Tsc22d4 (TSC22 domain family, member 4)

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Gene: Tsc22d4 (TSC22 domain family, member 4) Rattus norvegicus

Analyze

Symbol:

Tsc22d4

Name:

TSC22 domain family, member 4

RGD ID:

1584380

Description:

Predicted to be involved in response to osmotic stress. Predicted to localize to cytoplasm and nucleus. Orthologous to human TSC22D4 (TSC22 domain family member 4); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

LOC102550456; MGC125073; similar to TSC22 domain family protein 4 (TSC22-related-inducible leucine zipper protein 2); thg-1pit; Tilz2; TSC22 domain family protein 4; TSC22 domain family protein 4-like; TSC22-related-inducible leucine zipper protein 2; uncharacterized protein C7orf61 homolog

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	12	18,939,150 - 18,952,008 (-)	NCBI
Rnor_6.0 Ensembl	12	22,009,011 - 22,021,851 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0 Ensembl	12	21,722,075 - 21,761,487 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	12	22,008,956 - 22,021,814 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	12	24,017,638 - 24,039,147 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	19,814,586 - 19,826,254 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	12	20,744,972 - 20,757,750 (-)	NCBI		Celera
Cytogenetic Map	12	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

pleomorphic xanthoastrocytoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

2,3',4,4',5-Pentachlorobiphenyl (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

4-hydroxyphenyl retinamide (ISO)

6-propyl-2-thiouracil (EXP)

acrolein (ISO)

alpha-pinene (ISO)

Aroclor 1254 (ISO)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

Benzo[ghi]perylene (ISO)

bisphenol A (EXP,ISO)

carbon nanotube (ISO)

clobetasol (ISO)

clofibrate (ISO)

doxorubicin (ISO)

flutamide (EXP)

folic acid (ISO)

genistein (EXP)

hydrogen peroxide (ISO)

isoprenaline (ISO)

N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal (ISO)

ozone (ISO)

paracetamol (ISO)

rotenone (EXP)

selenomethionine (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

trichloroethene (EXP)

triptonide (ISO)

urethane (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

regulation of transcription by RNA polymerase II (IEA)

response to osmotic stress (IBA,ISO)

Cellular Component

cytoplasm (ISO)

nucleus (ISO)

Molecular Function

protein binding (ISO)

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.	RGD automated data pipeline
3.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:15057822	PMID:17147695	PMID:19084601

Genomics

Comparative Map Data

Tsc22d4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	12	18,939,150 - 18,952,008 (-)	NCBI
Rnor_6.0 Ensembl	12	22,009,011 - 22,021,851 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0 Ensembl	12	21,722,075 - 21,761,487 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	12	22,008,956 - 22,021,814 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	12	24,017,638 - 24,039,147 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	19,814,586 - 19,826,254 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	12	20,744,972 - 20,757,750 (-)	NCBI		Celera
Cytogenetic Map	12	q12	NCBI

TSC22D4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	7	100,463,359 - 100,479,232 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	7	100,466,519 - 100,479,214 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	7	100,064,142 - 100,076,837 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	99,902,078 - 99,914,838 (-)	NCBI	NCBI36		hg18	NCBI36
Celera	7	94,793,941 - 94,806,701 (-)	NCBI
Cytogenetic Map	7	q22.1	NCBI
HuRef	7	94,697,543 - 94,710,215 (-)	NCBI		HuRef
CHM1_1	7	99,994,757 - 100,007,518 (-)	NCBI		CHM1_1
CRA_TCAGchr7v2	7	99,424,226 - 99,436,987 (-)	NCBI

Tsc22d4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	137,744,231 - 137,766,715 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	5	137,743,992 - 137,766,712 (+)	Ensembl
GRCm38	5	137,745,969 - 137,768,453 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	137,745,730 - 137,768,450 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	138,187,224 - 138,200,975 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	5	137,975,784 - 137,989,539 (+)	NCBI			mm8
Celera	5	134,732,531 - 134,746,249 (+)	NCBI		Celera
Cytogenetic Map	5	G2	NCBI

Tsc22d4
(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_004955573	415,826 - 429,105 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955573	414,984 - 425,480 (+)	NCBI	ChiLan1.0	ChiLan1.0

TSC22D4
(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	7	105,887,295 - 105,909,981 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	7	105,896,307 - 105,909,967 (-)	Ensembl	panpan1.1		panPan2
PanPan1.1 Ensembl	7	105,887,295 - 105,894,117 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	7	92,495,407 - 92,508,204 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

