Aire (autoimmune regulator) - Rat Genome Database

Name: Aire
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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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 ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	AIRE (autoimmune regulator)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Aire (autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy))	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Aire (autoimmune regulator)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	AIRE (autoimmune regulator)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	AIRE (autoimmune regulator)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Aire (autoimmune regulator)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	AIRE (autoimmune regulator)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	AIRE (autoimmune regulator)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Aire (autoimmune regulator)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	AIRE (autoimmune regulator)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Aire (autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

Allele / Splice:

Aire^em1Ang

Genetic Models:

BN-Aire^em1Ang-/- SD.BN-Aire^em1Ang-/-

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	20	10,636,058 - 10,651,060 (+)	NCBI
Rnor_6.0 Ensembl	20	11,365,697 - 11,380,631 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	20	11,365,630 - 11,380,636 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	20	13,535,776 - 13,550,486 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	10,980,031 - 10,996,102 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	20	10,980,315 - 10,996,140 (+)	NCBI
Celera	20	12,141,888 - 12,156,863 (+)	NCBI		Celera
Cytogenetic Map	20	p12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

autoimmune polyendocrine syndrome (IMP,ISO)

autoimmune polyendocrine syndrome type 1 (ISO)

candidiasis (ISO)

Experimental Diabetes Mellitus (ISO)

Guillain-Barre syndrome (ISS)

Neurodevelopmental Disorders (ISO)

primary immunodeficiency disease (ISO)

Sjogren's syndrome (ISS)

Skin Neoplasms (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

acrylamide (EXP)

aflatoxin B2 (ISO)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP)

butanal (ISO)

cadmium dichloride (EXP)

chloropicrin (ISO)

crocidolite asbestos (ISO)

D-mannitol (ISO)

dimethylarsinic acid (ISO)

heptanal (ISO)

hexanal (ISO)

hydrogen peroxide (ISO)

menadione (ISO)

methapyrilene (ISO)

nonanal (ISO)

octanal (ISO)

paracetamol (ISO)

pentanal (ISO)

propanal (ISO)

trimellitic anhydride (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

central tolerance induction to self antigen (IBA,ISO)

humoral immune response (IBA,ISO)

negative thymic T cell selection (IBA,ISO)

peripheral T cell tolerance induction (IBA,ISO)

positive regulation of chemokine production (IEA,ISO)

positive regulation of transcription by RNA polymerase II (IBA,ISO)

positive regulation of transcription, DNA-templated (ISO)

regulation of thymocyte migration (IBA,ISO)

regulation of transcription, DNA-templated (ISO)

regulation of translation (IEA)

thymus epithelium morphogenesis (IBA,ISO)

Cellular Component

cellular_component (ND)

cytoplasm (ISO)

nuclear body (ISO)

nucleus (IBA,ISO)

Molecular Function

chromatin binding (IBA,ISO)

histone binding (IBA,ISO)

identical protein binding (ISO)

molecular_function (ND)

protein binding (ISO)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (IBA,ISO)

translation regulator activity (IEA)

zinc ion binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

primary immunodeficiency pathway (IEA)

ubiquitin/proteasome degradation pathway (IEA)

Phenotype Annotations Click to see Annotation Detail View

Mammalian Phenotype

abnormal NK cell number (IMP)

abnormal thymus morphology (IMP)

alopecia (IMP)

decreased circulating creatinine level (IMP)

decreased skin pigmentation (IMP)

enlarged paws (IMP)

increased autoantibody level (IMP)

nail dystrophy (IMP)

variable depigmentation (IMP)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	Hassler S, etal., Scand J Immunol. 2008 Jun;67(6):569-80. Epub 2008 Apr 8.
4.	MGD data from the GO Consortium
5.	OMIM Disease Annotation Pipeline
6.	Ossart J, etal., J Immunol. 2018 Aug 1;201(3):874-887. doi: 10.4049/jimmunol.1701318. Epub 2018 Jun 29.
7.	Pipeline to import KEGG annotations from KEGG into RGD
8.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9.	RGD automated import pipeline for gene-chemical interactions
10.	RGD comprehensive gene curation
11.	Wang CY, etal., Hum Genet. 1998 Dec;103(6):681-5.

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	20	10,636,058 - 10,651,060 (+)	NCBI
Rnor_6.0 Ensembl	20	11,365,697 - 11,380,631 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	20	11,365,630 - 11,380,636 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	20	13,535,776 - 13,550,486 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	10,980,031 - 10,996,102 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	20	10,980,315 - 10,996,140 (+)	NCBI
Celera	20	12,141,888 - 12,156,863 (+)	NCBI		Celera
Cytogenetic Map	20	p12	NCBI

AIRE
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	21	44,285,838 - 44,298,648 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	21	44,285,876 - 44,298,648 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	21	45,705,759 - 45,718,531 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	21	44,530,191 - 44,542,530 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	21	44,534,575 - 44,542,300	NCBI
Celera	21	30,811,017 - 30,823,364 (+)	NCBI
Cytogenetic Map	21	q22.3	NCBI
HuRef	21	31,076,211 - 31,088,675 (+)	NCBI		HuRef
CHM1_1	21	45,266,544 - 45,278,925 (+)	NCBI		CHM1_1

Aire
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	77,865,856 - 77,879,444 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	10	77,865,856 - 77,879,444 (-)	Ensembl
GRCm38	10	78,030,022 - 78,043,610 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	78,030,022 - 78,043,610 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	77,492,776 - 77,506,325 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	10	77,433,160 - 77,446,709 (-)	NCBI			mm8
Celera	10	79,069,034 - 79,082,580 (-)	NCBI		Celera
Cytogenetic Map	10	C1	NCBI
cM Map	10	39.72	NCBI

Aire
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955407	41,157,484 - 41,165,014 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955407	41,157,503 - 41,165,032 (-)	NCBI	ChiLan1.0	ChiLan1.0

AIRE
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	21	43,837,170 - 43,849,830 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	21	43,837,340 - 43,848,974 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	21	30,543,018 - 30,556,225 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

AIRE
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	31	38,139,513 - 38,149,294 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	31	38,139,099 - 38,149,296 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	31	37,296,701 - 37,307,469 (+)	NCBI
ROS_Cfam_1.0	31	37,686,832 - 37,697,601 (+)	NCBI
UMICH_Zoey_3.1	31	37,553,994 - 37,564,750 (+)	NCBI
UNSW_CanFamBas_1.0	31	37,534,760 - 37,545,522 (+)	NCBI
UU_Cfam_GSD_1.0	31	38,032,729 - 38,043,507 (+)	NCBI

Aire
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404971	37,330,752 - 37,342,258 (+)	NCBI
SpeTri2.0	NW_004936500	125,589 - 137,071 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

AIRE
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	207,148,380 - 207,158,354 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	13	207,148,401 - 207,158,355 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	217,028,220 - 217,038,176 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

AIRE
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	2	88,019,122 - 88,031,998 (+)	NCBI
ChlSab1.1 Ensembl	2	88,019,522 - 88,031,801 (+)	Ensembl

Aire
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624745	29,850,410 - 29,857,351 (-)	NCBI

