Taf5l (TATA-box binding protein associated factor 5 like) - Rat Genome Database

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Gene: Taf5l (TATA-box binding protein associated factor 5 like) Rattus norvegicus
Analyze
Symbol: Taf5l
Name: TATA-box binding protein associated factor 5 like
RGD ID: 1310215
Description: Predicted to have transcription coactivator activity. Predicted to be involved in histone H3 acetylation; regulation of somatic stem cell population maintenance; and regulation of transcription, DNA-templated. Predicted to localize to cytoplasmic ribonucleoprotein granule and nucleoplasm. Orthologous to human TAF5L (TATA-box binding protein associated factor 5 like); PARTICIPATES IN RNA polymerase II transcription initiation pathway; INTERACTS WITH acrylamide; bisphenol A; p-toluidine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC307927; TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L; TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor
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
mRatBN7.21951,991,704 - 52,011,001 (-)NCBI
Rnor_6.0 Ensembl1956,781,859 - 56,799,445 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01956,781,854 - 56,801,005 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01967,497,406 - 67,516,350 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41954,190,450 - 54,209,389 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11954,196,180 - 54,202,880 (-)NCBI
Celera1951,366,198 - 51,385,134 (-)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10373431   PMID:11564863   PMID:12477932   PMID:31005419  


Genomics

Comparative Map Data
Taf5l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21951,991,704 - 52,011,001 (-)NCBI
Rnor_6.0 Ensembl1956,781,859 - 56,799,445 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01956,781,854 - 56,801,005 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01967,497,406 - 67,516,350 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41954,190,450 - 54,209,389 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11954,196,180 - 54,202,880 (-)NCBI
Celera1951,366,198 - 51,385,134 (-)NCBICelera
Cytogenetic Map19q12NCBI
TAF5L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1229,593,121 - 229,626,047 (-)EnsemblGRCh38hg38GRCh38
GRCh381229,593,111 - 229,626,122 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371229,728,881 - 229,761,869 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361227,795,481 - 227,828,417 (-)NCBINCBI36hg18NCBI36
Build 341226,035,602 - 226,068,460NCBI
Celera1202,996,790 - 203,029,673 (-)NCBI
Cytogenetic Map1q42.13NCBI
HuRef1200,219,088 - 200,252,013 (-)NCBIHuRef
CHM1_11231,001,159 - 231,034,105 (-)NCBICHM1_1
Taf5l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398124,723,049 - 124,748,136 (-)NCBIGRCm39mm39
GRCm39 Ensembl8124,723,057 - 124,748,136 (-)Ensembl
GRCm388123,996,310 - 124,021,397 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8123,996,318 - 124,021,397 (-)EnsemblGRCm38mm10GRCm38
MGSCv378126,520,210 - 126,545,209 (-)NCBIGRCm37mm9NCBIm37
MGSCv368126,882,400 - 126,907,399 (-)NCBImm8
Celera8128,276,365 - 128,290,026 (-)NCBICelera
Cytogenetic Map8E2NCBI
Taf5l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554928,479,194 - 8,517,105 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554928,478,147 - 8,515,988 (+)NCBIChiLan1.0ChiLan1.0
TAF5L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11210,168,370 - 210,200,903 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1210,168,379 - 210,200,903 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01205,137,767 - 205,170,704 (-)NCBIMhudiblu_PPA_v0panPan3
TAF5L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.149,646,516 - 9,674,318 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl49,646,510 - 9,673,148 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha49,637,148 - 9,665,450 (+)NCBI
ROS_Cfam_1.049,676,557 - 9,704,884 (+)NCBI
UMICH_Zoey_3.149,680,590 - 9,708,468 (+)NCBI
UNSW_CanFamBas_1.049,794,777 - 9,823,249 (+)NCBI
UU_Cfam_GSD_1.0410,046,852 - 10,075,167 (+)NCBI
Taf5l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934443,955,747 - 43,976,730 (+)NCBI
SpeTri2.0NW_00493648420,123,039 - 20,143,063 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TAF5L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1460,223,432 - 60,302,958 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11460,254,502 - 60,286,368 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21465,077,397 - 65,109,260 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TAF5L
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12566,859,264 - 66,892,877 (-)NCBI
ChlSab1.1 Ensembl2566,858,911 - 66,881,081 (-)Ensembl
Vero_WHO_p1.0NW_02366605568,720,607 - 68,753,722 (-)NCBI
Taf5l
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477519,496,924 - 19,525,495 (+)NCBI

