Taf1 (TATA-box binding protein associated factor 1) - Rat Genome Database

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Gene: Taf1 (TATA-box binding protein associated factor 1) Rattus norvegicus
Analyze
Symbol: Taf1
Name: TATA-box binding protein associated factor 1
RGD ID: 1562050
Description: Is predicted to contribute to H3K27me3 modified histone binding activity. Involved in response to drug. Localizes to nucleus. Predicted to colocalize with nucleolus. Human ortholog(s) of this gene implicated in X-linked dystonia-parkinsonism and syndromic X-linked intellectual disability. Orthologous to human TAF1 (TATA-box binding protein associated factor 1); PARTICIPATES IN histone modification pathway; RNA polymerase II transcription initiation pathway; INTERACTS WITH 1,3-dinitrobenzene; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC102556339; LOC317256; RGD1562050; similar to CCG1; TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor; transcription initiation factor TFIID subunit 1; transcription initiation factor TFIID subunit 1-like
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
mRatBN7.2X66,640,915 - 66,716,543 (+)NCBI
Rnor_6.0 EnsemblX71,412,289 - 71,485,085 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X71,412,291 - 71,486,456 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X72,261,626 - 72,335,791 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X89,590,556 - 89,666,569 (+)NCBIRGSC3.4rn4RGSC3.4
CeleraX66,996,430 - 67,071,877 (+)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8625415   PMID:8980232   PMID:9660973   PMID:11592977   PMID:12498690   PMID:14580349   PMID:15053879   PMID:15607978   PMID:15960975   PMID:16822332   PMID:17237821   PMID:17996705  
PMID:18548200   PMID:18722179   PMID:20181722   PMID:21616129   PMID:22323595   PMID:24289924   PMID:24927529   PMID:25412659   PMID:26637982   PMID:27007846   PMID:31344492  


Genomics

Comparative Map Data
Taf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X66,640,915 - 66,716,543 (+)NCBI
Rnor_6.0 EnsemblX71,412,289 - 71,485,085 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X71,412,291 - 71,486,456 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X72,261,626 - 72,335,791 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X89,590,556 - 89,666,569 (+)NCBIRGSC3.4rn4RGSC3.4
CeleraX66,996,430 - 67,071,877 (+)NCBICelera
Cytogenetic MapXq22NCBI
TAF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX71,366,264 - 71,532,374 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 EnsemblX71,366,239 - 71,532,374 (+)EnsemblGRCh38hg38GRCh38
GRCh38X71,366,220 - 71,530,525 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X70,586,207 - 70,750,375 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X70,502,839 - 70,601,025 (+)NCBINCBI36hg18NCBI36
Build 34X70,369,134 - 70,467,321NCBI
CeleraX70,939,992 - 71,039,729 (+)NCBI
Cytogenetic MapXq13.1NCBI
HuRefX64,401,859 - 64,501,671 (+)NCBIHuRef
CHM1_1X70,479,113 - 70,642,732 (+)NCBICHM1_1
Taf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X100,576,335 - 100,645,395 (+)NCBIGRCm39mm39
GRCm39 EnsemblX100,576,340 - 100,645,395 (+)Ensembl
GRCm38X101,527,572 - 101,601,789 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX101,532,734 - 101,601,789 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X98,728,074 - 98,797,128 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X97,735,454 - 97,804,508 (+)NCBImm8
CeleraX88,450,587 - 88,519,292 (+)NCBICelera
Cytogenetic MapXDNCBI
cM MapX44.29NCBI
Taf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547510,930,192 - 11,005,724 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495547510,930,175 - 11,006,876 (+)NCBIChiLan1.0ChiLan1.0
TAF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X70,684,192 - 70,784,292 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX70,684,217 - 70,782,323 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X60,630,137 - 60,729,904 (+)NCBIMhudiblu_PPA_v0panPan3
TAF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X55,693,091 - 55,764,268 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX55,693,194 - 55,763,683 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX46,519,902 - 46,591,035 (+)NCBI
ROS_Cfam_1.0X56,662,169 - 56,733,328 (+)NCBI
UMICH_Zoey_3.1X54,629,611 - 54,700,758 (+)NCBI
UNSW_CanFamBas_1.0X55,961,540 - 56,032,713 (+)NCBI
UU_Cfam_GSD_1.0X55,888,952 - 55,960,089 (+)NCBI
Taf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X46,427,534 - 46,509,580 (-)NCBI
SpeTri2.0NW_004936762189,710 - 271,759 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TAF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX57,382,354 - 57,466,697 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X57,382,211 - 57,466,700 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TAF1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X61,167,743 - 61,269,000 (+)NCBI
ChlSab1.1 EnsemblX61,167,589 - 61,268,839 (+)Ensembl
Taf1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249031,698,201 - 1,774,607 (+)NCBI