Position Markers

D20Rat67

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	20	11,379,968 - 11,380,199	NCBI	Rnor6.0
Rnor_5.0	20	13,549,818 - 13,550,049	UniSTS	Rnor5.0
RGSC_v3.4	20	10,995,438 - 10,995,671	RGD	RGSC3.4
RGSC_v3.4	20	10,995,439 - 10,995,670	UniSTS	RGSC3.4
RGSC_v3.1	20	10,995,412 - 10,995,904	RGD
Celera	20	12,156,219 - 12,156,431	UniSTS
RH 3.4 Map	20	150.8	UniSTS
RH 3.4 Map	20	150.8	RGD
RH 2.0 Map	20	154.8	RGD
SHRSP x BN Map	20	11.54	RGD
Cytogenetic Map	20	p12	UniSTS

D20Got10

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	20	11,379,716 - 11,379,896	NCBI	Rnor6.0
Rnor_6.0	13	100,649,193 - 100,650,424	NCBI	Rnor6.0
Rnor_5.0	20	13,549,566 - 13,549,746	UniSTS	Rnor5.0
Rnor_5.0	13	105,583,034 - 105,584,265	UniSTS	Rnor5.0
RGSC_v3.4	13	98,225,241 - 98,226,472	UniSTS	RGSC3.4
RGSC_v3.4	20	10,995,189 - 10,995,367	RGD	RGSC3.4
RGSC_v3.4	20	10,995,190 - 10,995,367	UniSTS	RGSC3.4
RGSC_v3.1	20	10,995,417 - 10,995,594	RGD
Celera	13	93,463,578 - 93,464,809	UniSTS
Celera	20	12,155,967 - 12,156,147	UniSTS
RH 3.4 Map	20	144.9	UniSTS
RH 3.4 Map	20	144.9	RGD
RH 2.0 Map	20	155.9	RGD
Cytogenetic Map	20	p12	UniSTS

D20Ztm3

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	20	11,669,099 - 11,669,398	NCBI	Rnor6.0
Rnor_5.0	20	13,834,856 - 13,835,155	UniSTS	Rnor5.0
RGSC_v3.4	20	11,336,555 - 11,336,854	UniSTS	RGSC3.4
Celera	20	12,456,436 - 12,456,748	UniSTS
Cytogenetic Map	20	p12	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
61432	Cia1	Collagen induced arthritis QTL 1			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	20	4855475	15050565	Rat
631265	Iresp1	Immunoglobin response QTL1	8.3		blood anti-double stranded DNA antibody amount (VT:0004762)	serum anti-DNA antibody level (CMO:0001533)	20	9655642	14411641	Rat
70154	Insul2	Insulin level QTL 2	3.75		blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	20	5875448	18739210	Rat
1641893	Alcrsp7	Alcohol response QTL 7			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	1	26305996	Rat
1641915	Colcr9	Colorectal carcinoma resistance QTL 9	2.97	0.0024	intestine integrity trait (VT:0010554)	benign colorectal tumor number (CMO:0001795)	20	2999707	47999707	Rat
1581577	Pur15	Proteinuria QTL 15	4.38	0.0002	total urine protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	20	8654341	18872273	Rat
1598816	Memor12	Memory QTL 12	2.4		exploratory behavior trait (VT:0010471)	average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)	20	4108956	49108956	Rat
1600382	Edcs3	Endometrial carcinoma susceptibility QTL3	3.5	0.003	uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	20	1	25653396	Rat
2305926	Iddm37	Insulin dependent diabetes mellitus QTL 37	6		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	20	2018654	47018654	Rat
1354642	Despr15	Despair related QTL 15		0.0027	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	20	1	24652101	Rat
1558640	Prcs2	Prostate cancer susceptibility QTL 2	3.3		prostate integrity trait (VT:0010571)	percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)	20	4039113	18872273	Rat
2317057	Aia27	Adjuvant induced arthritis QTL 27	2.83		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	20	3402111	27968216	Rat
2317851	Alcrsp22	Alcohol response QTL 22	3.2	0.05	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	1	26305996	Rat
4889857	Pur27	Proteinuria QTL 27	12.2	0.001	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	20	4039113	18872273	Rat
4889870	Pur30	Proteinuria QTL 30	19	0.005	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	20	8654341	30991290	Rat
6893685	Bw111	Body weight QTL 111	2.7	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	20	1	33300419	Rat
7411668	Foco32	Food consumption QTL 32	8	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	1	37550487	Rat
8694189	Bw153	Body weight QTL 153	3.13	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	20	1	28375393	Rat
9590275	Scort15	Serum corticosterone level QTL 15	3.48	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	20	1	28375393	Rat
7411650	Foco23	Food consumption QTL 23	20.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	1	28375393	Rat
9590109	Sffal8	Serum free fatty acids level QTL 8	5.32	0.01	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	20	1	28375393	Rat
9590252	Scort12	Serum corticosterone level QTL 12	20.46	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	20	1	37550487	Rat
7387283	Uae44	Urinary albumin excretion QTL 44		0.1712	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	20	1	27357423	Rat
9589155	Insul32	Insulin level QTL 32	6.38	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	20	1	28375393	Rat

Genetic Models

This gene Aire is modified in the following models/strains

BN-Aire^em1Ang-/-

SD.BN-Aire^em1Ang-/-

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106379	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006256247	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017601597	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017601598	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017601599	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017601600	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017601601	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017601602	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC109383	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473988	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000324	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000001611 ⟹ ENSRNOP00000001611

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	11,365,697 - 11,380,631 (+)	Ensembl

RefSeq Acc Id:

NM_001106379 ⟹ NP_001099849

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	20	10,636,123 - 10,651,060 (+)	NCBI
Rnor_6.0	20	11,365,697 - 11,380,631 (+)	NCBI
Rnor_5.0	20	13,535,776 - 13,550,486 (+)	NCBI
RGSC_v3.4	20	10,980,031 - 10,996,102 (+)	RGD
Celera	20	12,141,888 - 12,156,863 (+)	RGD

Sequence:

