Taf1d (TATA-box binding protein associated factor, RNA polymerase I subunit D) - Rat Genome Database
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Gene: Taf1d (TATA-box binding protein associated factor, RNA polymerase I subunit D) Rattus norvegicus
Analyze
Symbol: Taf1d
Name: TATA-box binding protein associated factor, RNA polymerase I subunit D
RGD ID: 1309627
Description: Predicted to have identical protein binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to localize to cytosol; microtubule cytoskeleton; and nuclear lumen. Orthologous to human TAF1D (TATA-box binding protein associated factor, RNA polymerase I subunit D); PARTICIPATES IN RNA polymerase I transcription pathway; INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Josd3; Josephin domain containing 3; LOC363017; RGD1309627; similar to RIKEN cDNA 4930553M18; TATA box binding protein (Tbp)-associated factor, RNA polymerase I, D; TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa; TATA box-binding protein-associated factor 1D; TATA box-binding protein-associated factor RNA polymerase I subunit D; TBP-associated factor 1D; transcription initiation factor SL1/TIF-IB subunit D
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2812,146,511 - 12,156,647 (+)NCBI
Rnor_6.0 Ensembl813,861,459 - 13,871,354 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0813,861,242 - 13,871,508 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0813,800,779 - 13,811,374 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4812,107,144 - 12,117,177 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1812,108,474 - 12,117,177 (+)NCBI
Celera813,614,324 - 13,624,354 (+)NCBICelera
Cytogenetic Map8q12NCBI
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
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxyphenyl retinamide  (ISO)
aflatoxin M1  (ISO)
all-trans-retinoic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chloroprene  (EXP)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
cyclosporin A  (ISO)
DDT  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
fluoranthene  (ISO)
glafenine  (EXP)
glyphosate  (EXP)
leflunomide  (ISO)
methapyrilene  (EXP)
methoxyacetic acid  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (EXP,ISO)
methylparaben  (ISO)
Monobutylphthalate  (EXP)
oxaliplatin  (EXP)
paracetamol  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
rac-lactic acid  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP,ISO)
sodium fluoride  (ISO)
succimer  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
topotecan  (EXP)
trichostatin A  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
vitamin E  (ISO)

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

Additional References at PubMed
PMID:15489334  


Genomics

Comparative Map Data
Taf1d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2812,146,511 - 12,156,647 (+)NCBI
Rnor_6.0 Ensembl813,861,459 - 13,871,354 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0813,861,242 - 13,871,508 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0813,800,779 - 13,811,374 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4812,107,144 - 12,117,177 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1812,108,474 - 12,117,177 (+)NCBI
Celera813,614,324 - 13,624,354 (+)NCBICelera
Cytogenetic Map8q12NCBI
TAF1D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1193,729,948 - 93,784,391 (-)EnsemblGRCh38hg38GRCh38
GRCh381193,730,194 - 93,741,495 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371193,463,360 - 93,474,661 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361193,108,743 - 93,114,310 (-)NCBINCBI36hg18NCBI36
Celera1190,760,547 - 90,766,156 (-)NCBI
Cytogenetic Map11q21NCBI
HuRef1189,546,328 - 89,551,937 (-)NCBIHuRef
CHM1_11193,352,108 - 93,357,722 (-)NCBICHM1_1
Taf1d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39915,217,485 - 15,228,293 (+)NCBIGRCm39mm39
GRCm39 Ensembl915,217,510 - 15,228,287 (+)Ensembl
GRCm38915,305,953 - 15,316,997 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl915,306,214 - 15,316,991 (+)EnsemblGRCm38mm10GRCm38
MGSCv37915,110,658 - 15,121,441 (+)NCBIGRCm37mm9NCBIm37
MGSCv36915,056,653 - 15,067,390 (+)NCBImm8
Celera912,585,532 - 12,595,986 (+)NCBICelera
Cytogenetic Map9A2NCBI
Taf1d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955414799,138 - 803,005 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955414799,124 - 806,242 (+)NCBIChiLan1.0ChiLan1.0
TAF1D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11192,241,125 - 92,250,412 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1192,241,126 - 92,250,416 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01188,752,779 - 88,763,136 (-)NCBIMhudiblu_PPA_v0panPan3
TAF1D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1217,013,383 - 7,023,497 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Taf1d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366741,044,519 - 1,053,744 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TAF1D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl926,147,149 - 26,167,290 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1926,154,910 - 26,167,282 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2929,682,286 - 29,689,261 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TAF1D
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1184,982,364 - 84,993,601 (-)NCBI
ChlSab1.1 Ensembl184,988,280 - 84,994,290 (-)Ensembl
Taf1d
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473538,397,922 - 38,407,255 (-)NCBI