Position Markers
RH132036  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map19q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193791679960220451Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194883071260220581Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)195473521758072143Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:674
Count of miRNA genes:267
Interacting mature miRNAs:333
Transcripts:ENSRNOT00000014930, ENSRNOT00000024491, ENSRNOT00000058652
Prediction methods:Microtar, 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 26 39 33 15 33 1 66 20 39 10
Low 17 18 8 4 8 8 10 8 15 2 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024491   ⟹   ENSRNOP00000024491
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1956,781,859 - 56,799,445 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000058652   ⟹   ENSRNOP00000055446
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1956,783,574 - 56,789,404 (-)Ensembl
RefSeq Acc Id: NM_001107442   ⟹   NP_001100912
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21951,991,709 - 52,010,648 (-)NCBI
Rnor_6.01956,781,859 - 56,800,798 (-)NCBI
Rnor_5.01967,497,406 - 67,516,350 (-)NCBI
RGSC_v3.41954,190,450 - 54,209,389 (-)RGD
Celera1951,366,198 - 51,385,134 (-)RGD
Sequence:
RefSeq Acc Id: XM_006255812   ⟹   XP_006255874
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21951,991,704 - 52,010,401 (-)NCBI
Rnor_6.01956,781,854 - 56,800,613 (-)NCBI
Rnor_5.01967,497,406 - 67,516,350 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008772614   ⟹   XP_008770836
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21951,991,704 - 52,011,001 (-)NCBI
Rnor_6.01956,781,854 - 56,801,005 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008772615   ⟹   XP_008770837
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21951,991,704 - 52,010,702 (-)NCBI
Rnor_6.01956,781,854 - 56,800,830 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001100912   ⟸   NM_001107442
- Sequence:
RefSeq Acc Id: XP_006255874   ⟸   XM_006255812
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008770836   ⟸   XM_008772614
- Peptide Label: isoform X2
- UniProtKB: B1H284 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008770837   ⟸   XM_008772615
- Peptide Label: isoform X2
- UniProtKB: B1H284 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000024491   ⟸   ENSRNOT00000024491
RefSeq Acc Id: ENSRNOP00000055446   ⟸   ENSRNOT00000058652
Protein Domains
TFIID_NTD2   WD_REPEATS_REGION

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)
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: 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)
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/JrHsdMcwi (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)
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:1310215 AgrOrtholog
Ensembl Genes ENSRNOG00000018027 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024491 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000055446 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024491 UniProtKB/TrEMBL
  ENSRNOT00000058652 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.500 UniProtKB/TrEMBL
  2.130.10.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7380415 IMAGE-MGC_LOAD
  IMAGE:7454090 IMAGE-MGC_LOAD
InterPro G-protein_beta_WD-40_rep UniProtKB/TrEMBL
  Taf5 UniProtKB/TrEMBL
  TAF5L UniProtKB/TrEMBL
  TFIID-su_WD40-assoc_reg UniProtKB/TrEMBL
  TFIID_NTD2_sf UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WD40_repeat_CS UniProtKB/TrEMBL
  WD40_repeat_dom UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
MGC_CLONE MGC:112924 IMAGE-MGC_LOAD
  MGC:188626 IMAGE-MGC_LOAD
NCBI Gene 307927 ENTREZGENE
PANTHER PTHR19879 UniProtKB/TrEMBL
  PTHR19879:SF6 UniProtKB/TrEMBL
Pfam TFIID_90kDa UniProtKB/TrEMBL
  WD40 UniProtKB/TrEMBL
PhenoGen Taf5l PhenoGen
PRINTS GPROTEINBRPT UniProtKB/TrEMBL
PROSITE WD_REPEATS_1 UniProtKB/TrEMBL
  WD_REPEATS_2 UniProtKB/TrEMBL
  WD_REPEATS_REGION UniProtKB/TrEMBL
SMART WD40 UniProtKB/TrEMBL
Superfamily-SCOP SSF160897 UniProtKB/TrEMBL
  WD40_like UniProtKB/TrEMBL
UniProt B1H284 ENTREZGENE, UniProtKB/TrEMBL
  D3ZC58_RAT UniProtKB/TrEMBL
  Q4G004_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-11-02 Taf5l  TATA-box binding protein associated factor 5 like  Taf5l  TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Taf5l  TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor  Taf5l_predicted  TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Taf5l_predicted  TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor (predicted)      Symbol and Name status set to approved 70820 APPROVED