show sequence

GAACGCAAGCGCGCGGGGGGCCAGCAGGGGGCGCCGAAGCGCAGACCCTGTCTGGAGGATGGCT
GGTGGGGATGGGATGCTGCGCCGCCTGCTGAGGCTGCACCGCACCGAGATCGCAGTGGCCATAG
ACAGCGCCTTTCCGCTGCTGCATGCTCTGGCCGACCACGACGTGGTCCCTGAGGACAAGTTCCA
GGAGACACTCCGGCTGAAAGAGAAGGAAGGCTGCCCCCAGGCCTTCCACGCCCTGCTGTCCTGG
CTCCTGACTCGGGACAGTGGGGCCATCCTGGATTTCTGGAGGGTTCTCTTTAAGGACTACAATC
TGGAGCGGTACAGCCGCCTGCATACCATCCTGGACGGCTTTCCAAAAGATGTGGACCTTAGCCA
GCCTCGGAAAGGGAGGAAGCCCCTTGCTGGTCCCAAGGCTTCAGTAGTGCCACCCAGACCCCCC
ACAAAGAGAAGAGCCCTGGAAGAGCCTCGAGCCACCCCACCAGCAACTCTGGCCTCAAAGAGCA
TCTCTAGCCCAGGTTCCCACTCAAAGGCCAAACCCCCTAAGAAGCCAGAGGGCAACTTGGAGTC
ACAGCGCCTCCCACTGGGAAACGGAATCCAGACCATGGCAGCTTCTGTCCAGAGAGCTGTGACT
GTGTCCTCCGGGGATGTCCCAGGATCCCGAGGGGCTGTGGAAGGGATCCTTATCCAGCAAGTAT
TCGAGTCAGGAGGATCCAAGAAGTGCATCCAGGTTGGAGGGGAGTTTTATAAACCCAGCAAGTT
CGAAGACCCCAGTGGCAATTTGAAGAACAAGACCCGAGGTGGTAGCAGCCTAAAGCCAGTGATC
CGAGGAAAGGGAACCCAGGGTAGAGATGAGCAGAAAGTGAGCCAGCAGTGTGGGGTCCCTCCCC
TTCCACCTCTTCCCAATGAGCCCCAAGTTCACCAGAAGAACGAGGATGAATGCGCTGTGTGCCA
TGACGGAGGCGAGCTCATCTGCTGTGACGGCTGTCCCCGCGCCTTCCACCTGGCTTGCCTGTCC
CCACCTCTGCAGGAGATCCCCAGTGGCCTTTGGAGATGTTCGTGCTGCCTCCAGGGCAGAATCC
AGCAGAACCTGTCCCAGCCTGAGGAGTCCAGGCCCCTGGAGCCATCTGCAGAGACCCCGATTCT
CCTGGGACTGAGGTCAGCTTCCGAGAAAACCAGGGTCCTGTCCAGGGAGCTGCCAGCCGGCTCA
GATGCTGCAGTCACATATGCGAACCTGCTGGCCCCACCTTCCACAGCCCCTGTTCTGGAGCCTT
CAGCACTCTGCCCTCTACCGAGTGCTGGGGCGGAAGGGCAGCCGGGTCCGACACTGAGCGCGCG
ATGCGGTGTGTGCGGCGACTCCACCGACGTGCTGCGGTGCGCACACTGTGCCGCTGCCTTTCAC
TGGCGCTGCCACTTCCCGATGGCTGCTGTCCGGCCAGGGACCAATCTCCGCTGCAAGTCCTGCT
CGGCAGAACCGACTCCCACGCCAGGCGTGCCAGGCGAGGCTGTGCCCACCGCTGTGCGTCCCAC
ACCTGGGCTTGCCAAGGTAGGGGACGACTCTGCTAGTCATGACCCTGTTCTGCATAGGGATGAC
CTGGAGTCCCTCCTGAATGAGCACTCCTTTGACGGCATCCTGCAGTGGGCCATCCAGAGCATGT
CACGCCCGCTGGCCGAGACACCACCCTTTTCTTCCTGACTCCAGGCAGCATAGCACCAGCCCCC
ACCCCACCCCATCAGATGACGCCTTATACCTGCAGCCCCTCCGTTCTGAGAGGACTAGGCTAGT
TAGGGCCAAGAGCTGCAGGACTCAGCTGGCAGACGGCCCTGGTCTTTGTGGAGATGCAAGGCCA
CTCTGTGTCTTGAAATTAAAGTCACTTCTGTGTGC

hide sequence

RefSeq Acc Id:

XM_006256247 ⟹ XP_006256309

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	20	10,636,058 - 10,651,051 (+)	NCBI
Rnor_6.0	20	11,365,630 - 11,380,636 (+)	NCBI
Rnor_5.0	20	13,535,776 - 13,550,486 (+)	NCBI

Sequence:

show sequence

GGAGTAAGTATAAACGCTCACAGGTGCCTGCCTCTCCCGATAGCACCTAGACACCCAAGGGAGA
AGGGAACGCAAGCGCGCGGGGGGCCAGCAGGGGGCGCCGAAGCGCAGACCCTGTCTGGAGGATG
GCTGGTGGGGATGGGATGCTGCGCCGCCTGCTGAGGCTGCACCGCACCGAGATCGCAGTGGCCA
TAGACAGCGCCTTTCCGCTGCTGCATGCTCTGGCCGACCACGACGTGGTCCCTGAGGACAAGTT
CCAGGAGACACTCCGGCTGAAAGAGAAGGAAGGCTGCCCCCAGGCCTTCCACGCCCTGCTGTCC
TGGCTCCTGACTCGGGACAGTGGGGCCATCCTGGATTTCTGGAGGGTTCTCTTTAAGGACTACA
ATCTGGAGCGGTACAGCCGCCTGCATACCATCCTGGACGGCTTTCCAAAAGATGTGGACCTTAG
CCAGCCTCGGAAAGGGAGGAAGCCCCTTGCTGGTCCCAAGGCTTCAGTAGTGCCACCCAGACCC
CCCACAAAGAGAAGAGCCCTGGAAGAGCCTCGAGCCACCCCACCAGCAACTCTGGCCTCAAAGA
GCATCTCTAGCCCAGGTTCCCACTCAAAGGCCAAACCCCCTAAGAAGCCAGAGGGCAACTTGGA
GTCACAGCGCCTCCCACTGGGAAACGGAATCCAGACCATGGCAGCTTCTGTCCAGAGAGCTGTG
ACTGTGTCCTCCGGGGATGTCCCAGGATCCCGAGGGGCTGTGGAAGGGATCCTTATCCAGCAAG
TATTCGAGTCAGGAGGATCCAAGAAGTGCATCCAGGTTGGAGGGGAGTTTTATAAACCCAGCAA
GTTCGAAGACCCCAGTGGCAATTTGAAGAACAAGACCCGAGGTGGTAGCAGCCTAAAGCCAGTG
ATCCGAGGAAAGGGAACCCAGGTCACTATACCTGGTAGAGATGAGCAGAAAGTGAGCCAGCAGT
GTGGGGTCCCTCCCCTTCCACCTCTTCCCAATGAGCCCCAAGTTCACCAGAAGAACGAGGATGA
ATGCGCTGTGTGCCATGACGGAGGCGAGCTCATCTGCTGTGACGGCTGTCCCCGCGCCTTCCAC
CTGGCTTGCCTGTCCCCACCTCTGCAGGAGATCCCCAGTGGCCTTTGGAGATGTTCGTGCTGCC
TCCAGGGCAGAATCCAGCAGAACCTGTCCCAGCCTGAGGAGTCCAGGCCCCTGGAGCCATCTGC
AGAGACCCCGATTCTCCTGGGACTGAGGTCAGCTTCCGAGAAAACCAGGGTCCTGTCCAGGGAG
CTGCCAGCCGGCTCAGATGCTGCAGTCACATATGCGAACCTGCTGGCCCCACCTTCCACAGCCC
CTGTTCTGGAGCCTTCAGCACTCTGCCCTCTACCGAGTGCTGGGGCGGAAGGGCAGCCGGGTCC
GACACTGAGCGCGCGATGCGGTGTGTGCGGCGACTCCACCGACGTGCTGCGGTGCGCACACTGT
GCCGCTGCCTTTCACTGGCGCTGCCACTTCCCGATGGCTGCTGTCCGGCCAGGGACCAATCTCC
GCTGCAAGTCCTGCTCGGCAGAACCGACTCCCACGCCAGGCGTGCCAGGCGAGGCTGTGCCCAC
CGCTGTGCGTCCCACACCTGGGCTTGCCAAGGTAGGGGACGACTCTGCTAGTCATGACCCTGTT
CTGCATAGGGATGACCTGGAGTCCCTCCTGAATGAGCACTCCTTTGACGGCATCCTGCAGTGGG
CCATCCAGAGCATGTCACGCCCGCTGGCCGAGACACCACCCTTTTCTTCCTGACTCCAGGCAGC
ATAGCACCAGCCCCCACCCCACCCCATCAGATGACGCCTTATACCTGCAGCCCCTCCGTTCTGA
GAGGACTAGGCTAGTTAGGGCCAAGAGCTGCAGGACTCAGCTGGCAGACGGCCCTGGTCTTTGT
GGAGATGCAAGGCCACTCTGTGTCTTGAAATTAAAGTCACTTCTGTGTGCTTTGA

