Taf9b (TATA-box binding protein associated factor 9b) - Rat Genome Database

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Gene: Taf9b (TATA-box binding protein associated factor 9b) Rattus norvegicus
Analyze
Symbol: Taf9b
Name: TATA-box binding protein associated factor 9b
RGD ID: 621116
Description: Is predicted to contribute to RNA polymerase II general transcription initiation factor activity. Involved in programmed cell death and response to organic cyclic compound. Predicted to localize to transcription factor TFIID complex and transcription factor TFTC complex. Orthologous to human TAF9B (TATA-box binding protein associated factor 9b); INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 17alpha-ethynylestradiol; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: DN-7; Dn7; neuronal cell death-related gene in neuron 7; neuronal cell death-related gene in neuron-7; TAF9-like RNA polymerase II TATA box binding protein (TBP)-associated factor 31 kD; TAF9-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31 kD; TAF9-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa; TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor; Taf9l; TAFII31; transcription initiation factor TFIID subunit 9-like; transcription initiation factor TFIID subunit 9B; transcription-associated factor TAFII31L
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
mRatBN7.2X71,289,290 - 71,300,142 (-)NCBI
Rnor_6.0 EnsemblX77,281,210 - 77,295,426 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X77,281,234 - 77,295,238 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X56,401,294 - 56,416,018 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X94,342,071 - 94,351,927 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X94,415,515 - 94,425,356 (-)NCBI
CeleraX72,601,506 - 72,610,854 (-)NCBICelera
Cytogenetic MapXq22NCBI
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
References

Additional References at PubMed
PMID:12477932   PMID:12837753   PMID:15489334   PMID:15899866  


Genomics

Comparative Map Data
Taf9b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X71,289,290 - 71,300,142 (-)NCBI
Rnor_6.0 EnsemblX77,281,210 - 77,295,426 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X77,281,234 - 77,295,238 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X56,401,294 - 56,416,018 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X94,342,071 - 94,351,927 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X94,415,515 - 94,425,356 (-)NCBI
CeleraX72,601,506 - 72,610,854 (-)NCBICelera
Cytogenetic MapXq22NCBI
TAF9B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX78,129,748 - 78,139,650 (-)EnsemblGRCh38hg38GRCh38
GRCh38X78,129,748 - 78,139,650 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X77,385,245 - 77,395,147 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X77,271,901 - 77,281,835 (-)NCBINCBI36hg18NCBI36
CeleraX77,626,326 - 77,636,254 (-)NCBI
Cytogenetic MapXq21.1NCBI
HuRefX70,971,528 - 70,981,808 (-)NCBIHuRef
CHM1_1X77,277,938 - 77,287,872 (-)NCBICHM1_1
Taf9b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X105,250,480 - 105,264,764 (-)NCBIGRCm39mm39
GRCm39 EnsemblX105,250,489 - 105,264,764 (-)Ensembl
GRCm38X106,206,874 - 106,221,158 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX106,206,883 - 106,221,158 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X103,402,213 - 103,416,497 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X102,409,593 - 102,422,352 (-)NCBImm8
CeleraX93,060,248 - 93,074,689 (-)NCBICelera
Cytogenetic MapXDNCBI
Taf9b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555571,605,669 - 1,617,999 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555571,607,589 - 1,617,748 (-)NCBIChiLan1.0ChiLan1.0
TAF9B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X77,417,232 - 77,427,193 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX77,417,232 - 77,427,193 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X67,305,754 - 67,315,714 (-)NCBIMhudiblu_PPA_v0panPan3
TAF9B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X60,399,638 - 60,410,004 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX60,401,419 - 60,410,027 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX51,412,746 - 51,423,112 (-)NCBI
ROS_Cfam_1.0X61,638,375 - 61,648,741 (-)NCBI
UMICH_Zoey_3.1X59,344,509 - 59,354,875 (-)NCBI
UNSW_CanFamBas_1.0X60,954,492 - 60,964,857 (-)NCBI
UU_Cfam_GSD_1.0X60,542,584 - 60,552,950 (-)NCBI
Taf9b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X53,992,158 - 54,001,078 (-)NCBI
SpeTri2.0NW_004936547312,909 - 321,424 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TAF9B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX62,207,464 - 62,229,021 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X62,214,331 - 62,228,782 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X71,321,322 - 71,333,905 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TAF9B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X67,097,313 - 67,106,076 (-)NCBI
ChlSab1.1 EnsemblX67,099,147 - 67,106,262 (-)Ensembl
Taf9b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248362,623,924 - 2,636,330 (+)NCBI

