Taf1c (TATA-box binding protein associated factor, RNA polymerase 1 subunit C) - Rat Genome Database
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Gene: Taf1c (TATA-box binding protein associated factor, RNA polymerase 1 subunit C) Rattus norvegicus
Analyze
Symbol: Taf1c
Name: TATA-box binding protein associated factor, RNA polymerase 1 subunit C
RGD ID: 1305658
Description: Predicted to have RNA polymerase I core promoter sequence-specific DNA binding activity and RNA polymerase I general transcription initiation factor activity. Predicted to be involved in RNA polymerase I preinitiation complex assembly. Predicted to localize to fibrillar center and nucleoplasm. Orthologous to human TAF1C (TATA-box binding protein associated factor, RNA polymerase I subunit C); PARTICIPATES IN RNA polymerase I transcription pathway; INTERACTS WITH 2,4-dinitrotoluene; aflatoxin B1; benzo[a]pyrene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC361420; LOC361421; similar to TAFI95; TATA box binding protein (Tbp)-associated factor, RNA polymerase I, C; TATA box-binding protein-associated factor 1C; TATA box-binding protein-associated factor, RNA polymerase I, subunit C; TBP-associated factor 1C; transcription initiation factor SL1/TIF-IB subunit C
Orthologs:
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01952,246,061 - 52,252,642 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1952,246,068 - 52,252,587 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01962,994,275 - 63,000,801 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41949,842,371 - 49,848,891 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11949,851,555 - 49,853,756 (-)NCBI
Celera1946,911,512 - 46,918,032 (-)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

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12498690   PMID:15489334   PMID:22368283  


Genomics

Comparative Map Data
Taf1c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01952,246,061 - 52,252,642 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1952,246,068 - 52,252,587 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01962,994,275 - 63,000,801 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41949,842,371 - 49,848,891 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11949,851,555 - 49,853,756 (-)NCBI
Celera1946,911,512 - 46,918,032 (-)NCBICelera
Cytogenetic Map19q12NCBI
TAF1C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1684,177,847 - 84,187,070 (-)EnsemblGRCh38hg38GRCh38
GRCh381684,177,852 - 84,187,065 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371684,211,453 - 84,220,676 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361682,768,962 - 82,778,163 (-)NCBINCBI36hg18NCBI36
Build 341682,768,962 - 82,778,163NCBI
Celera1668,513,270 - 68,522,472 (-)NCBI
Cytogenetic Map16q24.1NCBI
HuRef1669,965,230 - 69,974,453 (-)NCBIHuRef
CHM1_11685,622,840 - 85,632,064 (-)NCBICHM1_1
Taf1c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398120,324,713 - 120,331,945 (-)NCBI
GRCm388119,597,974 - 119,605,206 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8119,597,871 - 119,605,222 (-)EnsemblGRCm38mm10GRCm38
MGSCv378122,121,874 - 122,129,140 (-)NCBIGRCm37mm9NCBIm37
MGSCv368122,483,951 - 122,491,160 (-)NCBImm8
Celera8123,815,454 - 123,822,720 (-)NCBICelera
Cytogenetic Map8E1NCBI
Taf1c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495556487,452 - 134,650 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955564121,988 - 132,347 (+)NCBIChiLan1.0ChiLan1.0
TAF1C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11684,184,928 - 84,194,147 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1684,184,928 - 84,194,147 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01664,843,197 - 64,852,408 (-)NCBIMhudiblu_PPA_v0panPan3
TAF1C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl568,175,014 - 68,184,277 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1568,175,196 - 68,184,267 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Taf1c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366413,649,177 - 3,653,798 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TAF1C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl64,448,780 - 4,457,499 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.164,448,672 - 4,457,109 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.265,030,498 - 5,038,769 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TAF1C
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl569,587,769 - 69,593,814 (-)Ensembl
ChlSab1.1569,587,592 - 69,596,312 (-)NCBI
Taf1c
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247463,403,122 - 3,412,709 (+)NCBI

Position Markers
RH134909  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01952,246,199 - 52,246,389NCBIRnor6.0
Rnor_5.01962,994,413 - 62,994,603UniSTSRnor5.0
RGSC_v3.41949,842,503 - 49,842,693UniSTSRGSC3.4
Celera1946,911,644 - 46,911,834UniSTS
Cytogenetic Map19q12UniSTS
RH 3.4 Map19649.0UniSTS
AI145291  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01952,245,678 - 52,245,895NCBIRnor6.0
Rnor_5.01962,993,892 - 62,994,109UniSTSRnor5.0
RGSC_v3.41949,841,982 - 49,842,199UniSTSRGSC3.4
Celera1946,911,123 - 46,911,340UniSTS
Cytogenetic Map19q12UniSTS
RH 3.4 Map19653.0UniSTS
BE115013  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01952,246,440 - 52,246,609NCBIRnor6.0
Rnor_5.01962,994,654 - 62,994,823UniSTSRnor5.0
RGSC_v3.41949,842,744 - 49,842,913UniSTSRGSC3.4
Celera1946,911,885 - 46,912,054UniSTS
Cytogenetic Map19q12UniSTS
RH 3.4 Map19647.9UniSTS


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
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191702800352538299Rat
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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:326
Count of miRNA genes:208
Interacting mature miRNAs:245
Transcripts:ENSRNOT00000020990
Prediction methods:Microtar, Miranda, Rnahybrid
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 16 11 6 7 6 57 20 36 1
Low 2 27 46 35 12 35 8 11 17 15 5 10 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020990   ⟹   ENSRNOP00000020990
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1952,246,068 - 52,252,587 (-)Ensembl
RefSeq Acc Id: NM_001014155   ⟹   NP_001014177
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01952,246,067 - 52,252,587 (-)NCBI
Rnor_5.01962,994,275 - 63,000,801 (-)NCBI
RGSC_v3.41949,842,371 - 49,848,891 (-)RGD
Celera1946,911,512 - 46,918,032 (-)RGD
Sequence:
RefSeq Acc Id: XM_008772623   ⟹   XP_008770845
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01952,246,061 - 52,252,642 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008772625   ⟹   XP_008770847
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01952,246,061 - 52,250,371 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601324   ⟹   XP_017456813
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01952,246,061 - 52,252,642 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001014177 (Get FASTA)   NCBI Sequence Viewer  
  XP_008770845 (Get FASTA)   NCBI Sequence Viewer  
  XP_008770847 (Get FASTA)   NCBI Sequence Viewer  
  XP_017456813 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH61804 (Get FASTA)   NCBI Sequence Viewer  
  Q6P773 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001014177   ⟸   NM_001014155
- UniProtKB: Q6P773 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008770845   ⟸   XM_008772623
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008770847   ⟸   XM_008772625
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017456813   ⟸   XM_017601324
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000020990   ⟸   ENSRNOT00000020990

Transcriptome

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

Promoters
RGD ID:13701183
Promoter ID:EPDNEW_R11705
Type:initiation region
Name:Taf1c_1
Description:TATA-box binding protein associated factor, RNA polymerase 1subunit C
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_6.01952,252,583 - 52,252,643EPDNEW

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)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 62995868 62995869 G A snv SBH/Ygl (MCW), ZF (KyushuU), SR/JrHsd (MCW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MR/N (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), BN/SsN (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), M520/N (KNAW), LE/OrlBarth (UDEL), SBN/Ygl (MCW), KFRS3B/Kyo (KyushuU), F344/Jcl (KyushuU), F344/Stm (KyushuU), F344/DuCrlCrlj (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU)
19 62997563 62997564 G A snv DOB/Oda (KyushuU), IS-Tlk/Kyo (KyushuU), IS/Kyo (KyushuU)
19 62998964 62998965 G A snv BDIX/NemOda (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 52247654 52247655 G A snv SBH/Ygl (MCW), SR/JrHsd (RGD), SHRSP/Gcrc (RGD), SBN/Ygl (RGD), SBH/Ygl (RGD), LL/MavRrrc (RGD), LN/MavRrrc (RGD), F344/NCrl (RGD), MR/N (MCW), M520/N (MCW), F344/NRrrc (MCW), CDR, SR/JrHsd (MCW), SBN/Ygl (MCW)
19 52250690 52250691 C T snv WKY/N (MCW), SBH/Ygl (MCW), SR/JrHsd (RGD), GK/Ox (RGD), LN/MavRrrc (RGD), MR/N (MCW), SBN/Ygl (RGD), WKY/Gcrc (RGD), M520/N (MCW), SBH/Ygl (RGD), F344/NRrrc (MCW), CDR, LL/MavRrrc (RGD), SR/JrHsd (MCW), SHRSP/Gcrc (RGD), WKY/NCrl (RGD), SBN/Ygl (MCW), WKY/NHsd (RGD), F344/NCrl (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 49843958 49843959 G A snv SHRSP/Gcrc (MDC), F344/NHsd (ICAHN), F344/NRrrc (KNAW), M520/N (KNAW), MR/N (KNAW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), F344/NCrl (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), SHRSP/Gcrc (ICL), SR/JrHsd (ICL), SS/Jr (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), SS/JrHsdMcwi (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305658 AgrOrtholog
Ensembl Genes ENSRNOG00000015632 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000020990 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000020990 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.130.10.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5598458 IMAGE-MGC_LOAD
  IMAGE:5599601 IMAGE-MGC_LOAD
InterPro TAF1C UniProtKB/Swiss-Prot
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot
  WD40_repeat_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:361420 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72580 IMAGE-MGC_LOAD
  MGC:72608 IMAGE-MGC_LOAD
NCBI Gene 361420 ENTREZGENE
PANTHER PTHR15319 UniProtKB/Swiss-Prot
PhenoGen Taf1c PhenoGen
Superfamily-SCOP SSF50978 UniProtKB/Swiss-Prot
UniGene Rn.146984 ENTREZGENE
UniProt Q6P773 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-18 Taf1c  TATA-box binding protein associated factor, RNA polymerase 1 subunit C  Taf1c  TATA box binding protein (Tbp)-associated factor, RNA polymerase I, C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-02-07 Taf1c  TATA box binding protein (Tbp)-associated factor, RNA polymerase I, C  Taf1c_predicted  TATA box binding protein (Tbp)-associated factor, RNA polymerase I, C (predicted)  Symbol and Name updated 1299863 APPROVED
2007-02-07 Taf1c_predicted  TATA box binding protein (Tbp)-associated factor, RNA polymerase I, C (predicted)  LOC361420  similar to TAFI95  Data Merged 737654 PROVISIONAL
2005-09-15 LOC361420  similar to TAFI95      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-12 Taf1c_predicted  TATA box binding protein (Tbp)-associated factor, RNA polymerase I, C (predicted)      Symbol and Name status set to approved 70820 APPROVED