Taf9 (TATA-box binding protein associated factor 9) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Taf9 (TATA-box binding protein associated factor 9) Rattus norvegicus
Analyze
Symbol: Taf9
Name: TATA-box binding protein associated factor 9
RGD ID: 727861
Description: Predicted to enable several functions, including ATPase binding activity; C2H2 zinc finger domain binding activity; and p53 binding activity. Predicted to contribute to RNA polymerase II general transcription initiation factor activity and histone acetyltransferase activity. Involved in positive regulation of transcription by RNA polymerase II and response to L-glutamate. Predicted to be located in nucleoplasm. Predicted to be part of nucleoplasm and pre-snoRNP complex. Orthologous to human TAF9 (TATA-box binding protein associated factor 9); PARTICIPATES IN de novo purine biosynthetic pathway; RNA polymerase II transcription initiation pathway; ribosome biogenesis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: CINAP; LOC294694; MGC108535; MGC109428; RNA polymerase II TBP-associated factor subunit G; TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor; TAF9 RNA polymerase II, TATA box binding protein-associated factor; TAFII-31; TAFII-32; TAFII31; TAFII32; transcription initiation factor TFIID 31 kDa subunit; transcription initiation factor TFIID 32 kDa subunit; transcription initiation factor TFIID subunit 9
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Taf9-ps  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2231,794,316 - 31,798,324 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl231,794,142 - 31,798,769 (+)Ensembl
Rnor_6.0230,664,407 - 30,668,414 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl230,664,639 - 30,668,414 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0249,824,043 - 49,828,050 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4231,454,557 - 31,466,611 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1231,374,959 - 31,386,977 (+)NCBI
Celera227,807,006 - 27,811,013 (+)NCBICelera
Cytogenetic Map2q12NCBI
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

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Rat TAFII31 gene is induced upon programmed cell death in differentiated PC12 cells deprived of NGF. Aoki T, etal., Biochem Biophys Res Commun 1997 May 8;234(1):230-4.
2. In vivo functional analysis of the histone 3-like TAF9 and a TAF9-related factor, TAF9L. Chen Z and Manley JL, J Biol Chem 2003 Sep 12;278(37):35172-83. Epub 2003 Jul 01.
3. 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.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Structural bioinformatics of the general transcription factor TFIID. Malkowska M, etal., Biochimie. 2013 Apr;95(4):680-91. doi: 10.1016/j.biochi.2012.10.024. Epub 2012 Nov 9.
6. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
7. Dynamics of nucleotide metabolism as a supporter of life phenomena. Noma T J Med Invest. 2005 Aug;52(3-4):127-36.
8. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
9. GOA pipeline RGD automated data pipeline
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Comprehensive gene review and curation RGD comprehensive gene curation
12. ATAC-king the complexity of SAGA during evolution. Spedale G, etal., Genes Dev. 2012 Mar 15;26(6):527-41. doi: 10.1101/gad.184705.111.
13. Transcriptional modification by a CASK-interacting nucleosome assembly protein. Wang GS, etal., Neuron. 2004 Apr 8;42(1):113-28.
Additional References at PubMed
PMID:8889548   PMID:9171108   PMID:9674425   PMID:11278372   PMID:11564863   PMID:12477932   PMID:14580349   PMID:14766980   PMID:15309719   PMID:15489227   PMID:15489334   PMID:15601843  
PMID:15899866   PMID:15960975   PMID:17636026   PMID:18722179   PMID:19251649  


