Taf1a (TATA-box binding protein associated factor, RNA polymerase I subunit A) - Rat Genome Database

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Gene: Taf1a (TATA-box binding protein associated factor, RNA polymerase I subunit A) Rattus norvegicus
Analyze
Symbol: Taf1a
Name: TATA-box binding protein associated factor, RNA polymerase I subunit A
RGD ID: 1305698
Description: Predicted to enable DNA binding activity. Predicted to be involved in transcription by RNA polymerase I. Predicted to be located in microtubule cytoskeleton; nucleolus; and nucleoplasm. Predicted to be part of RNA polymerase transcription factor SL1 complex. Orthologous to human TAF1A (TATA-box binding protein associated factor, RNA polymerase I subunit A); PARTICIPATES IN RNA polymerase I transcription pathway; INTERACTS WITH (+)-schisandrin B; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC360893; MGC125031; TATA box binding protein (Tbp)-associated factor, RNA polymerase I, A; TATA box-binding protein-associated factor 1A; TATA box-binding protein-associated factor RNA polymerase I subunit A; TBP-associated factor 1A; transcription initiation factor SL1/TIF-IB subunit A
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
GRCr81397,543,772 - 97,579,742 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1397,560,820 - 97,579,737 (+)EnsemblGRCr8
mRatBN7.21395,012,160 - 95,048,131 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1395,029,225 - 95,048,087 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1397,517,521 - 97,552,491 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01398,917,328 - 98,952,276 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01396,099,474 - 96,134,437 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.013101,770,278 - 101,807,975 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13101,790,865 - 101,806,900 (+)Ensemblrn6Rnor6.0
Rnor_5.013100,975,811 - 101,010,982 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41399,475,709 - 99,484,662 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1394,538,515 - 94,573,430 (+)NCBICelera
RGSC_v3.11399,528,622 - 99,673,546 (+)NCBI
Cytogenetic Map13q26NCBI
JBrowse:




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. TFIIB-related factors in RNA polymerase I transcription. Knutson BA and Hahn S, Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):265-73. doi: 10.1016/j.bbagrm.2012.08.003. Epub 2012 Aug 30.
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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
6. RNA polymerase I activity is regulated at multiple steps in the transcription cycle: recent insights into factors that influence transcription elongation. Schneider DA Gene. 2012 Feb 10;493(2):176-84. doi: 10.1016/j.gene.2011.08.006. Epub 2011 Aug 26.
Additional References at PubMed
PMID:12477932   PMID:15489334  


