Ncoa6 (nuclear receptor coactivator 6) - Rat Genome Database
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Gene: Ncoa6 (nuclear receptor coactivator 6) Rattus norvegicus
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Symbol: Ncoa6
Name: nuclear receptor coactivator 6
RGD ID: 620111
Description: Exhibits several functions, including nuclear hormone receptor binding activity; nuclear receptor transcription coactivator activity; and peroxisome proliferator activated receptor binding activity. Involved in ovarian follicle development; positive regulation of insulin secretion involved in cellular response to glucose stimulus; and positive regulation of transcription by RNA polymerase II. Localizes to nucleus and protein-containing complex. Biomarker of type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in breast cancer; colon cancer; and lung cancer. Orthologous to human NCOA6 (nuclear receptor coactivator 6); PARTICIPATES IN estrogen signaling pathway; histone modification pathway; INTERACTS WITH 17beta-estradiol; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: activating signal cointegrator 2; Aib3; amplified in breast cancer protein 3; ASC-2; cancer-amplified transcriptional coactivator ASC-2; NRC; nuclear receptor coactivator RAP250; nuclear receptor-activating protein, 250 kDa; peroxisome proliferator-activated receptor-interacting protein; PPAR-interacting protein; PRIP; RAP250; thyroid hormone receptor binding protein; thyroid hormone receptor-binding protein; Trbp
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
mRatBN7.23143,890,896 - 143,961,916 (-)NCBI
Rnor_6.0 Ensembl3150,919,317 - 150,960,030 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03150,919,317 - 150,990,391 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03157,287,434 - 157,358,499 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43145,886,874 - 145,957,928 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13145,808,879 - 145,815,141 (-)NCBI
Celera3142,616,753 - 142,657,466 (-)NCBICelera
Cytogenetic Map3q41-q42NCBI
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 Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10681503   PMID:10788465   PMID:11302752   PMID:11443112   PMID:12039952   PMID:12368298   PMID:12446761   PMID:17021013   PMID:17500065   PMID:21700703   PMID:22311984   PMID:23341457  
PMID:29263199  


Genomics

Comparative Map Data
Ncoa6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23143,890,896 - 143,961,916 (-)NCBI
Rnor_6.0 Ensembl3150,919,317 - 150,960,030 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03150,919,317 - 150,990,391 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03157,287,434 - 157,358,499 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43145,886,874 - 145,957,928 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13145,808,879 - 145,815,141 (-)NCBI
Celera3142,616,753 - 142,657,466 (-)NCBICelera
Cytogenetic Map3q41-q42NCBI
NCOA6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2034,689,097 - 34,825,651 (-)EnsemblGRCh38hg38GRCh38
GRCh382034,714,774 - 34,825,651 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372033,302,578 - 33,413,454 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh372033,302,578 - 33,413,433 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362032,766,239 - 32,877,094 (-)NCBINCBI36hg18NCBI36
Build 342032,766,238 - 32,877,094NCBI
Celera2030,051,663 - 30,162,529 (-)NCBI
Cytogenetic Map20q11.22NCBI
HuRef2030,081,569 - 30,192,220 (-)NCBIHuRef
CHM1_12033,204,060 - 33,314,842 (-)NCBICHM1_1
Ncoa6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392155,232,576 - 155,315,831 (-)NCBIGRCm39mm39
GRCm382155,390,656 - 155,473,911 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2155,390,656 - 155,473,894 (-)EnsemblGRCm38mm10GRCm38
MGSCv372155,216,401 - 155,266,519 (-)NCBIGRCm37mm9NCBIm37
MGSCv362155,082,112 - 155,129,567 (-)NCBImm8
Celera2161,323,189 - 161,373,222 (-)NCBICelera
Cytogenetic Map2H1NCBI
Ncoa6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542226,564,037 - 26,632,675 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542226,564,535 - 26,639,516 (+)NCBIChiLan1.0ChiLan1.0
NCOA6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12032,170,583 - 32,247,167 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2032,170,583 - 32,247,167 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02031,044,339 - 31,154,798 (-)NCBIMhudiblu_PPA_v0panPan3
NCOA6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2423,802,351 - 23,866,792 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12423,802,360 - 23,877,986 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ncoa6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365615,905,905 - 5,982,824 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NCOA6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1738,114,291 - 38,221,901 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11738,114,284 - 38,221,904 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21743,309,959 - 43,393,797 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NCOA6
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1239,013,364 - 39,129,723 (-)NCBI
ChlSab1.1 Ensembl239,013,232 - 39,129,658 (-)Ensembl
Ncoa6
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248424,570,758 - 4,665,517 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)348561928155263151Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)381136227154416635Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3102152812155263151Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3114376250159376250Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3119471263164471263Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3125848628170848628Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3126575595153412619Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3126575595165355668Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128986468173986468Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3129787213177699992Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3130006659175006659Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3132875075176418101Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3136876155170935007Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3138374177177699992Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3138374177177699992Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3139578365177699992Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3146232777177699992Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3147072047154807958Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3148034701177699992Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3148348517171467264Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3148348739163640325Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3150368003177699992Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:272
Count of miRNA genes:107
Interacting mature miRNAs:112
Transcripts:ENSRNOT00000024714, ENSRNOT00000074304
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 3 28 30 14 19 14 67 33 41 11
Low 15 27 27 27 8 11 7 2 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024714   ⟹   ENSRNOP00000024714
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3150,919,317 - 150,960,030 (-)Ensembl
RefSeq Acc Id: NM_001276714   ⟹   NP_001263643
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23143,890,896 - 143,931,612 (-)NCBI
Rnor_6.03150,919,317 - 150,960,030 (-)NCBI
Rnor_5.03157,287,434 - 157,358,499 (-)NCBI
Celera3142,616,753 - 142,657,466 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235296   ⟹   XP_006235358
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23143,890,896 - 143,961,914 (-)NCBI
Rnor_6.03150,919,317 - 150,990,391 (-)NCBI
Rnor_5.03157,287,434 - 157,358,499 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762295   ⟹   XP_008760517
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23143,890,930 - 143,961,916 (-)NCBI
Rnor_6.03150,919,317 - 150,990,391 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762296   ⟹   XP_008760518
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03150,919,317 - 150,971,957 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762297   ⟹   XP_008760519
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03150,919,317 - 150,971,957 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762298   ⟹   XP_008760520
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03150,919,317 - 150,971,957 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762299   ⟹   XP_008760521
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03150,919,317 - 150,971,955 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039104103   ⟹   XP_038960031
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23143,890,896 - 143,961,914 (-)NCBI
RefSeq Acc Id: XM_039104104   ⟹   XP_038960032
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23143,890,896 - 143,961,914 (-)NCBI
RefSeq Acc Id: XM_039104105   ⟹   XP_038960033
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23143,890,896 - 143,961,914 (-)NCBI
RefSeq Acc Id: XM_039104106   ⟹   XP_038960034
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23143,890,896 - 143,961,914 (-)NCBI
RefSeq Acc Id: XM_039104107   ⟹   XP_038960035
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23143,890,896 - 143,961,914 (-)NCBI
RefSeq Acc Id: XR_005501749
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23143,898,839 - 143,961,914 (-)NCBI
RefSeq Acc Id: XR_005501750
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23143,898,839 - 143,961,914 (-)NCBI
RefSeq Acc Id: XR_591737
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03150,930,333 - 150,971,957 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001263643   ⟸   NM_001276714
- UniProtKB: G3V8C9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006235358   ⟸   XM_006235296
- Peptide Label: isoform X1
- UniProtKB: G3V8C9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760517   ⟸   XM_008762295
- Peptide Label: isoform X1
- UniProtKB: G3V8C9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760520   ⟸   XM_008762298
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008760519   ⟸   XM_008762297
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008760521   ⟸   XM_008762299
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_008760518   ⟸   XM_008762296
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000024714   ⟸   ENSRNOT00000024714
RefSeq Acc Id: XP_038960033   ⟸   XM_039104105
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038960032   ⟸   XM_039104104
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038960035   ⟸   XM_039104107
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038960034   ⟸   XM_039104106
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038960031   ⟸   XM_039104103
- Peptide Label: isoform X2
Protein Domains
Nucleic_acid_bd

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)
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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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/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
SBN/Ygl (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: 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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 157317386 157317387 A T snv COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), ZFDM (KyushuU), SBN/Ygl (MCW), HTX/Kyo (KyushuU), ZF (KyushuU)
3 157320209 157320210 C T snv DA/BklArbNsi (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 150933218 150933219 C T snv ACI/N (MCW)
3 150949269 150949270 A T snv FHH/EurMcwi (MCW), SBN/Ygl (MCW), COP/CrCrl (MCW & UW), FHL/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620111 AgrOrtholog
Ensembl Genes ENSRNOG00000018288 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024714 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024714 ENTREZGENE, UniProtKB/TrEMBL
InterPro NCOA6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NCOA6_nucleic_acid_bd UniProtKB/TrEMBL
KEGG Report rno:116464 UniProtKB/TrEMBL
NCBI Gene 116464 ENTREZGENE
PANTHER PTHR15690 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Nucleic_acid_bd UniProtKB/TrEMBL
PhenoGen Ncoa6 PhenoGen
UniProt G3V8C9 ENTREZGENE, UniProtKB/TrEMBL
  NCOA6_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q9JIH6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Ncoa6  nuclear receptor coactivator 6      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Ncoa6  nuclear receptor coactivator 6      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains a LXXLL motif 633379
gene_protein 2063 amino acid residues 633379