hide sequence

RefSeq Acc Id:

XM_017601597 ⟹ XP_017457086

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	20	11,365,630 - 11,380,636 (+)	NCBI

Sequence:

show sequence

GGAGTAAGTATAAACGCTCACAGGTGCCTGCCTCTCCCGATAGCACCTAGACACCCAAGGGAGA
AGGGAACGCAAGCGCGCGGGGGGCCAGCAGGGGGCGCCGAAGCGCAGACCCTGTCTGGAGGATG
GCTGGTGGGGATGGGATGCTGCGCCGCCTGCTGAGGCTGCACCGCACCGAGATCGCAGTGGCCA
TAGACAGCGCCTTTCCGCTGCTGCATGCTCTGGCCGACCACGACGTGGTCCCTGAGGACAAGTT
CCAGGAGACACTCCGGCTGAAAGAGAAGGAAGGCTGCCCCCAGGCCTTCCACGCCCTGCTGTCC
TGGCTCCTGACTCGGGACAGTGGGGCCATCCTGGATTTCTGGAGGGTTCTCTTTAAGGACTACA
ATCTGGAGCGGTACAGCCGCCTGCATACCATCCTGGACGGCTTTCCAAAAGATGTGGACCTTAG
CCAGCCTCGGAAAGGGAGGAAGCCCCTTGCTGGTCCCAAGGCTTCAGTAGTGCCACCCAGACCC
CCCACAAAGAGAAGAGCCCTGGAAGAGCCTCGAGCCACCCCACCAGCAACTCTGGCCTCAAAGA
GCATCTCTAGCCCAGGTTCCCACTCAAAGGCCAAACCCCCTAAGAAGCCAGAGGGCAACTTGGA
GTCACAGCGCCTCCCACTGGGAAACGGAATCCAGACCATGGCAGCTTCTGTCCAGAGAGCTGTG
ACTGTGTCCTCCGGGGATGTCCCAGGATCCCGAGGGGCTGTGGAAGGGATCCTTATCCAGCAAG
TATTCGAGTCAGGAGGATCCAAGAAGTGCATCCAGGTTGGAGGGGAGTTTTATAAACCCAGCAA
GTTCGAAGACCCCAGTGGCAATTTGAAGAACAAGACCCGAGGTGGTAGCAGCCTAAAGCCAGTG
ATCCGAGGAAAGGGAACCCAGGTCACTATACCTGGTAGAGATGAGCAGAAAGTGAGCCAGCAGT
GTGGGGTCCCTCCCCTTCCACCTCTTCCCAATGAGCCCCAAGTTCACCAGAACGAGGATGAATG
CGCTGTGTGCCATGACGGAGGCGAGCTCATCTGCTGTGACGGCTGTCCCCGCGCCTTCCACCTG
GCTTGCCTGTCCCCACCTCTGCAGGAGATCCCCAGTGGCCTTTGGAGATGTTCGTGCTGCCTCC
AGGGCAGAATCCAGCAGAACCTGTCCCAGCCTGAGGAGTCCAGGCCCCTGGAGCCATCTGCAGA
GACCCCGATTCTCCTGGGACTGAGGTCAGCTTCCGAGAAAACCAGGGTCCTGTCCAGGGAGCTG
CCAGCCGGCTCAGATGCTGCAGTCACATATGCGAACCTGCTGGCCCCACCTTCCACAGCCCCTG
TTCTGGAGCCTTCAGCACTCTGCCCTCTACCGAGTGCTGGGGCGGAAGGGCAGCCGGGTCCGAC
ACTGAGCGCGCGATGCGGTGTGTGCGGCGACTCCACCGACGTGCTGCGGTGCGCACACTGTGCC
GCTGCCTTTCACTGGCGCTGCCACTTCCCGATGGCTGCTGTCCGGCCAGGGACCAATCTCCGCT
GCAAGTCCTGCTCGGCAGAACCGACTCCCACGCCAGGCGTGCCAGGCGAGGCTGTGCCCACCGC
TGTGCGTCCCACACCTGGGCTTGCCAAGGTAGGGGACGACTCTGCTAGTCATGACCCTGTTCTG
CATAGGGATGACCTGGAGTCCCTCCTGAATGAGCACTCCTTTGACGGCATCCTGCAGTGGGCCA
TCCAGAGCATGTCACGCCCGCTGGCCGAGACACCACCCTTTTCTTCCTGACTCCAGGCAGCATA
GCACCAGCCCCCACCCCACCCCATCAGATGACGCCTTATACCTGCAGCCCCTCCGTTCTGAGAG
GACTAGGCTAGTTAGGGCCAAGAGCTGCAGGACTCAGCTGGCAGACGGCCCTGGTCTTTGTGGA
GATGCAAGGCCACTCTGTGTCTTGAAATTAAAGTCACTTCTGTGTGCTTTGA

hide sequence

RefSeq Acc Id:

XM_017601598 ⟹ XP_017457087

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	20	11,365,630 - 11,380,636 (+)	NCBI