Position Markers
RH130449  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map8q12UniSTS
RH132383  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0813,871,572 - 13,871,778NCBIRnor6.0
Rnor_5.0813,811,137 - 13,811,343UniSTSRnor5.0
RGSC_v3.4812,117,394 - 12,117,600UniSTSRGSC3.4
Celera813,624,571 - 13,624,777UniSTS
RH 3.4 Map8111.9UniSTS
Cytogenetic Map8q12UniSTS
RH138545  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0813,874,235 - 13,874,384NCBIRnor6.0
Rnor_5.0813,813,806 - 13,813,955UniSTSRnor5.0
RGSC_v3.4812,120,057 - 12,120,206UniSTSRGSC3.4
Celera813,627,234 - 13,627,383UniSTS
RH 3.4 Map8111.1UniSTS
Cytogenetic Map8q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124608226Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125942267Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8210812847108128Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8210812847108128Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8210812847108128Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8210812847108128Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8736807652368076Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8736807652368076Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8736807652368076Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8873867753738677Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)89531047119211942Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)81038843955388439Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)81038843955388439Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810938911120496129Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81137326757541668Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81137350945712344Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81137350945712344Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81144825156448251Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81144825156448251Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:36
Count of miRNA genes:34
Interacting mature miRNAs:36
Transcripts:ENSRNOT00000014605
Prediction methods: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.


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 3 37 47 31 19 31 8 8 74 35 41 11 8
Low 6 10 10 10 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000014605   ⟹   ENSRNOP00000014605
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl813,862,651 - 13,871,354 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078161   ⟹   ENSRNOP00000068730
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl813,861,459 - 13,867,749 (+)Ensembl
RefSeq Acc Id: NM_001014207   ⟹   NP_001014229
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2812,146,614 - 12,156,647 (+)NCBI
Rnor_6.0813,861,322 - 13,871,355 (+)NCBI
Rnor_5.0813,800,779 - 13,811,374 (+)NCBI
RGSC_v3.4812,107,144 - 12,117,177 (+)RGD
Celera813,614,324 - 13,624,354 (+)RGD
Sequence:
RefSeq Acc Id: XM_008765946   ⟹   XP_008764168
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0813,861,726 - 13,871,395 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595713   ⟹   XP_017451202
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0813,861,242 - 13,871,395 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595714   ⟹   XP_017451203
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0813,861,338 - 13,871,508 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595715   ⟹   XP_017451204
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0813,861,726 - 13,871,395 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595716   ⟹   XP_017451205
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0813,861,726 - 13,871,395 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595717   ⟹   XP_017451206
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0813,861,726 - 13,871,395 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039081695   ⟹   XP_038937623
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2812,146,511 - 12,154,255 (+)NCBI
RefSeq Acc Id: XR_005487862
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2812,146,511 - 12,156,633 (+)NCBI
RefSeq Acc Id: XR_005487863
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2812,146,623 - 12,156,633 (+)NCBI
RefSeq Acc Id: XR_005487864
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2812,146,511 - 12,156,021 (+)NCBI
RefSeq Acc Id: XR_005487865
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2812,146,511 - 12,156,015 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001014229   ⟸   NM_001014207
- UniProtKB: Q5M948 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008764168   ⟸   XM_008765946
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017451202   ⟸   XM_017595713
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451203   ⟸   XM_017595714
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451204   ⟸   XM_017595715
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451205   ⟸   XM_017595716
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451206   ⟸   XM_017595717
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000014605   ⟸   ENSRNOT00000014605
RefSeq Acc Id: ENSRNOP00000068730   ⟸   ENSRNOT00000078161
RefSeq Acc Id: XP_038937623   ⟸   XM_039081695
- Peptide Label: isoform X1

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309627 AgrOrtholog
Ensembl Genes ENSRNOG00000010921 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000014605 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068730 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014605 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000078161 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7311303 IMAGE-MGC_LOAD
InterPro TAF1D UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:363017 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105574 IMAGE-MGC_LOAD
NCBI Gene 363017 ENTREZGENE
PANTHER PTHR14562 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TAF1D UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Taf1d PhenoGen
UniProt G3V7G4_RAT UniProtKB/TrEMBL
  Q5M948 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-16 Taf1d  TATA-box binding protein associated factor, RNA polymerase I subunit D  Taf1d  TATA box binding protein (Tbp)-associated factor, RNA polymerase I, D  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-04-27 Taf1d  TATA box binding protein (Tbp)-associated factor, RNA polymerase I, D  Taf1d  TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-17 Taf1d  TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa  Josd3  Josephin domain containing 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Josd3  Josephin domain containing 3  RGD1309627  similar to RIKEN cDNA 4930553M18  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1309627  similar to RIKEN cDNA 4930553M18  RGD1309627_predicted  similar to RIKEN cDNA 4930553M18 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1309627_predicted  similar to RIKEN cDNA 4930553M18 (predicted)  LOC363017_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC363017_predicted  similar to RIKEN cDNA 4930553M18 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL