Set (SET nuclear proto-oncogene) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Set (SET nuclear proto-oncogene) Rattus norvegicus
Analyze
Symbol: Set
Name: SET nuclear proto-oncogene
RGD ID: 1307467
Description: Predicted to have DNA binding activity. Predicted to be involved in negative regulation of neuron apoptotic process and negative regulation of transcription, DNA-templated. Predicted to localize to several cellular components, including lipid droplet; nucleoplasm; and perinuclear region of cytoplasm. Human ortholog(s) of this gene implicated in autosomal dominant non-syndromic intellectual disability. Orthologous to several human genes including SET (SET nuclear proto-oncogene); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Ab1-115; I-2PP2A; liver regeneration-related protein LRRGR00002; LOC307947; phosphatase 2A inhibitor I2PP2A; SET nuclear oncogene; SET translocation; TAF-I; template-activating factor I
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
mRatBN7.21953,561,262 - 53,562,780 (+)NCBI
Rnor_6.0 Ensembl1958,419,961 - 58,421,504 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01958,420,635 - 58,422,153 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01969,119,722 - 69,121,240 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41955,797,060 - 55,798,578 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11955,801,940 - 55,803,459 (+)NCBI
Celera1952,922,285 - 52,923,803 (+)NCBICelera
Cytogenetic Map19q12NCBI
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
(+)-schisandrin B  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
aflatoxin B1  (ISO)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
enzyme inhibitor  (ISO)
ethanol  (EXP)
finasteride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
hydrogen sulfide  (ISO)
indometacin  (ISO)
isoprenaline  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
methoxychlor  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nefazodone  (EXP)
nimesulide  (EXP)
ochratoxin A  (EXP)
paraoxon  (ISO)
paraquat  (EXP)
pentachlorophenol  (ISO)
perfluorooctanoic acid  (ISO)
progesterone  (ISO)
rotenone  (EXP)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (EXP)
sulindac  (EXP)
T-2 toxin  (EXP)
tamoxifen  (ISO)
tetrachloromethane  (EXP,ISO)
thapsigargin  (ISO)
titanium dioxide  (ISO)
tributylstannane  (EXP)
trichloroethene  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:7508204   PMID:8889548   PMID:10715114   PMID:10716735   PMID:11078917   PMID:11555662   PMID:11909973   PMID:12477932   PMID:12524539   PMID:16162853   PMID:16396499   PMID:16791210  
PMID:17065150   PMID:18374643   PMID:19343227   PMID:20651003   PMID:23233674  


Genomics

Comparative Map Data
Set
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21953,561,262 - 53,562,780 (+)NCBI
Rnor_6.0 Ensembl1958,419,961 - 58,421,504 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01958,420,635 - 58,422,153 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01969,119,722 - 69,121,240 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41955,797,060 - 55,798,578 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11955,801,940 - 55,803,459 (+)NCBI
Celera1952,922,285 - 52,923,803 (+)NCBICelera
Cytogenetic Map19q12NCBI
SET
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9128,683,424 - 128,696,400 (+)EnsemblGRCh38hg38GRCh38
GRCh389128,683,424 - 128,696,396 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh379131,445,703 - 131,458,675 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369130,491,682 - 130,498,488 (+)NCBINCBI36hg18NCBI36
Build 349128,531,414 - 128,538,221NCBI
Celera9102,096,741 - 102,109,482 (+)NCBI
Cytogenetic Map9q34.11NCBI
HuRef9101,055,484 - 101,068,248 (+)NCBIHuRef
CHM1_19131,596,913 - 131,609,662 (+)NCBICHM1_1
Set
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39229,952,008 - 29,962,589 (+)NCBIGRCm39mm39
GRCm39 Ensembl229,947,390 - 29,962,589 (+)Ensembl
GRCm38230,061,996 - 30,072,577 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl230,057,378 - 30,072,577 (+)EnsemblGRCm38mm10GRCm38
MGSCv37229,917,563 - 29,927,315 (+)NCBIGRCm37mm9NCBIm37
MGSCv36229,884,052 - 29,893,804 (+)NCBImm8
Celera229,765,516 - 29,775,301 (+)NCBICelera
Cytogenetic Map2BNCBI
Set
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555701,104,447 - 1,117,682 (+)NCBIChiLan1.0ChiLan1.0
SET
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19128,473,334 - 128,486,295 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9128,473,806 - 128,484,563 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0999,806,876 - 99,819,825 (+)NCBIMhudiblu_PPA_v0panPan3
SET
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1954,896,464 - 54,907,698 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Set
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493648716,181,764 - 16,184,706 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SET
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11269,050,447 - 269,064,462 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21303,081,846 - 303,088,281 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SET
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1129,446,265 - 9,453,991 (-)NCBI
Set
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247606,293,452 - 6,304,237 (-)NCBI


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 glucose level (CMO:0000543)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)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:224
Count of miRNA genes:152
Interacting mature miRNAs:161
Transcripts:ENSRNOT00000051397
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 2 26 25 22 6 22 65 21 31 2
Low 1 17 32 19 13 19 8 11 9 14 10 9 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000051397   ⟹   ENSRNOP00000039454
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1958,419,961 - 58,421,504 (+)Ensembl
RefSeq Acc Id: NM_001012504   ⟹   NP_001012522
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21953,561,262 - 53,562,780 (+)NCBI
Rnor_6.01958,420,635 - 58,422,153 (+)NCBI
Rnor_5.01969,119,722 - 69,121,240 (+)NCBI
RGSC_v3.41955,797,060 - 55,798,578 (+)RGD
Celera1952,922,285 - 52,923,803 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001012522 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC60681 (Get FASTA)   NCBI Sequence Viewer  
  AAP92538 (Get FASTA)   NCBI Sequence Viewer  
  Q63945 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001012522   ⟸   NM_001012504
- UniProtKB: Q63945 (UniProtKB/Swiss-Prot),   A0A0G2JSU3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000039454   ⟸   ENSRNOT00000051397