Position Markers
RH131488  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X66,715,633 - 66,715,832 (+)MAPPER
Rnor_6.0X71,485,547 - 71,485,745NCBIRnor6.0
Rnor_5.0X72,334,882 - 72,335,080UniSTSRnor5.0
RGSC_v3.4X89,665,660 - 89,665,858UniSTSRGSC3.4
CeleraX67,070,968 - 67,071,166UniSTS
Cytogenetic MapXq31UniSTS
AI548344  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X66,660,107 - 66,660,296 (+)MAPPER
Rnor_6.0X72,708,987 - 72,709,175NCBIRnor6.0
Rnor_6.0X71,431,417 - 71,431,605NCBIRnor6.0
Rnor_5.0X72,280,752 - 72,280,940UniSTSRnor5.0
Rnor_5.0X73,544,320 - 73,544,508UniSTSRnor5.0
RGSC_v3.4X89,609,682 - 89,609,870UniSTSRGSC3.4
CeleraX67,015,557 - 67,015,745UniSTS
Cytogenetic MapXq31UniSTS
px-35c7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X66,650,626 - 66,650,791 (+)MAPPER
Rnor_6.0X71,421,936 - 71,422,100NCBIRnor6.0
Rnor_5.0X72,271,271 - 72,271,435UniSTSRnor5.0
RGSC_v3.4X89,600,201 - 89,600,365UniSTSRGSC3.4
CeleraX67,006,075 - 67,006,239UniSTS
Cytogenetic MapXq31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:761
Count of miRNA genes:303
Interacting mature miRNAs:410
Transcripts:ENSRNOT00000003494
Prediction methods:Microtar, Miranda, Pita, Pita,Targetscan, 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 2 24 32 16 19 16 1 1 74 28 34 11 1
Low 1 19 25 25 25 7 10 7 7 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003494
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX71,412,303 - 71,484,890 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076799
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX71,412,289 - 71,485,085 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079320
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX72,705,039 - 72,713,249 (+)Ensembl
RefSeq Acc Id: NM_001191723   ⟹   NP_001178652
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,640,982 - 66,716,543 (+)NCBI
Rnor_6.0X71,412,291 - 71,486,456 (+)NCBI
Rnor_5.0X72,261,626 - 72,335,791 (+)NCBI
CeleraX66,996,430 - 67,071,877 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099742   ⟹   XP_038955670
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,640,915 - 66,716,416 (+)NCBI
RefSeq Acc Id: XM_039099743   ⟹   XP_038955671
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,640,994 - 66,714,977 (+)NCBI
RefSeq Acc Id: XM_039099744   ⟹   XP_038955672
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,640,915 - 66,716,416 (+)NCBI
RefSeq Acc Id: XM_039099745   ⟹   XP_038955673
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,640,916 - 66,714,977 (+)NCBI
RefSeq Acc Id: XM_039099746   ⟹   XP_038955674
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,640,915 - 66,707,320 (+)NCBI
RefSeq Acc Id: XR_005497977
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,640,915 - 66,704,814 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001178652   ⟸   NM_001191723
- Sequence:
RefSeq Acc Id: XP_038955670   ⟸   XM_039099742
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955672   ⟸   XM_039099744
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955674   ⟸   XM_039099746
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038955673   ⟸   XM_039099745
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038955671   ⟸   XM_039099743
- Peptide Label: isoform X2

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)
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)
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)
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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: 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)
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: 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)
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
SHRSP/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
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)
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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/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)
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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
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)
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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/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
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)
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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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562050 AgrOrtholog
Ensembl Genes ENSRNOG00000002565 Ensembl, ENTREZGENE
  ENSRNOG00000060509 Ensembl
Ensembl Transcript ENSRNOT00000076799 ENTREZGENE
NCBI Gene 317256 ENTREZGENE
PhenoGen Taf1 PhenoGen


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Taf1  TATA-box binding protein associated factor 1  LOC102556339  transcription initiation factor TFIID subunit 1-like  Data Merged 737654 PROVISIONAL
2016-05-18 Taf1  TATA-box binding protein associated factor 1  Taf1  TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-17 LOC102556339  transcription initiation factor TFIID subunit 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Taf1  TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor   Taf1_predicted  TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Taf1_predicted  TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor (predicted)  RGD1562050_predicted  similar to CCG1 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1562050_predicted  similar to CCG1 (predicted)  LOC317256  similar to CCG1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317256  similar to CCG1      Symbol and Name status set to provisional 70820 PROVISIONAL