Sequence:

show sequence

GGAGTAAGTATAAACGCTCACAGGTGCCTGCCTCTCCCGATAGCACCTAGACACCCAAGGGAGA
AGGGAACGCAAGCGCGCGGGGGGCCAGCAGGGGGCGCCGAAGCGCAGACCCTGTCTGGAGGATG
GCTGGTGGGGATGGGATGCTGCGCCGCCTGCTGAGGCTGCACCGCACCGAGATCGCAGTGGCCA
TAGACAGCGCCTTTCCGCTGCTGCATGCTCTGGCCGACCACGACGTGGTCCCTGAGGACAAGTT
CCAGGAGACACTCCGGCTGAAAGAGAAGGAAGGCTGCCCCCAGGCCTTCCACGCCCTGCTGTCC
TGGCTCCTGACTCGGGACAGTGGGGCCATCCTGGATTTCTGGAGGGTTCTCTTTAAGGACTACA
ATCTGGAGCGGTACAGCCGCCTGCATACCATCCTGGACGGCTTTCCAAAAGATGTGGACCTTAG
CCAGCCTCGGAAAGGGAGGAAGCCCCTTGCTGGTCCCAAGGCTTCAGTAGTGCCACCCAGACCC
CCCACAAAGAGAAGAGCCCTGGAAGAGCCTCGAGCCACCCCACCAGCAACTCTGGCCTCAAAGA
GCATCTCTAGCCCAGGTTCCCACTCAAAGGCCAAACCCCCTAAGAAGCCAGAGGGCAACTTGGA
GTCACAGCGCCTCCCACTGGGAAACGGAATCCAGACCATGGCAGCTTCTGTCCAGAGAGCTGTG
ACTGTGTCCTCCGGGGATGTCCCAGGATCCCGAGGGGCTGTGGAAGGGATCCTTATCCAGCAAG
TATTCGAGTCAGGAGGATCCAAGAAGTGCATCCAGGTTGGAGGGGAGTTTTATAAACCCAGCAA
GTTCGAAGACCCCAGTGGCAATTTGAAGAACAAGACCCGAGGTGGTAGCAGCCTAAAGCCAGTG
ATCCGAGGAAAGGGAACCCAGGGTAGAGATGAGCAGAAAGTGAGCCAGCAGTGTGGGGTCCCTC
CCCTTCCACCTCTTCCCAATGAGCCCCAAGTTCACCAGAACGAGGATGAATGCGCTGTGTGCCA
TGACGGAGGCGAGCTCATCTGCTGTGACGGCTGTCCCCGCGCCTTCCACCTGGCTTGCCTGTCC
CCACCTCTGCAGGAGATCCCCAGTGGCCTTTGGAGATGTTCGTGCTGCCTCCAGGGCAGAATCC
AGCAGAACCTGTCCCAGCCTGAGGAGTCCAGGCCCCTGGAGCCATCTGCAGAGACCCCGATTCT
CCTGGGACTGAGGTCAGCTTCCGAGAAAACCAGGGTCCTGTCCAGGGAGCTGCCAGCCGGCTCA
GATGCTGCAGTCACATATGCGAACCTGCTGGCCCCACCTTCCACAGCCCCTGTTCTGGAGCCTT
CAGCACTCTGCCCTCTACCGAGTGCTGGGGCGGAAGGGCAGCCGGGTCCGACACTGAGCGCGCG
ATGCGGTGTGTGCGGCGACTCCACCGACGTGCTGCGGTGCGCACACTGTGCCGCTGCCTTTCAC
TGGCGCTGCCACTTCCCGATGGCTGCTGTCCGGCCAGGGACCAATCTCCGCTGCAAGTCCTGCT
CGGCAGAACCGACTCCCACGCCAGGCGTGCCAGGCGAGGCTGTGCCCACCGCTGTGCGTCCCAC
ACCTGGGCTTGCCAAGGTAGGGGACGACTCTGCTAGTCATGACCCTGTTCTGCATAGGGATGAC
CTGGAGTCCCTCCTGAATGAGCACTCCTTTGACGGCATCCTGCAGTGGGCCATCCAGAGCATGT
CACGCCCGCTGGCCGAGACACCACCCTTTTCTTCCTGACTCCAGGCAGCATAGCACCAGCCCCC
ACCCCACCCCATCAGATGACGCCTTATACCTGCAGCCCCTCCGTTCTGAGAGGACTAGGCTAGT
TAGGGCCAAGAGCTGCAGGACTCAGCTGGCAGACGGCCCTGGTCTTTGTGGAGATGCAAGGCCA
CTCTGTGTCTTGAAATTAAAGTCACTTCTGTGTGCTTTGA

hide sequence

RefSeq Acc Id:

XM_017601599 ⟹ XP_017457088

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	20	10,636,058 - 10,649,758 (+)	NCBI
Rnor_6.0	20	11,365,630 - 11,378,553 (+)	NCBI

Sequence:

show sequence

GGAGTAAGTATAAACGCTCACAGGTGCCTGCCTCTCCCGATAGCACCTAGACACCCAAGGGAGA
AGGGAACGCAAGCGCGCGGGGGGCCAGCAGGGGGCGCCGAAGCGCAGACCCTGTCTGGAGGATG
GCTGGTGGGGATGGGATGCTGCGCCGCCTGCTGAGGCTGCACCGCACCGAGATCGCAGTGGCCA
TAGACAGCGCCTTTCCGCTGCTGCATGCTCTGGCCGACCACGACGTGGTCCCTGAGGACAAGTT
CCAGGAGACACTCCGGCTGAAAGAGAAGGAAGGCTGCCCCCAGGCCTTCCACGCCCTGCTGTCC
TGGCTCCTGACTCGGGACAGTGGGGCCATCCTGGATTTCTGGAGGGTTCTCTTTAAGGACTACA
ATCTGGAGCGGTACAGCCGCCTGCATACCATCCTGGACGGCTTTCCAAAAGATGTGGACCTTAG
CCAGCCTCGGAAAGGGAGGAAGCCCCTTGCTGGTCCCAAGGCTTCAGTAGTGCCACCCAGACCC
CCCACAAAGAGAAGAGCCCTGGAAGAGCCTCGAGCCACCCCACCAGCAACTCTGGCCTCAAAGA
GCATCTCTAGCCCAGGTTCCCACTCAAAGGCCAAACCCCCTAAGAAGCCAGAGGGCAACTTGGA
GTCACAGCGCCTCCCACTGGGAAACGGAATCCAGACCATGGCAGCTTCTGTCCAGAGAGCTGTG
ACTGTGTCCTCCGGGGATGTCCCAGGATCCCGAGGGGCTGTGGAAGGGATCCTTATCCAGCAAG
TATTCGAGTCAGGAGGATCCAAGAAGTGCATCCAGGTTGGAGGGGAGTTTTATAAACCCAGCAA
GTTCGAAGACCCCAGTGGCAATTTGAAGAACAAGACCCGAGGTGGTAGCAGCCTAAAGCCAGTG
ATCCGAGGAAAGGGAACCCAGGTCACTATACCTGGTAGAGATGAGCAGAAAGTGAGCCAGCAGT
GTGGGGTCCCTCCCCTTCCACCTCTTCCCAATGAGCCCCAAGTTCACCAGAAGAACGAGGATGA
ATGCGCTGTGTGCCATGACGGAGGCGAGCTCATCTGCTGTGACGGCTGTCCCCGCGCCTTCCAC
CTGGCTTGCCTGTCCCCACCTCTGCAGGAGATCCCCAGTGGCCTTTGGAGATGTTCGTGCTGCC
TCCAGGGCAGAATCCAGCAGAACCTGTCCCAGCCTGAGGAGTCCAGGCCCCTGGAGCCATCTGC
AGAGACCCCGGACCAATCTCCGCTGCAAGTCCTGCTCGGCAGAACCGACTCCCACGCCAGGCGT
GCCAGGCGAGGCTGTGCCCACCGCTGTGCGTCCCACACCTGGGCTTGCCAAGGTAGGGGACGAC
TCTGCTAG

hide sequence

RefSeq Acc Id:

XM_017601600 ⟹ XP_017457089

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	20	11,365,630 - 11,378,553 (+)	NCBI

Sequence:

show sequence

GGAGTAAGTATAAACGCTCACAGGTGCCTGCCTCTCCCGATAGCACCTAGACACCCAAGGGAGA
AGGGAACGCAAGCGCGCGGGGGGCCAGCAGGGGGCGCCGAAGCGCAGACCCTGTCTGGAGGATG
GCTGGTGGGGATGGGATGCTGCGCCGCCTGCTGAGGCTGCACCGCACCGAGATCGCAGTGGCCA
TAGACAGCGCCTTTCCGCTGCTGCATGCTCTGGCCGACCACGACGTGGTCCCTGAGGACAAGTT
CCAGGAGACACTCCGGCTGAAAGAGAAGGAAGGCTGCCCCCAGGCCTTCCACGCCCTGCTGTCC
TGGCTCCTGACTCGGGACAGTGGGGCCATCCTGGATTTCTGGAGGGTTCTCTTTAAGGACTACA
ATCTGGAGCGGTACAGCCGCCTGCATACCATCCTGGACGGCTTTCCAAAAGATGTGGACCTTAG
CCAGCCTCGGAAAGGGAGGAAGCCCCTTGCTGGTCCCAAGGCTTCAGTAGTGCCACCCAGACCC
CCCACAAAGAGAAGAGCCCTGGAAGAGCCTCGAGCCACCCCACCAGCAACTCTGGCCTCAAAGA
GCATCTCTAGCCCAGGTTCCCACTCAAAGGCCAAACCCCCTAAGAAGCCAGAGGGCAACTTGGA
GTCACAGCGCCTCCCACTGGGAAACGGAATCCAGACCATGGCAGCTTCTGTCCAGAGAGCTGTG
ACTGTGTCCTCCGGGGATGTCCCAGGATCCCGAGGGGCTGTGGAAGGGATCCTTATCCAGCAAG
TATTCGAGTCAGGAGGATCCAAGAAGTGCATCCAGGTTGGAGGGGAGTTTTATAAACCCAGCAA
GTTCGAAGACCCCAGTGGCAATTTGAAGAACAAGACCCGAGGTGGTAGCAGCCTAAAGCCAGTG
ATCCGAGGAAAGGGAACCCAGGTCACTATACCTGGTAGAGATGAGCAGAAAGTGAGCCAGCAGT
GTGGGGTCCCTCCCCTTCCACCTCTTCCCAATGAGCCCCAAGTTCACCAGAACGAGGATGAATG
CGCTGTGTGCCATGACGGAGGCGAGCTCATCTGCTGTGACGGCTGTCCCCGCGCCTTCCACCTG
GCTTGCCTGTCCCCACCTCTGCAGGAGATCCCCAGTGGCCTTTGGAGATGTTCGTGCTGCCTCC
AGGGCAGAATCCAGCAGAACCTGTCCCAGCCTGAGGAGTCCAGGCCCCTGGAGCCATCTGCAGA
GACCCCGGACCAATCTCCGCTGCAAGTCCTGCTCGGCAGAACCGACTCCCACGCCAGGCGTGCC
AGGCGAGGCTGTGCCCACCGCTGTGCGTCCCACACCTGGGCTTGCCAAGGTAGGGGACGACTCT
GCTAG

hide sequence

RefSeq Acc Id:

XM_017601601 ⟹ XP_017457090

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	20	10,636,058 - 10,649,758 (+)	NCBI
Rnor_6.0	20	11,365,630 - 11,378,553 (+)	NCBI

Sequence:

show sequence

GGAGTAAGTATAAACGCTCACAGGTGCCTGCCTCTCCCGATAGCACCTAGACACCCAAGGGAGA
AGGGAACGCAAGCGCGCGGGGGGCCAGCAGGGGGCGCCGAAGCGCAGACCCTGTCTGGAGGATG
GCTGGTGGGGATGGGATGCTGCGCCGCCTGCTGAGGCTGCACCGCACCGAGATCGCAGTGGCCA
TAGACAGCGCCTTTCCGCTGCTGCATGCTCTGGCCGACCACGACGTGGTCCCTGAGGACAAGTT
CCAGGAGACACTCCGGCTGAAAGAGAAGGAAGGCTGCCCCCAGGCCTTCCACGCCCTGCTGTCC
TGGCTCCTGACTCGGGACAGTGGGGCCATCCTGGATTTCTGGAGGGTTCTCTTTAAGGACTACA
ATCTGGAGCGGTACAGCCGCCTGCATACCATCCTGGACGGCTTTCCAAAAGATGTGGACCTTAG
CCAGCCTCGGAAAGGGAGGAAGCCCCTTGCTGGTCCCAAGGCTTCAGTAGTGCCACCCAGACCC
CCCACAAAGAGAAGAGCCCTGGAAGAGCCTCGAGCCACCCCACCAGCAACTCTGGCCTCAAAGA
GCATCTCTAGCCCAGGTTCCCACTCAAAGGCCAAACCCCCTAAGAAGCCAGAGGGCAACTTGGA
GTCACAGCGCCTCCCACTGGGAAACGGAATCCAGACCATGGCAGCTTCTGTCCAGAGAGCTGTG
ACTGTGTCCTCCGGGGATGTCCCAGGATCCCGAGGGGCTGTGGAAGGGATCCTTATCCAGCAAG
TATTCGAGTCAGGAGGATCCAAGAAGTGCATCCAGGTTGGAGGGGAGTTTTATAAACCCAGCAA
GTTCGAAGACCCCAGTGGCAATTTGAAGAACAAGACCCGAGGTGGTAGCAGCCTAAAGCCAGTG
ATCCGAGGAAAGGGAACCCAGGGTAGAGATGAGCAGAAAGTGAGCCAGCAGTGTGGGGTCCCTC
CCCTTCCACCTCTTCCCAATGAGCCCCAAGTTCACCAGAAGAACGAGGATGAATGCGCTGTGTG
CCATGACGGAGGCGAGCTCATCTGCTGTGACGGCTGTCCCCGCGCCTTCCACCTGGCTTGCCTG
TCCCCACCTCTGCAGGAGATCCCCAGTGGCCTTTGGAGATGTTCGTGCTGCCTCCAGGGCAGAA
TCCAGCAGAACCTGTCCCAGCCTGAGGAGTCCAGGCCCCTGGAGCCATCTGCAGAGACCCCGGA
CCAATCTCCGCTGCAAGTCCTGCTCGGCAGAACCGACTCCCACGCCAGGCGTGCCAGGCGAGGC
TGTGCCCACCGCTGTGCGTCCCACACCTGGGCTTGCCAAGGTAGGGGACGACTCTGCTAG

hide sequence

RefSeq Acc Id:

XM_017601602 ⟹ XP_017457091

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	20	11,365,630 - 11,378,553 (+)	NCBI