Genomics

Comparative Map Data
Taf1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81397,543,772 - 97,579,742 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1397,560,820 - 97,579,737 (+)EnsemblGRCr8
mRatBN7.21395,012,160 - 95,048,131 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1395,029,225 - 95,048,087 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1397,517,521 - 97,552,491 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01398,917,328 - 98,952,276 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01396,099,474 - 96,134,437 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.013101,770,278 - 101,807,975 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13101,790,865 - 101,806,900 (+)Ensemblrn6Rnor6.0
Rnor_5.013100,975,811 - 101,010,982 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41399,475,709 - 99,484,662 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1394,538,515 - 94,573,430 (+)NCBICelera
RGSC_v3.11399,528,622 - 99,673,546 (+)NCBI
Cytogenetic Map13q26NCBI
TAF1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381222,554,105 - 222,589,933 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1222,557,902 - 222,590,162 (-)Ensemblhg38GRCh38
GRCh371222,731,244 - 222,763,275 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361220,798,288 - 220,829,878 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1195,950,756 - 195,982,347 (-)NCBICelera
Cytogenetic Map1q41NCBI
HuRef1193,405,361 - 193,437,394 (-)NCBIHuRef
CHM1_11224,003,859 - 224,035,892 (-)NCBICHM1_1
T2T-CHM13v2.01221,788,155 - 221,823,679 (-)NCBIT2T-CHM13v2.0
Taf1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391183,170,251 - 183,195,776 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1183,170,325 - 183,191,020 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381183,388,885 - 183,410,201 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1183,388,981 - 183,410,198 (+)Ensemblmm10GRCm38
Celera1190,389,770 - 190,410,706 (+)NCBICelera
Cytogenetic Map1H5NCBI
Taf1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555201,901,405 - 1,921,900 (+)Ensembl
ChiLan1.0NW_0049555201,900,802 - 1,921,350 (+)NCBIChiLan1.0ChiLan1.0
TAF1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2126,730,903 - 26,768,465 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1126,684,291 - 26,720,548 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01198,227,332 - 198,263,133 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11203,244,796 - 203,276,849 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1203,244,796 - 203,276,872 (-)EnsemblpanPan2panpan1.1
TAF1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13816,827,853 - 16,858,506 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3816,828,205 - 16,858,432 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3816,883,269 - 16,914,352 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03816,873,236 - 16,904,338 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3816,873,247 - 16,904,285 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13816,878,704 - 16,909,772 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03817,228,367 - 17,259,637 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03817,522,309 - 17,553,821 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Taf1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934454,751,797 - 54,756,740 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366507 - 6,758 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TAF1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1011,340,642 - 11,362,432 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11011,340,637 - 11,362,432 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21013,449,697 - 13,471,491 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TAF1A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1256,982,714 - 7,014,699 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl256,982,784 - 7,014,877 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660557,221,347 - 7,253,346 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Taf1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248355,121,299 - 5,144,732 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248355,121,496 - 5,144,904 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Taf1a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11061,645,900 - 61,663,354 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Taf1a
365 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:189
Count of miRNA genes:148
Interacting mature miRNAs:168
Transcripts:ENSRNOT00000068036
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
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)1365613454109350286Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1321120177109350286Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1368983334109350286Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1367635937109350286Rat
1576318Schws5Schwannoma susceptibility QTL 50.0351nervous system integrity trait (VT:0010566)post-insult time to trigeminal nerve neurilemmoma formation (CMO:0002019)1364497900109350286Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1311081740103588154Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1338975045103588154Rat
8655951Rf63Renal function QTL 6312.2blood urea nitrogen amount (VT:0005265)plasma urea nitrogen level (CMO:0000586)1371610804109350286Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1383286150109350286Rat
8655959Pur32Proteinuria QTL 328.4urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137298450699745408Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1367635937109350286Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1364375743109350286Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131103588154Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1367635937109350286Rat

Markers in Region
RH131815  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81397,558,216 - 97,558,424 (+)Marker Load Pipeline
mRatBN7.21395,026,602 - 95,026,810 (+)MAPPERmRatBN7.2
Rnor_6.013101,786,098 - 101,786,305NCBIRnor6.0
Rnor_5.013100,990,128 - 100,990,335UniSTSRnor5.0
Celera1394,552,860 - 94,553,067UniSTS
RH 3.4 Map13652.0UniSTS
Cytogenetic Map13q26UniSTS
RH138784  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21395,034,535 - 95,034,677 (+)MAPPERmRatBN7.2
Rnor_6.013101,794,614 - 101,794,755NCBIRnor6.0
Rnor_5.013100,998,644 - 100,998,785UniSTSRnor5.0
Celera1394,560,793 - 94,560,934UniSTS
RH 3.4 Map13651.9UniSTS
Cytogenetic Map13q26UniSTS


