Taf4b (TATA-box binding protein associated factor 4b) - Rat Genome Database
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Gene: Taf4b (TATA-box binding protein associated factor 4b) Rattus norvegicus
Analyze
Symbol: Taf4b
Name: TATA-box binding protein associated factor 4b
RGD ID: 1562997
Description: Predicted to have DNA binding activity and NF-kappaB binding activity. Predicted to be involved in positive regulation of stem cell proliferation. Predicted to localize to fibrillar center and transcription factor TFIID complex. Human ortholog(s) of this gene implicated in spermatogenic failure 13. Orthologous to human TAF4B (TATA-box binding protein associated factor 4b); INTERACTS WITH amphetamine; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC291773; RGD1562997; similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105); similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (TAFII105); TAF4B RNA polymerase II, TATA box binding protein (TBP)-associated factor; TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa; transcription initiation factor TFIID subunit 4B
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
mRatBN7.2185,952,737 - 6,086,408 (+)NCBI
Rnor_6.0 Ensembl186,207,280 - 6,318,219 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0186,206,939 - 6,338,794 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0186,168,668 - 6,280,010 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4186,071,848 - 6,168,486 (+)NCBIRGSC3.4rn4RGSC3.4
Celera185,982,341 - 6,115,631 (+)NCBICelera
Cytogenetic Map18p13NCBI
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

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:10849440   PMID:15601843   PMID:23350932  


Genomics

Comparative Map Data
Taf4b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2185,952,737 - 6,086,408 (+)NCBI
Rnor_6.0 Ensembl186,207,280 - 6,318,219 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0186,206,939 - 6,338,794 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0186,168,668 - 6,280,010 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4186,071,848 - 6,168,486 (+)NCBIRGSC3.4rn4RGSC3.4
Celera185,982,341 - 6,115,631 (+)NCBICelera
Cytogenetic Map18p13NCBI
TAF4B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1826,225,936 - 26,391,685 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1826,226,445 - 26,391,685 (+)EnsemblGRCh38hg38GRCh38
GRCh381826,226,445 - 26,391,685 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371823,806,409 - 23,971,649 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361822,060,407 - 22,225,647 (+)NCBINCBI36hg18NCBI36
Build 341822,061,093 - 22,224,126NCBI
Celera1820,617,414 - 20,782,254 (+)NCBI
Cytogenetic Map18q11.2NCBI
HuRef1820,657,331 - 20,821,816 (+)NCBIHuRef
CHM1_11823,734,161 - 23,899,102 (+)NCBICHM1_1
Taf4b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391814,916,302 - 15,035,160 (+)NCBIGRCm39mm39
GRCm39 Ensembl1814,916,302 - 15,033,416 (+)Ensembl
GRCm381814,783,201 - 14,960,424 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1814,783,245 - 14,900,359 (+)EnsemblGRCm38mm10GRCm38
MGSCv371814,941,754 - 15,058,868 (+)NCBIGRCm37mm9NCBIm37
MGSCv361814,926,263 - 15,043,377 (+)NCBImm8
Celera1815,005,590 - 15,122,615 (+)NCBICelera
Cytogenetic Map18A1NCBI
Taf4b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540214,296,202 - 14,425,321 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540214,296,202 - 14,425,298 (+)NCBIChiLan1.0ChiLan1.0
TAF4B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11823,089,239 - 23,254,247 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1823,089,736 - 23,254,518 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01819,480,844 - 19,648,936 (+)NCBIMhudiblu_PPA_v0panPan3
TAF4B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl762,278,061 - 62,402,375 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1762,276,885 - 62,402,838 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Taf4b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365505,396,239 - 5,527,540 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TAF4B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6110,855,636 - 110,971,994 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16110,855,636 - 110,972,798 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26103,817,752 - 103,934,684 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TAF4B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11854,198,730 - 54,357,101 (-)NCBI
ChlSab1.1 Ensembl1854,200,414 - 54,356,611 (-)Ensembl
Taf4b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247705,955,159 - 6,163,060 (-)NCBI