Sequence:

show sequence

GGAGTAAGTATAAACGCTCACAGGTGCCTGCCTCTCCCGATAGCACCTAGACACCCAAGGGAGA
AGGGAACGCAAGCGCGCGGGGGGCCAGCAGGGGGCGCCGAAGCGCAGACCCTGTCTGGAGGATG
GCTGGTGGGGATGGGATGCTGCGCCGCCTGCTGAGGCTGCACCGCACCGAGATCGCAGTGGCCA
TAGACAGCGCCTTTCCGCTGCTGCATGCTCTGGCCGACCACGACGTGGTCCCTGAGGACAAGTT
CCAGGAGACACTCCGGCTGAAAGAGAAGGAAGGCTGCCCCCAGGCCTTCCACGCCCTGCTGTCC
TGGCTCCTGACTCGGGACAGTGGGGCCATCCTGGATTTCTGGAGGGTTCTCTTTAAGGACTACA
ATCTGGAGCGGTACAGCCGCCTGCATACCATCCTGGACGGCTTTCCAAAAGATGTGGACCTTAG
CCAGCCTCGGAAAGGGAGGAAGCCCCTTGCTGGTCCCAAGGCTTCAGTAGTGCCACCCAGACCC
CCCACAAAGAGAAGAGCCCTGGAAGAGCCTCGAGCCACCCCACCAGCAACTCTGGCCTCAAAGA
GCATCTCTAGCCCAGGTTCCCACTCAAAGGCCAAACCCCCTAAGAAGCCAGAGGGCAACTTGGA
GTCACAGCGCCTCCCACTGGGAAACGGAATCCAGACCATGGCAGCTTCTGTCCAGAGAGCTGTG
ACTGTGTCCTCCGGGGATGTCCCAGGATCCCGAGGGGCTGTGGAAGGGATCCTTATCCAGCAAG
TATTCGAGTCAGGAGGATCCAAGAAGTGCATCCAGGTTGGAGGGGAGTTTTATAAACCCAGCAA
GTTCGAAGACCCCAGTGGCAATTTGAAGAACAAGACCCGAGGTGGTAGCAGCCTAAAGCCAGTG
ATCCGAGGAAAGGGAACCCAGGGTAGAGATGAGCAGAAAGTGAGCCAGCAGTGTGGGGTCCCTC
CCCTTCCACCTCTTCCCAATGAGCCCCAAGTTCACCAGAACGAGGATGAATGCGCTGTGTGCCA
TGACGGAGGCGAGCTCATCTGCTGTGACGGCTGTCCCCGCGCCTTCCACCTGGCTTGCCTGTCC
CCACCTCTGCAGGAGATCCCCAGTGGCCTTTGGAGATGTTCGTGCTGCCTCCAGGGCAGAATCC
AGCAGAACCTGTCCCAGCCTGAGGAGTCCAGGCCCCTGGAGCCATCTGCAGAGACCCCGGACCA
ATCTCCGCTGCAAGTCCTGCTCGGCAGAACCGACTCCCACGCCAGGCGTGCCAGGCGAGGCTGT
GCCCACCGCTGTGCGTCCCACACCTGGGCTTGCCAAGGTAGGGGACGACTCTGCTAG

hide sequence

Protein Sequences


Protein RefSeqs	NP_001099849	(Get FASTA)	NCBI Sequence Viewer
	XP_006256309	(Get FASTA)	NCBI Sequence Viewer
	XP_017457088	(Get FASTA)	NCBI Sequence Viewer
	XP_017457090	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL97063	(Get FASTA)	NCBI Sequence Viewer
	EDL97064	(Get FASTA)	NCBI Sequence Viewer
	EDL97065	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001099849 ⟸ NM_001106379

- UniProtKB:

D3ZV49 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAGGDGMLRRLLRLHRTEIAVAIDSAFPLLHALADHDVVPEDKFQETLRLKEKEGCPQAFHALL
SWLLTRDSGAILDFWRVLFKDYNLERYSRLHTILDGFPKDVDLSQPRKGRKPLAGPKASVVPPR
PPTKRRALEEPRATPPATLASKSISSPGSHSKAKPPKKPEGNLESQRLPLGNGIQTMAASVQRA
VTVSSGDVPGSRGAVEGILIQQVFESGGSKKCIQVGGEFYKPSKFEDPSGNLKNKTRGGSSLKP
VIRGKGTQGRDEQKVSQQCGVPPLPPLPNEPQVHQKNEDECAVCHDGGELICCDGCPRAFHLAC
LSPPLQEIPSGLWRCSCCLQGRIQQNLSQPEESRPLEPSAETPILLGLRSASEKTRVLSRELPA
GSDAAVTYANLLAPPSTAPVLEPSALCPLPSAGAEGQPGPTLSARCGVCGDSTDVLRCAHCAAA
FHWRCHFPMAAVRPGTNLRCKSCSAEPTPTPGVPGEAVPTAVRPTPGLAKVGDDSASHDPVLHR
DDLESLLNEHSFDGILQWAIQSMSRPLAETPPFSS

hide sequence

RefSeq Acc Id:

XP_006256309 ⟸ XM_006256247

- Peptide Label:

isoform X1

- Sequence:

show sequence

MAGGDGMLRRLLRLHRTEIAVAIDSAFPLLHALADHDVVPEDKFQETLRLKEKEGCPQAFHALL
SWLLTRDSGAILDFWRVLFKDYNLERYSRLHTILDGFPKDVDLSQPRKGRKPLAGPKASVVPPR
PPTKRRALEEPRATPPATLASKSISSPGSHSKAKPPKKPEGNLESQRLPLGNGIQTMAASVQRA
VTVSSGDVPGSRGAVEGILIQQVFESGGSKKCIQVGGEFYKPSKFEDPSGNLKNKTRGGSSLKP
VIRGKGTQVTIPGRDEQKVSQQCGVPPLPPLPNEPQVHQKNEDECAVCHDGGELICCDGCPRAF
HLACLSPPLQEIPSGLWRCSCCLQGRIQQNLSQPEESRPLEPSAETPILLGLRSASEKTRVLSR
ELPAGSDAAVTYANLLAPPSTAPVLEPSALCPLPSAGAEGQPGPTLSARCGVCGDSTDVLRCAH
CAAAFHWRCHFPMAAVRPGTNLRCKSCSAEPTPTPGVPGEAVPTAVRPTPGLAKVGDDSASHDP
VLHRDDLESLLNEHSFDGILQWAIQSMSRPLAETPPFSS

hide sequence

RefSeq Acc Id:

XP_017457086 ⟸ XM_017601597

- Peptide Label:

isoform X2

- Sequence:

show sequence

MAGGDGMLRRLLRLHRTEIAVAIDSAFPLLHALADHDVVPEDKFQETLRLKEKEGCPQAFHALL
SWLLTRDSGAILDFWRVLFKDYNLERYSRLHTILDGFPKDVDLSQPRKGRKPLAGPKASVVPPR
PPTKRRALEEPRATPPATLASKSISSPGSHSKAKPPKKPEGNLESQRLPLGNGIQTMAASVQRA
VTVSSGDVPGSRGAVEGILIQQVFESGGSKKCIQVGGEFYKPSKFEDPSGNLKNKTRGGSSLKP
VIRGKGTQVTIPGRDEQKVSQQCGVPPLPPLPNEPQVHQNEDECAVCHDGGELICCDGCPRAFH
LACLSPPLQEIPSGLWRCSCCLQGRIQQNLSQPEESRPLEPSAETPILLGLRSASEKTRVLSRE
LPAGSDAAVTYANLLAPPSTAPVLEPSALCPLPSAGAEGQPGPTLSARCGVCGDSTDVLRCAHC
AAAFHWRCHFPMAAVRPGTNLRCKSCSAEPTPTPGVPGEAVPTAVRPTPGLAKVGDDSASHDPV
LHRDDLESLLNEHSFDGILQWAIQSMSRPLAETPPFSS

hide sequence

RefSeq Acc Id:

XP_017457087 ⟸ XM_017601598

- Peptide Label:

isoform X3

- Sequence:

show sequence

MAGGDGMLRRLLRLHRTEIAVAIDSAFPLLHALADHDVVPEDKFQETLRLKEKEGCPQAFHALL
SWLLTRDSGAILDFWRVLFKDYNLERYSRLHTILDGFPKDVDLSQPRKGRKPLAGPKASVVPPR
PPTKRRALEEPRATPPATLASKSISSPGSHSKAKPPKKPEGNLESQRLPLGNGIQTMAASVQRA
VTVSSGDVPGSRGAVEGILIQQVFESGGSKKCIQVGGEFYKPSKFEDPSGNLKNKTRGGSSLKP
VIRGKGTQGRDEQKVSQQCGVPPLPPLPNEPQVHQNEDECAVCHDGGELICCDGCPRAFHLACL
SPPLQEIPSGLWRCSCCLQGRIQQNLSQPEESRPLEPSAETPILLGLRSASEKTRVLSRELPAG
SDAAVTYANLLAPPSTAPVLEPSALCPLPSAGAEGQPGPTLSARCGVCGDSTDVLRCAHCAAAF
HWRCHFPMAAVRPGTNLRCKSCSAEPTPTPGVPGEAVPTAVRPTPGLAKVGDDSASHDPVLHRD
DLESLLNEHSFDGILQWAIQSMSRPLAETPPFSS

hide sequence

RefSeq Acc Id:

XP_017457088 ⟸ XM_017601599

- Peptide Label:

isoform X2

- Sequence:

show sequence

MAGGDGMLRRLLRLHRTEIAVAIDSAFPLLHALADHDVVPEDKFQETLRLKEKEGCPQAFHALL
SWLLTRDSGAILDFWRVLFKDYNLERYSRLHTILDGFPKDVDLSQPRKGRKPLAGPKASVVPPR
PPTKRRALEEPRATPPATLASKSISSPGSHSKAKPPKKPEGNLESQRLPLGNGIQTMAASVQRA
VTVSSGDVPGSRGAVEGILIQQVFESGGSKKCIQVGGEFYKPSKFEDPSGNLKNKTRGGSSLKP
VIRGKGTQVTIPGRDEQKVSQQCGVPPLPPLPNEPQVHQKNEDECAVCHDGGELICCDGCPRAF
HLACLSPPLQEIPSGLWRCSCCLQGRIQQNLSQPEESRPLEPSAETPDQSPLQVLLGRTDSHAR
RARRGCAHRCASHTWACQGRGRLC

hide sequence

RefSeq Acc Id:

XP_017457089 ⟸ XM_017601600

- Peptide Label:

isoform X5

- Sequence:

show sequence

MAGGDGMLRRLLRLHRTEIAVAIDSAFPLLHALADHDVVPEDKFQETLRLKEKEGCPQAFHALL
SWLLTRDSGAILDFWRVLFKDYNLERYSRLHTILDGFPKDVDLSQPRKGRKPLAGPKASVVPPR
PPTKRRALEEPRATPPATLASKSISSPGSHSKAKPPKKPEGNLESQRLPLGNGIQTMAASVQRA
VTVSSGDVPGSRGAVEGILIQQVFESGGSKKCIQVGGEFYKPSKFEDPSGNLKNKTRGGSSLKP
VIRGKGTQVTIPGRDEQKVSQQCGVPPLPPLPNEPQVHQNEDECAVCHDGGELICCDGCPRAFH
LACLSPPLQEIPSGLWRCSCCLQGRIQQNLSQPEESRPLEPSAETPDQSPLQVLLGRTDSHARR
ARRGCAHRCASHTWACQGRGRLC

hide sequence

RefSeq Acc Id:

XP_017457090 ⟸ XM_017601601

- Peptide Label:

isoform X3

- Sequence:

show sequence

MAGGDGMLRRLLRLHRTEIAVAIDSAFPLLHALADHDVVPEDKFQETLRLKEKEGCPQAFHALL
SWLLTRDSGAILDFWRVLFKDYNLERYSRLHTILDGFPKDVDLSQPRKGRKPLAGPKASVVPPR
PPTKRRALEEPRATPPATLASKSISSPGSHSKAKPPKKPEGNLESQRLPLGNGIQTMAASVQRA
VTVSSGDVPGSRGAVEGILIQQVFESGGSKKCIQVGGEFYKPSKFEDPSGNLKNKTRGGSSLKP
VIRGKGTQGRDEQKVSQQCGVPPLPPLPNEPQVHQKNEDECAVCHDGGELICCDGCPRAFHLAC
LSPPLQEIPSGLWRCSCCLQGRIQQNLSQPEESRPLEPSAETPDQSPLQVLLGRTDSHARRARR
GCAHRCASHTWACQGRGRLC

hide sequence

RefSeq Acc Id:

XP_017457091 ⟸ XM_017601602

- Peptide Label:

isoform X7

- Sequence:

show sequence

MAGGDGMLRRLLRLHRTEIAVAIDSAFPLLHALADHDVVPEDKFQETLRLKEKEGCPQAFHALL
SWLLTRDSGAILDFWRVLFKDYNLERYSRLHTILDGFPKDVDLSQPRKGRKPLAGPKASVVPPR
PPTKRRALEEPRATPPATLASKSISSPGSHSKAKPPKKPEGNLESQRLPLGNGIQTMAASVQRA
VTVSSGDVPGSRGAVEGILIQQVFESGGSKKCIQVGGEFYKPSKFEDPSGNLKNKTRGGSSLKP
VIRGKGTQGRDEQKVSQQCGVPPLPPLPNEPQVHQNEDECAVCHDGGELICCDGCPRAFHLACL
SPPLQEIPSGLWRCSCCLQGRIQQNLSQPEESRPLEPSAETPDQSPLQVLLGRTDSHARRARRG
CAHRCASHTWACQGRGRLC

hide 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)

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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)

ACI/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

ACI/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

BBDP/Wor (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

BN/SsN (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

Buf/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

COP/CrCrl (MCW & UW)

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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)

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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

F344/NRrrc (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

FHH/EurMcwi (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)

FHH/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

FHL/EurMcwi (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)

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_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

External Database Links

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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

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MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

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Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)