Position Markers
AI059951  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X77,281,301 - 77,281,483NCBIRnor6.0
Rnor_5.0X56,401,361 - 56,401,543UniSTSRnor5.0
RGSC_v3.4X94,342,121 - 94,342,303UniSTSRGSC3.4
CeleraX72,601,556 - 72,601,738UniSTS
Cytogenetic MapXq31UniSTS
BF386911  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X77,282,953 - 77,283,123NCBIRnor6.0
Rnor_5.0X56,403,013 - 56,403,183UniSTSRnor5.0
RGSC_v3.4X94,343,773 - 94,343,943UniSTSRGSC3.4
CeleraX72,603,208 - 72,603,378UniSTS
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:375
Count of miRNA genes:227
Interacting mature miRNAs:272
Transcripts:ENSRNOT00000003335
Prediction methods:Microtar, Miranda, Pita
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 1 26 9 2 16 2 70 27 26 11
Low 2 17 48 39 3 39 8 11 4 8 15 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000088077   ⟹   ENSRNOP00000070237
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX77,281,234 - 77,293,395 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089640   ⟹   ENSRNOP00000069372
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX77,281,253 - 77,293,386 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000090833   ⟹   ENSRNOP00000073996
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX77,281,234 - 77,295,426 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091234   ⟹   ENSRNOP00000073891
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX77,281,210 - 77,293,497 (-)Ensembl
RefSeq Acc Id: NM_133615   ⟹   NP_598299
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X71,289,307 - 71,298,563 (-)NCBI
Rnor_6.0X77,281,251 - 77,293,385 (-)NCBI
Rnor_5.0X56,401,294 - 56,416,018 (-)NCBI
RGSC_v3.4X94,342,071 - 94,351,927 (-)RGD
CeleraX72,601,506 - 72,610,854 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256993   ⟹   XP_006257055
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X71,289,290 - 71,300,142 (-)NCBI
Rnor_6.0X77,281,234 - 77,295,237 (-)NCBI
Rnor_5.0X56,401,294 - 56,416,018 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256994   ⟹   XP_006257056
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X71,289,290 - 71,300,141 (-)NCBI
Rnor_6.0X77,281,234 - 77,295,238 (-)NCBI
Rnor_5.0X56,401,294 - 56,416,018 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099438   ⟹   XP_038955366
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X71,291,211 - 71,300,142 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_598299   ⟸   NM_133615
- Sequence:
RefSeq Acc Id: XP_006257056   ⟸   XM_006256994
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006257055   ⟸   XM_006256993
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000069372   ⟸   ENSRNOT00000089640
RefSeq Acc Id: ENSRNOP00000073996   ⟸   ENSRNOT00000090833
RefSeq Acc Id: ENSRNOP00000073891   ⟸   ENSRNOT00000091234
RefSeq Acc Id: ENSRNOP00000070237   ⟸   ENSRNOT00000088077
RefSeq Acc Id: XP_038955366   ⟸   XM_039099438
- Peptide Label: isoform X2

Transcriptome

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

Promoters
RGD ID:13701905
Promoter ID:EPDNEW_R12427
Type:initiation region
Name:Taf9b_1
Description:TATA-box binding protein associated factor 9b
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_6.0X77,293,401 - 77,293,461EPDNEW

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:621116 AgrOrtholog
Ensembl Genes ENSRNOG00000061102 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000069372 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070237 UniProtKB/TrEMBL
  ENSRNOP00000073891 UniProtKB/Swiss-Prot
  ENSRNOP00000073996 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000088077 UniProtKB/TrEMBL
  ENSRNOT00000089640 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000090833 UniProtKB/TrEMBL
  ENSRNOT00000091234 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.20.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7193160 IMAGE-MGC_LOAD
InterPro Histone-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIID-31 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171152 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105328 IMAGE-MGC_LOAD
NCBI Gene 171152 ENTREZGENE
Pfam TFIID-31kDa UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Taf9b PhenoGen
Superfamily-SCOP SSF47113 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JV70_RAT UniProtKB/TrEMBL
  A0A0G2JXE2_RAT UniProtKB/TrEMBL
  A0A0G2K6Z1_RAT UniProtKB/TrEMBL
  Q62880 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q5EAN8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-14 Taf9b  TATA-box binding protein associated factor 9b  Taf9b  TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-22 Taf9b  TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor  Taf9l  TAF9-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Taf9l  TAF9-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa    TAF9-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31 kD  Name updated 1299863 APPROVED
2002-08-07 Taf9l  TAF9-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31 kD      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_process involved in various growth regulatory processes including cell cycle progression 634165