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 67 165 91 90 59 90 59 6 354 190 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000087784   ⟹   ENSRNOP00000068899
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1397,560,820 - 97,579,737 (+)Ensembl
mRatBN7.2 Ensembl1395,029,225 - 95,048,087 (+)Ensembl
Rnor_6.0 Ensembl13101,790,865 - 101,806,900 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000113534   ⟹   ENSRNOP00000095744
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1395,029,225 - 95,048,087 (+)Ensembl
RefSeq Acc Id: NM_001037204   ⟹   NP_001032281
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81397,543,772 - 97,578,719 (+)NCBI
mRatBN7.21395,012,160 - 95,047,108 (+)NCBI
Rnor_6.013101,770,278 - 101,806,952 (+)NCBI
Rnor_5.013100,975,811 - 101,010,982 (+)NCBI
RGSC_v3.41399,475,709 - 99,484,662 (+)RGD
Celera1394,538,515 - 94,573,430 (+)RGD
Sequence:
RefSeq Acc Id: XM_039090934   ⟹   XP_038946862
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81397,560,771 - 97,579,742 (+)NCBI
mRatBN7.21395,029,149 - 95,048,131 (+)NCBI
RefSeq Acc Id: XM_039090935   ⟹   XP_038946863
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81397,560,779 - 97,579,742 (+)NCBI
mRatBN7.21395,029,165 - 95,048,131 (+)NCBI
RefSeq Acc Id: XM_039090936   ⟹   XP_038946864
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81397,560,942 - 97,579,742 (+)NCBI
mRatBN7.21395,029,330 - 95,048,131 (+)NCBI
RefSeq Acc Id: XM_039090937   ⟹   XP_038946865
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81397,562,387 - 97,579,742 (+)NCBI
mRatBN7.21395,031,306 - 95,048,131 (+)NCBI
RefSeq Acc Id: NP_001032281   ⟸   NM_001037204
- UniProtKB: Q3B7U2 (UniProtKB/Swiss-Prot),   A6JGN7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000068899   ⟸   ENSRNOT00000087784
RefSeq Acc Id: XP_038946862   ⟸   XM_039090934
- Peptide Label: isoform X1
- UniProtKB: A6JGN7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038946863   ⟸   XM_039090935
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038946864   ⟸   XM_039090936
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038946865   ⟸   XM_039090937
- Peptide Label: isoform X3
- UniProtKB: A6JGN7 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000095744   ⟸   ENSRNOT00000113534

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q3B7U2-F1-model_v2 AlphaFold Q3B7U2 1-453 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305698 AgrOrtholog
BioCyc Gene G2FUF-17033 BioCyc
Ensembl Genes ENSRNOG00000061139 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000087784 ENTREZGENE
  ENSRNOT00000087784.2 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7460374 IMAGE-MGC_LOAD
InterPro RNA_pol_I_TAF1A/TAFI48 UniProtKB/Swiss-Prot
  SL1/TIF-IB_Component UniProtKB/Swiss-Prot
  TAF1A-like UniProtKB/Swiss-Prot
KEGG Report rno:360893 UniProtKB/Swiss-Prot
MGC_CLONE MGC:125031 IMAGE-MGC_LOAD
NCBI Gene 360893 ENTREZGENE
PANTHER TATA BOX-BINDING PROTEIN ASSOCIATED FACTOR RNA POLYMERASE I SUBUNIT A UniProtKB/Swiss-Prot
  TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR RNA POLYMERASE I SUBUNIT A UniProtKB/Swiss-Prot
Pfam TAF1_subA UniProtKB/Swiss-Prot
PhenoGen Taf1a PhenoGen
PIRSF TAFI48 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000061139 RatGTEx
UniProt A0A0G2JTZ3_RAT UniProtKB/TrEMBL
  A6JGN7 ENTREZGENE, UniProtKB/TrEMBL
  Q3B7U2 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-16 Taf1a  TATA-box binding protein associated factor, RNA polymerase I subunit A  Taf1a  TATA box binding protein (Tbp)-associated factor, RNA polymerase I, A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Taf1a  TATA box binding protein (Tbp)-associated factor, RNA polymerase I, A  Taf1a_predicted  TATA box binding protein (Tbp)-associated factor, RNA polymerase I, A (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Taf1a_predicted  TATA box binding protein (Tbp)-associated factor, RNA polymerase I, A (predicted)      Symbol and Name status set to approved 70820 APPROVED