Genomics

Comparative Map Data
Taf9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2231,794,316 - 31,798,324 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl231,794,142 - 31,798,769 (+)Ensembl
Rnor_6.0230,664,407 - 30,668,414 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl230,664,639 - 30,668,414 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0249,824,043 - 49,828,050 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4231,454,557 - 31,466,611 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1231,374,959 - 31,386,977 (+)NCBI
Celera227,807,006 - 27,811,013 (+)NCBICelera
Cytogenetic Map2q12NCBI
TAF9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38569,364,743 - 69,369,824 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl569,362,026 - 69,370,013 (-)EnsemblGRCh38hg38GRCh38
GRCh37568,660,570 - 68,665,651 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36568,683,309 - 68,701,596 (-)NCBINCBI36hg18NCBI36
Build 34568,683,310 - 68,701,122NCBI
Celera565,650,213 - 65,668,504 (-)NCBI
Cytogenetic Map5q13.2NCBI
HuRef565,603,597 - 65,621,883 (-)NCBIHuRef
CHM1_1568,647,401 - 68,665,684 (-)NCBICHM1_1
T2T-CHM13v2.0570,190,530 - 70,195,609 (-)NCBI
Taf9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3913100,787,851 - 100,792,568 (+)NCBIGRCm39mm39
GRCm39 Ensembl13100,788,087 - 100,792,568 (+)Ensembl
GRCm39 Ensembl13100,787,487 - 100,802,867 (+)Ensembl
GRCm3813100,651,343 - 100,656,060 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl13100,651,579 - 100,656,060 (+)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl13100,650,979 - 100,666,359 (+)EnsemblGRCm38mm10GRCm38
MGSCv3713101,421,298 - 101,436,368 (+)NCBIGRCm37mm9NCBIm37
MGSCv3613101,751,631 - 101,766,616 (+)NCBImm8
Celera13104,261,518 - 104,276,056 (+)NCBICelera
Cytogenetic Map13D1NCBI
Taf9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495557574,506 - 76,272 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495557574,506 - 76,272 (-)NCBIChiLan1.0ChiLan1.0
TAF9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1546,201,985 - 46,207,254 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0544,630,503 - 44,635,760 (+)NCBIMhudiblu_PPA_v0panPan3
TAF9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1254,403,908 - 54,406,857 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl254,390,411 - 54,406,872 (-)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.03619,339,518 - 19,340,582 (-)NCBI
ROS_Cfam_1.0 Ensembl254,914,940 - 54,917,901 (-)Ensembl
UMICH_Zoey_3.1447,834,795 - 47,835,859 (+)NCBI
UU_Cfam_GSD_1.03619,524,389 - 19,525,453 (-)NCBI
Taf9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213191,315,967 - 191,320,141 (+)NCBI
SpeTri2.0NW_004936480252,435 - 256,609 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TAF9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1647,488,941 - 47,499,542 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11647,494,841 - 47,499,568 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21651,338,769 - 51,343,462 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TAF9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1465,451,038 - 65,455,896 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604914,187,417 - 14,192,526 (-)NCBIVero_WHO_p1.0
Taf9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624905240,760 - 244,656 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_004624905240,760 - 244,656 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH128995  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2231,797,926 - 31,798,125 (+)MAPPERmRatBN7.2
Rnor_6.0230,668,017 - 30,668,215NCBIRnor6.0
Rnor_5.0249,827,653 - 49,827,851UniSTSRnor5.0
RGSC_v3.4231,458,167 - 31,458,365UniSTSRGSC3.4
Celera227,810,616 - 27,810,814UniSTS
RH 3.4 Map263.88UniSTS
Cytogenetic Map2q12UniSTS
RH142847  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2231,794,893 - 31,795,007 (+)MAPPERmRatBN7.2
Rnor_6.0230,664,985 - 30,665,098NCBIRnor6.0
Rnor_5.0249,824,621 - 49,824,734UniSTSRnor5.0
RGSC_v3.4231,455,135 - 31,455,248UniSTSRGSC3.4
Celera227,807,584 - 27,807,697UniSTS
RH 3.4 Map278.3UniSTS
Cytogenetic Map2q12UniSTS
RH136869  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2231,806,049 - 31,806,200 (+)MAPPERmRatBN7.2
mRatBN7.22025,577,081 - 25,577,232 (+)MAPPERmRatBN7.2
Rnor_6.02027,129,890 - 27,130,040NCBIRnor6.0
Rnor_6.0230,676,139 - 30,676,289NCBIRnor6.0
Rnor_5.02028,970,428 - 28,970,578UniSTSRnor5.0
Rnor_5.0249,835,775 - 49,835,925UniSTSRnor5.0
RGSC_v3.4231,466,289 - 31,466,439UniSTSRGSC3.4
RGSC_v3.42025,401,745 - 25,401,895UniSTSRGSC3.4
Celera2026,872,950 - 26,873,100UniSTS
Celera227,818,538 - 27,818,688UniSTS
Cytogenetic Map2q12UniSTS
Cytogenetic Map20p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22691781781754745Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
1331764Bp205Blood pressure QTL 2053.476arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22699957143154682Rat
1643006Pain1Pain QTL 13.630.005mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)22699957148268661Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22715716072157160Rat
1300160Hrtrt3Heart rate QTL 33.62heart pumping trait (VT:2000009)absolute change in heart rate (CMO:0000534)22997159351729300Rat
10755434Coatc7Coat color QTL 70.04794coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23064806575648065Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:36
Count of miRNA genes:34
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000061166
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.