Position Markers
RH128256  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0186,317,961 - 6,318,127NCBIRnor6.0
Rnor_5.0186,279,755 - 6,279,921UniSTSRnor5.0
RGSC_v3.4186,168,231 - 6,168,397UniSTSRGSC3.4
Celera186,094,839 - 6,095,005UniSTS
RH 3.4 Map1842.3UniSTS
Cytogenetic Map18p13UniSTS
BM392071  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0186,316,958 - 6,317,142NCBIRnor6.0
Rnor_5.0186,278,752 - 6,278,936UniSTSRnor5.0
RGSC_v3.4186,167,227 - 6,167,411UniSTSRGSC3.4
Celera186,093,835 - 6,094,019UniSTS
RH 3.4 Map1880.7UniSTS
Cytogenetic Map18p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590248Scort10Serum corticosterone level QTL 1019.710.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)18125999214Rat
8552968Pigfal19Plasma insulin-like growth factor 1 level QTL 1911.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)18125999214Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135097280Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18138195967Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18138195967Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18138753381Rat
1641910Colcr3Colorectal carcinoma resistance QTL 35.020.000007intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor surface area measurement (CMO:0002078)18247709623184414Rat
1641910Colcr3Colorectal carcinoma resistance QTL 35.020.000007intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)18247709623184414Rat
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18371954732487870Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18440751362570466Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18543013441781619Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:12
Count of miRNA genes:11
Interacting mature miRNAs:12
Transcripts:ENSRNOT00000037955
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 2 1 29 19 1
Low 3 43 55 41 18 41 8 11 74 6 22 10 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000037955   ⟹   ENSRNOP00000031359
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl186,207,280 - 6,318,219 (+)Ensembl
RefSeq Acc Id: XM_006222506   ⟹   XP_006222568
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera185,982,342 - 6,096,201 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006222507   ⟹   XP_006222569
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera185,982,878 - 6,096,201 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006254439   ⟹   XP_006254501
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2185,952,738 - 6,065,820 (+)NCBI
Rnor_6.0186,206,940 - 6,319,323 (+)NCBI
Rnor_5.0186,168,668 - 6,280,010 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006254440   ⟹   XP_006254502
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2185,953,357 - 6,065,820 (+)NCBI
Rnor_6.0186,207,476 - 6,319,323 (+)NCBI
Rnor_5.0186,168,668 - 6,280,010 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771990   ⟹   XP_008770212
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2185,952,737 - 6,086,407 (+)NCBI
Rnor_6.0186,206,939 - 6,338,794 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008774091   ⟹   XP_008772313
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera185,982,341 - 6,115,631 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039097304   ⟹   XP_038953232
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2185,952,737 - 6,086,408 (+)NCBI
Protein Sequences
Protein RefSeqs XP_006254501 (Get FASTA)   NCBI Sequence Viewer  
  XP_006254502 (Get FASTA)   NCBI Sequence Viewer  
  XP_008770212 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953232 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006222568   ⟸   XM_006222506
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006222569   ⟸   XM_006222507
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006254501   ⟸   XM_006254439
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006254502   ⟸   XM_006254440
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008772313   ⟸   XM_008774091
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008770212   ⟸   XM_008771990
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000031359   ⟸   ENSRNOT00000037955
RefSeq Acc Id: XP_038953232   ⟸   XM_039097304
- Peptide Label: isoform X2
Protein Domains
TAFH

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)
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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
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)
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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:1562997 AgrOrtholog
Ensembl Genes ENSRNOG00000026023 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000031359 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037955 UniProtKB/TrEMBL
Gene3D-CATH 1.10.20.10 UniProtKB/TrEMBL
  1.20.120.1110 UniProtKB/TrEMBL
InterPro Histone-fold UniProtKB/TrEMBL
  TAF4 UniProtKB/TrEMBL
  TAFH/NHR1_dom_sf UniProtKB/TrEMBL
  TAFH_NHR1 UniProtKB/TrEMBL
NCBI Gene 291773 ENTREZGENE
Pfam TAF4 UniProtKB/TrEMBL
  TAFH UniProtKB/TrEMBL
PhenoGen Taf4b PhenoGen
PROSITE TAFH UniProtKB/TrEMBL
SMART TAFH UniProtKB/TrEMBL
Superfamily-SCOP Histone-fold UniProtKB/TrEMBL
  SSF158553 UniProtKB/TrEMBL
UniProt F1LT11_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Taf4b  TATA-box binding protein associated factor 4b  Taf4b  TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-12 Taf4b  TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa  RGD1562997  similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1562997  similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105)   RGD1562997_predicted  similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-10 RGD1562997_predicted  similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (predicted)    similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (TAFII105) (predicted)  Name updated 1299863 APPROVED
2006-03-07 RGD1562997_predicted  similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (TAFII105) (predicted)  LOC291773  similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (TAFII105)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC291773  similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (TAFII105)      Symbol and Name status set to provisional 70820 PROVISIONAL