788,577,031 - 88,623,478 (+)NCBIMGSCv36mm8
Celera1793,080,296 - 93,126,242 (+)NCBICelera
Cytogenetic Map17E4NCBI
cM Map1758.22NCBI
Gtf2a1l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544115,142,216 - 15,192,976 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544115,142,906 - 15,193,089 (+)NCBIChiLan1.0ChiLan1.0
GTF2A1L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21277,643,653 - 77,764,767 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A77,645,848 - 77,768,731 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A48,739,807 - 48,801,670 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A49,659,979 - 49,721,845 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A49,577,562 - 49,721,845 (+)Ensemblpanpan1.1panPan2
Gtf2a1l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629232,560,885 - 32,621,393 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365083,989,647 - 4,048,286 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365083,989,492 - 4,049,975 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GTF2A1L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl392,035,341 - 92,093,096 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1391,991,690 - 92,083,062 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2397,868,205 - 97,879,284 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Gtf2a1l
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473829,818,046 - 29,872,612 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473829,817,883 - 29,872,773 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gtf2a1l
297 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:25
Count of miRNA genes:23
Interacting mature miRNAs:23
Transcripts:ENSRNOT00000022380
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6127574569Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6127574569Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6127574569Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6127574569Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6127574569Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
2293706Bmd20Bone mineral density QTL 204.30.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6507449719988050Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat


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 8
Low 1 1 2 2 2 13 25 11 2
Below cutoff 2 39 25 12 15 12 6 8 59 30 8 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022380   ⟹   ENSRNOP00000022380
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl65,752,823 - 5,836,472 (-)Ensembl
Rnor_6.0 Ensembl612,415,805 - 12,468,596 (+)Ensembl
RefSeq Acc Id: NM_001012136   ⟹   NP_001012136
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8611,506,362 - 11,562,072 (-)NCBI
mRatBN7.265,752,822 - 5,808,530 (-)NCBI
Rnor_6.0612,415,886 - 12,468,587 (+)NCBI
Rnor_5.0622,367,835 - 22,431,365 (+)NCBI
RGSC_v3.4612,527,076 - 12,583,946 (+)RGD
Celera65,532,314 - 5,581,303 (-)RGD
Sequence:
RefSeq Acc Id: XM_039112432   ⟹   XP_038968360
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8611,506,362 - 11,589,974 (-)NCBI
mRatBN7.265,752,816 - 5,834,787 (-)NCBI
RefSeq Acc Id: XM_039112433   ⟹   XP_038968361
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8611,506,362 - 11,589,974 (-)NCBI
mRatBN7.265,752,814 - 5,834,787 (-)NCBI
RefSeq Acc Id: XM_039112434   ⟹   XP_038968362
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8611,506,362 - 11,532,736 (-)NCBI
mRatBN7.265,752,814 - 5,780,651 (-)NCBI
RefSeq Acc Id: XM_039112435   ⟹   XP_038968363
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8611,510,122 - 11,589,992 (-)NCBI
mRatBN7.265,756,575 - 5,834,797 (-)NCBI
RefSeq Acc Id: XM_063262031   ⟹   XP_063118101
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8611,506,362 - 11,591,604 (-)NCBI
RefSeq Acc Id: XM_063262032   ⟹   XP_063118102
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8611,506,362 - 11,572,751 (-)NCBI
RefSeq Acc Id: XM_063262033   ⟹   XP_063118103
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8611,506,362 - 11,591,622 (-)NCBI
RefSeq Acc Id: XM_063262034   ⟹   XP_063118104
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8611,506,362 - 11,591,331 (-)NCBI
RefSeq Acc Id: XR_005505531
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8611,510,136 - 11,589,991 (-)NCBI
mRatBN7.265,756,594 - 5,834,796 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001012136   ⟸   NM_001012136
- UniProtKB: Q641W8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022380   ⟸   ENSRNOT00000022380
RefSeq Acc Id: XP_038968361   ⟸   XM_039112433
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038968362   ⟸   XM_039112434
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968360   ⟸   XM_039112432
- Peptide Label: isoform X1
- UniProtKB: F7F7R8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038968363   ⟸   XM_039112435
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063118103   ⟸   XM_063262033
- Peptide Label: isoform X1
- UniProtKB: F7F7R8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063118101   ⟸   XM_063262031
- Peptide Label: isoform X1
- UniProtKB: F7F7R8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063118104   ⟸   XM_063262034
- Peptide Label: isoform X1
- UniProtKB: F7F7R8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063118102   ⟸   XM_063262032
- Peptide Label: isoform X1
- UniProtKB: F7F7R8 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q641W8-F1-model_v2 AlphaFold Q641W8 1-468 view protein structure

Transcriptome

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

Promoters
RGD ID:13694402
Promoter ID:EPDNEW_R4926
Type:initiation region
Name:Gtf2a1l_1
Description:general transcription factor 2A subunit 1 like
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_6.0612,415,875 - 12,415,935EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308625 AgrOrtholog
BioCyc Gene G2FUF-38777 BioCyc
Ensembl Genes ENSRNOG00000016703 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022380.7 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.100 UniProtKB/TrEMBL
  2.30.18.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7134703 IMAGE-MGC_LOAD
InterPro TFIIA_asu/bsu UniProtKB/TrEMBL
  TFIIA_b-brl UniProtKB/TrEMBL
KEGG Report rno:316711 UniProtKB/TrEMBL
MGC_CLONE MGC:95300 IMAGE-MGC_LOAD
NCBI Gene 316711 ENTREZGENE
PANTHER PTHR12694 UniProtKB/TrEMBL
  TFIIA-ALPHA AND BETA-LIKE FACTOR UniProtKB/TrEMBL
Pfam TFIIA UniProtKB/TrEMBL
PhenoGen Gtf2a1l PhenoGen
RatGTEx ENSRNOG00000016703 RatGTEx
SMART TFIIA UniProtKB/TrEMBL
Superfamily-SCOP TFIIA_betabarrel UniProtKB/TrEMBL
  Transcription factor IIA (TFIIA), alpha-helical domain UniProtKB/TrEMBL
UniProt F7F7R8 ENTREZGENE, UniProtKB/TrEMBL
  Q641W8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-04 Gtf2a1l  general transcription factor 2A subunit 1 like  Gtf2a1l  general transcription factor IIA, 1-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Gtf2a1l  general transcription factor IIA, 1-like  Gtf2a1lf  general transcription factor II A, 1-like factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Gtf2a1lf  general transcription factor II A, 1-like factor  Gtf2a1lf_predicted  general transcription factor II A, 1-like factor (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Gtf2a1lf_predicted  general transcription factor II A, 1-like factor (predicted)      Symbol and Name status set to approved 70820 APPROVED