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 7
Low 3 33 46 30 19 30 3 4 74 34 34 11 3
Below cutoff 10 11 11 11 5 7 1 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000076061   ⟹   ENSRNOP00000068116
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl230,666,475 - 30,668,185 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076294   ⟹   ENSRNOP00000068206
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl230,664,642 - 30,667,868 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076372   ⟹   ENSRNOP00000068315
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl230,664,639 - 30,667,456 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076434   ⟹   ENSRNOP00000067916
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl230,664,690 - 30,667,873 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076484   ⟹   ENSRNOP00000068397
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl230,664,695 - 30,668,414 (+)Ensembl
RefSeq Acc Id: NM_001037310   ⟹   NP_001032387
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2231,794,571 - 31,798,324 (+)NCBI
Rnor_6.0230,664,662 - 30,668,414 (+)NCBI
Rnor_5.0249,824,043 - 49,828,050 (+)NCBI
RGSC_v3.4231,454,557 - 31,466,611 (+)RGD
Celera227,807,261 - 27,811,013 (+)NCBI
Sequence:
RefSeq Acc Id: NM_184048   ⟹   NP_908937
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2231,794,316 - 31,798,324 (+)NCBI
Rnor_6.0230,664,407 - 30,668,414 (+)NCBI
Rnor_5.0249,824,043 - 49,828,050 (+)NCBI
RGSC_v3.4231,454,557 - 31,466,611 (+)RGD
Celera227,807,006 - 27,811,013 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_908937   ⟸   NM_184048
- UniProtKB: Q5BKE0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001032387   ⟸   NM_001037310
- UniProtKB: Q5BKE0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068206   ⟸   ENSRNOT00000076294
RefSeq Acc Id: ENSRNOP00000068315   ⟸   ENSRNOT00000076372
RefSeq Acc Id: ENSRNOP00000068116   ⟸   ENSRNOT00000076061
RefSeq Acc Id: ENSRNOP00000068397   ⟸   ENSRNOT00000076484
RefSeq Acc Id: ENSRNOP00000067916   ⟸   ENSRNOT00000076434

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5BKE0-F1-model_v2 AlphaFold Q5BKE0 1-264 view protein structure

Transcriptome

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

Promoters
RGD ID:13691112
Promoter ID:EPDNEW_R1633
Type:multiple initiation site
Name:Taf9_1
Description:TATA-box binding protein associated factor 9
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_6.0230,664,685 - 30,664,745EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727861 AgrOrtholog
BioCyc Gene G2FUF-54655 BioCyc
Ensembl Genes ENSRNOG00000039848 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00000051258 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000068116 ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOP00000068424 ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000076061 ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOT00000076786 ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Gene3D-CATH 1.10.20.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7319327 IMAGE-MGC_LOAD
  IMAGE:7322630 IMAGE-MGC_LOAD
InterPro Depp_CoAkinase UniProtKB/TrEMBL
  Histone-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  TFIID-31 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:373541 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108535 IMAGE-MGC_LOAD
  MGC:109428 IMAGE-MGC_LOAD
NCBI Gene 373541 ENTREZGENE
Pfam TFIID-31kDa UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Taf9 PhenoGen
PROSITE DPCK UniProtKB/TrEMBL
Superfamily-SCOP SSF47113 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt A0A096MJG1_RAT UniProtKB/TrEMBL
  A0A096MK91_RAT UniProtKB/TrEMBL
  Q5BKE0 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q6UV34 UniProtKB/Swiss-Prot
  Q7TP20 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-11-29 Taf9  TATA-box binding protein associated factor 9  Taf9  TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-11 Taf9  TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor  Taf9_predicted  TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor (predicted)  Data Merged 737654 APPROVED
2005-07-08 Taf9  TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor      Symbol and Name status set to approved 1299863 APPROVED
2005-01-12 Taf9_predicted  TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor (predicted)      Symbol and Name status set to approved 70820 APPROVED

RGD Curation Notes
Note Type Note Reference