Aire (autoimmune regulator) - Rat Genome Database

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Gene: Aire (autoimmune regulator) Rattus norvegicus
Analyze
Symbol: Aire
Name: autoimmune regulator
RGD ID: 1311139
Description: Predicted to have several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; identical protein binding activity; and zinc ion binding activity. Predicted to be involved in several processes, including immune system development; positive regulation of transcription by RNA polymerase II; and regulation of thymocyte migration. Predicted to localize to cytoplasm and nuclear body. Used to study autoimmune polyendocrine syndrome. Human ortholog(s) of this gene implicated in autoimmune polyendocrine syndrome and autoimmune polyendocrine syndrome type 1. Orthologous to human AIRE (autoimmune regulator); PARTICIPATES IN primary immunodeficiency pathway; ubiquitin/proteasome degradation pathway; INTERACTS WITH acrylamide; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy); LOC294328
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Aireem1Ang  
Genetic Models: BN-Aireem1Ang-/- SD.BN-Aireem1Ang-/-
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22010,636,058 - 10,651,060 (+)NCBI
Rnor_6.0 Ensembl2011,365,697 - 11,380,631 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02011,365,630 - 11,380,636 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02013,535,776 - 13,550,486 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42010,980,031 - 10,996,102 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12010,980,315 - 10,996,140 (+)NCBI
Celera2012,141,888 - 12,156,863 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11156688   PMID:11274163   PMID:11533054   PMID:11854172   PMID:15712268   PMID:17599412   PMID:18292755   PMID:19015306   PMID:19446523   PMID:19923453   PMID:20185822   PMID:23382543  
PMID:23993652   PMID:26084028   PMID:28540407  


Genomics

Candidate Gene Status
Aire is a candidate Gene for QTL Iddm23
Comparative Map Data
Aire
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22010,636,058 - 10,651,060 (+)NCBI
Rnor_6.0 Ensembl2011,365,697 - 11,380,631 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02011,365,630 - 11,380,636 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02013,535,776 - 13,550,486 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42010,980,031 - 10,996,102 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12010,980,315 - 10,996,140 (+)NCBI
Celera2012,141,888 - 12,156,863 (+)NCBICelera
Cytogenetic Map20p12NCBI
AIRE
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2144,285,838 - 44,298,648 (+)EnsemblGRCh38hg38GRCh38
GRCh382144,285,876 - 44,298,648 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372145,705,759 - 45,718,531 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362144,530,191 - 44,542,530 (+)NCBINCBI36hg18NCBI36
Build 342144,534,575 - 44,542,300NCBI
Celera2130,811,017 - 30,823,364 (+)NCBI
Cytogenetic Map21q22.3NCBI
HuRef2131,076,211 - 31,088,675 (+)NCBIHuRef
CHM1_12145,266,544 - 45,278,925 (+)NCBICHM1_1
Aire
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391077,865,856 - 77,879,444 (-)NCBIGRCm39mm39
GRCm39 Ensembl1077,865,856 - 77,879,444 (-)Ensembl
GRCm381078,030,022 - 78,043,610 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1078,030,022 - 78,043,610 (-)EnsemblGRCm38mm10GRCm38
MGSCv371077,492,776 - 77,506,325 (-)NCBIGRCm37mm9NCBIm37
MGSCv361077,433,160 - 77,446,709 (-)NCBImm8
Celera1079,069,034 - 79,082,580 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Aire
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540741,157,484 - 41,165,014 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540741,157,503 - 41,165,032 (-)NCBIChiLan1.0ChiLan1.0
AIRE
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12143,837,170 - 43,849,830 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2143,837,340 - 43,848,974 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02130,543,018 - 30,556,225 (+)NCBIMhudiblu_PPA_v0panPan3
AIRE
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13138,139,513 - 38,149,294 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3138,139,099 - 38,149,296 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3137,296,701 - 37,307,469 (+)NCBI
ROS_Cfam_1.03137,686,832 - 37,697,601 (+)NCBI
UMICH_Zoey_3.13137,553,994 - 37,564,750 (+)NCBI
UNSW_CanFamBas_1.03137,534,760 - 37,545,522 (+)NCBI
UU_Cfam_GSD_1.03138,032,729 - 38,043,507 (+)NCBI
Aire
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497137,330,752 - 37,342,258 (+)NCBI
SpeTri2.0NW_004936500125,589 - 137,071 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AIRE
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13207,148,380 - 207,158,354 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113207,148,401 - 207,158,355 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213217,028,220 - 217,038,176 (+)NCBISscrofa10.2Sscrofa10.2susScr3
AIRE
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1288,019,122 - 88,031,998 (+)NCBI
ChlSab1.1 Ensembl288,019,522 - 88,031,801 (+)Ensembl
Aire
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474529,850,410 - 29,857,351 (-)NCBI

Position Markers
D20Rat67  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02011,379,968 - 11,380,199NCBIRnor6.0
Rnor_5.02013,549,818 - 13,550,049UniSTSRnor5.0
RGSC_v3.42010,995,438 - 10,995,671RGDRGSC3.4
RGSC_v3.42010,995,439 - 10,995,670UniSTSRGSC3.4
RGSC_v3.12010,995,412 - 10,995,904RGD
Celera2012,156,219 - 12,156,431UniSTS
RH 3.4 Map20150.8UniSTS
RH 3.4 Map20150.8RGD
RH 2.0 Map20154.8RGD
SHRSP x BN Map2011.54RGD
Cytogenetic Map20p12UniSTS
D20Got10  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02011,379,716 - 11,379,896NCBIRnor6.0
Rnor_6.013100,649,193 - 100,650,424NCBIRnor6.0
Rnor_5.02013,549,566 - 13,549,746UniSTSRnor5.0
Rnor_5.013105,583,034 - 105,584,265UniSTSRnor5.0
RGSC_v3.41398,225,241 - 98,226,472UniSTSRGSC3.4
RGSC_v3.42010,995,189 - 10,995,367RGDRGSC3.4
RGSC_v3.42010,995,190 - 10,995,367UniSTSRGSC3.4
RGSC_v3.12010,995,417 - 10,995,594RGD
Celera1393,463,578 - 93,464,809UniSTS
Celera2012,155,967 - 12,156,147UniSTS
RH 3.4 Map20144.9UniSTS
RH 3.4 Map20144.9RGD
RH 2.0 Map20155.9RGD
Cytogenetic Map20p12UniSTS
D20Ztm3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02011,669,099 - 11,669,398NCBIRnor6.0
Rnor_5.02013,834,856 - 13,835,155UniSTSRnor5.0
RGSC_v3.42011,336,555 - 11,336,854UniSTSRGSC3.4
Celera2012,456,436 - 12,456,748UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20965564214411641Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20587544818739210Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
1581577Pur15Proteinuria QTL 154.380.0002total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20865434118872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20403911318872273Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat


Genetic Models
This gene Aire is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:42
Count of miRNA genes:39
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000001611
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system nervous system renal system reproductive system respiratory system
High
Medium
Low 1 4 8 8 4
Below cutoff 1 6 10 10 5 10 15 8 10 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001611   ⟹   ENSRNOP00000001611
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2011,365,697 - 11,380,631 (+)Ensembl
RefSeq Acc Id: NM_001106379   ⟹   NP_001099849
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22010,636,123 - 10,651,060 (+)NCBI
Rnor_6.02011,365,697 - 11,380,631 (+)NCBI
Rnor_5.02013,535,776 - 13,550,486 (+)NCBI
RGSC_v3.42010,980,031 - 10,996,102 (+)RGD
Celera2012,141,888 - 12,156,863 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256247   ⟹   XP_006256309
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22010,636,058 - 10,651,051 (+)NCBI
Rnor_6.02011,365,630 - 11,380,636 (+)NCBI
Rnor_5.02013,535,776 - 13,550,486 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601597   ⟹   XP_017457086
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02011,365,630 - 11,380,636 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601598   ⟹   XP_017457087
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02011,365,630 - 11,380,636 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601599   ⟹   XP_017457088
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22010,636,058 - 10,649,758 (+)NCBI
Rnor_6.02011,365,630 - 11,378,553 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601600   ⟹   XP_017457089
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02011,365,630 - 11,378,553 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601601   ⟹   XP_017457090
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22010,636,058 - 10,649,758 (+)NCBI
Rnor_6.02011,365,630 - 11,378,553 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601602   ⟹   XP_017457091
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02011,365,630 - 11,378,553 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001099849   ⟸   NM_001106379
- UniProtKB: D3ZV49 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256309   ⟸   XM_006256247
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457086   ⟸   XM_017601597
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017457087   ⟸   XM_017601598
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017457088   ⟸   XM_017601599
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017457089   ⟸   XM_017601600
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017457090   ⟸   XM_017601601
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017457091   ⟸   XM_017601602
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: ENSRNOP00000001611   ⟸   ENSRNOT00000001611
Protein Domains
HSR   PHD-type   SAND

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)
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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_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 11375790 11375791 C A snv Buf/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311139 AgrOrtholog
Ensembl Genes ENSRNOG00000001213 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001611 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001611 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.10.390.10 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
InterPro AIRE UniProtKB/TrEMBL
  AIRE_PHD2 UniProtKB/TrEMBL
  SAND_dom UniProtKB/TrEMBL
  SAND_dom-like UniProtKB/TrEMBL
  Sp100 UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:294328 UniProtKB/TrEMBL
NCBI Gene 294328 ENTREZGENE
Pfam PHD UniProtKB/TrEMBL
  Sp100 UniProtKB/TrEMBL
PhenoGen Aire PhenoGen
PRINTS AIREGULATOR UniProtKB/TrEMBL
PROSITE HSR UniProtKB/TrEMBL
  SAND UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/TrEMBL
SMART PHD UniProtKB/TrEMBL
  SAND UniProtKB/TrEMBL
Superfamily-SCOP FYVE_PHD_ZnF UniProtKB/TrEMBL
  SAND_like UniProtKB/TrEMBL
UniProt D3ZV49 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-26 Aire  autoimmune regulator  Aire  autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Aire  autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)   Aire_predicted  autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Aire_predicted  autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy) (predicted)      Symbol and Name status set to approved 70820 APPROVED