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)
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
WAG/Rij (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
WKY/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
WKY/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
WKY/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
WKY/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
WN/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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 69120056 69120057 A T snv F344/Jcl (KyushuU), HTX/Kyo (KyushuU), LEC/Tj (KyushuU), F344/DuCrlCrlj (KyushuU), HWY/Slc (KyushuU), NIG-III/Hok (KyushuU), F344/Stm (KyushuU), GH/OmrMcwi (MCW), IS-Tlk/Kyo (KyushuU), ACI/EurMcwi (MCW), BUF/MNa (KyushuU), RCS/Kyo (KyushuU), SDLEF7/Barth (UDEL), BN/SsNSlc (KyushuU), DOB/Oda (KyushuU), SBH/Ygl (MCW), F344/NSlc (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), COP/CrCrl (MCW & UW), SBN/Ygl (MCW), ZFDM (KyushuU), ZF (KyushuU), KFRS3B/Kyo (KyushuU), SS/JrHsdMcwi (MCW), LE/Stm (KyushuU), BDIX/NemOda (KyushuU)
19 69120071 69120072 A T snv LEC/Tj (KyushuU), HWY/Slc (KyushuU), F344/Stm (KyushuU), IS-Tlk/Kyo (KyushuU), RCS/Kyo (KyushuU), BN/SsNSlc (KyushuU), F344/NSlc (KyushuU), HTX/Kyo (KyushuU), LE/Stm (KyushuU), F344/DuCrlCrlj (KyushuU), NIG-III/Hok (KyushuU), BUF/MNa (KyushuU), SDLEF7/Barth (UDEL), SS/JrHsdMcwi (MCW), SBN/Ygl (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), ZFDM (KyushuU), ACI/EurMcwi (MCW), ZF (KyushuU), KFRS3B/Kyo (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX/NemOda (KyushuU), F344/Jcl (KyushuU)
19 69120370 69120371 G C snv F344/Jcl (KyushuU)
19 69120389 69120390 A G snv F344/DuCrlCrlj (KyushuU), F344/Jcl (KyushuU)
19 69120397 69120398 C T snv F344/Jcl (KyushuU), F344/NSlc (KyushuU), F344/DuCrlCrlj (KyushuU)
19 69120403 69120404 C T snv F344/Jcl (KyushuU), ZFDM (KyushuU), F344/DuCrlCrlj (KyushuU), F344/NSlc (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 58420969 58420970 A T snv ACI/EurMcwi (MCW), MR/N (MCW), M520/N (MCW), CDS, CDR, SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), WN/N (MCW)
19 58420984 58420985 A T snv FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), SBH/Ygl (MCW), COP/CrCrl (MCW & UW), CDS, SS/JrHsdMcwi (MCW), CDR, SR/JrHsd (MCW), GH/OmrMcwi (MCW)
19 58421247 58421248 T C snv SBN/Ygl (MCW)
19 58421283 58421284 G C snv FHH/EurMcwi (MCW), SBH/Ygl (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), SBN/Ygl (MCW)
19 58421302 58421303 A G snv SBH/Ygl (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), ACI/EurMcwi (MCW), GH/OmrMcwi (MCW), FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW), SR/JrHsd (MCW), FHH/EurMcwi (MCW)
19 58421310 58421311 C T snv FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), SBN/Ygl (MCW), COP/CrCrl (MCW & UW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), ACI/EurMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 55797305 55797306 G T snv SS/JrHsdMcwi (MCW)
19 55797394 55797395 A T snv SHR/OlaIpcv (ICL), COP/CrCrl (MCW & UW), MR/N (KNAW), WN/N (KNAW), LEW/Crl (ICL), GK/Ox (ICL), ACI/EurMcwi (MCW), M520/N (KNAW), GH/OmrMcwi (MCW), SS/JrHsdMcwi (MCW)
19 55797409 55797410 A T snv SHR/OlaIpcv (ICL), SBN/Ygl (ICL), SBH/Ygl (ICL), LL/MavRrrc (ICL), LEW/Crl (ICL), LE/Stm (ICL), ACI/EurMcwi (ICL), WKY/NCrl (ICL), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), GH/OmrMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307467 AgrOrtholog
Ensembl Genes ENSRNOG00000025892 UniProtKB/Swiss-Prot
  ENSRNOG00000034241 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000039454 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070331 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000051397 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000081787 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:9089104 IMAGE-MGC_LOAD
InterPro NAP-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NAP_family UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:307947 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:187306 IMAGE-MGC_LOAD
NCBI Gene 307947 ENTREZGENE
PANTHER PTHR11875 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam NAP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Set PhenoGen
Superfamily-SCOP SSF143113 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JSU3 ENTREZGENE, UniProtKB/TrEMBL
  B0BMV1_RAT UniProtKB/TrEMBL
  Q63945 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q7TPA3 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-10 Set  SET nuclear proto-oncogene  Set  SET nuclear oncogene  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-14 Set  SET nuclear oncogene  Set  SET translocation   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Set  SET translocation   Set_predicted  SET translocation (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Set_predicted  SET translocation (predicted)      Symbol and Name status set to approved 70820 APPROVED