TSC22D4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	6	9,196,199 - 9,206,929 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	6	9,197,197 - 9,211,885 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	6	10,900,933 - 10,911,479 (+)	NCBI
ROS_Cfam_1.0	6	9,130,449 - 9,140,993 (+)	NCBI
UMICH_Zoey_3.1	6	8,982,924 - 8,993,466 (+)	NCBI
UNSW_CanFamBas_1.0	6	8,960,443 - 8,971,023 (+)	NCBI
UU_Cfam_GSD_1.0	6	9,142,821 - 9,153,385 (+)	NCBI

Tsc22d4
(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_024409344	133,486,985 - 133,497,302 (+)	NCBI
SpeTri2.0	NW_004936543	539,222 - 549,542 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LOC100514038
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	8,390,945 - 8,406,218 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	8,390,945 - 8,406,240 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	7,734,046 - 7,750,006 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

TSC22D4
(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	28	12,729,798 - 12,744,222 (+)	NCBI
ChlSab1.1 Ensembl	28	12,730,714 - 12,745,483 (+)	Ensembl

Tsc22d4
(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_004624740	16,582,726 - 16,598,477 (+)	NCBI

Position Markers

RH133351

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	12	21,748,808 - 21,749,009	NCBI	Rnor6.0
Rnor_6.0	12	22,009,162 - 22,009,363	NCBI	Rnor6.0
Rnor_5.0	12	24,026,448 - 24,026,649	UniSTS	Rnor5.0
Rnor_5.0	12	23,769,676 - 23,769,877	UniSTS	Rnor5.0
RGSC_v3.4	12	19,825,869 - 19,826,070	UniSTS	RGSC3.4
Celera	12	20,745,178 - 20,745,379	UniSTS
Cytogenetic Map	12	q12	UniSTS

RH142348

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	12	22,009,123 - 22,009,309	NCBI	Rnor6.0
Rnor_6.0	12	21,748,769 - 21,748,955	NCBI	Rnor6.0
Rnor_5.0	12	24,026,409 - 24,026,595	UniSTS	Rnor5.0
Rnor_5.0	12	23,769,637 - 23,769,823	UniSTS	Rnor5.0
RGSC_v3.4	12	19,825,923 - 19,826,109	UniSTS	RGSC3.4
Celera	12	20,745,139 - 20,745,325	UniSTS
RH 3.4 Map	12	263.8	UniSTS
Cytogenetic Map	12	q12	UniSTS

RH143037

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	12	22,016,325 - 22,016,582	NCBI	Rnor6.0
Rnor_6.0	12	21,755,971 - 21,756,228	NCBI	Rnor6.0
Rnor_5.0	12	24,033,611 - 24,033,868	UniSTS	Rnor5.0
Rnor_5.0	12	23,776,839 - 23,777,096	UniSTS	Rnor5.0
RGSC_v3.4	12	19,818,650 - 19,818,907	UniSTS	RGSC3.4
Celera	12	20,752,342 - 20,752,599	UniSTS
RH 3.4 Map	12	264.3	UniSTS
Cytogenetic Map	12	q12	UniSTS

RH136799

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	12	21,740,404 - 21,740,525	NCBI	Rnor6.0
Rnor_6.0	12	22,000,913 - 22,001,034	NCBI	Rnor6.0
Rnor_5.0	12	24,017,961 - 24,018,082	UniSTS	Rnor5.0
Rnor_5.0	12	23,761,272 - 23,761,393	UniSTS	Rnor5.0
RGSC_v3.4	12	19,834,353 - 19,834,474	UniSTS	RGSC3.4
Celera	12	20,736,866 - 20,736,987	UniSTS
RH 3.4 Map	12	268.1	UniSTS
Cytogenetic Map	12	q12	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
2312418	Kidm41	Kidney mass QTL 41	3.7	0.0001	kidney mass (VT:0002707)	single kidney wet weight to body weight ratio (CMO:0000622)	12	1	22650917	Rat
10450854	Stl34	Serum triglyceride level QTL 34	3.5	0.05	blood LDL triglyceride amount (VT:0010699)	blood lipoprotein triglyceride level (CMO:0002685)	12	1	22853017	Rat
10755457	Coatc14	Coat color QTL 14		0.01759	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	12	1	23035872	Rat
6893681	Bw109	Body weight QTL 109	2.3	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	12	1	23758197	Rat
1581516	Cm56	Cardiac mass QTL 56	4.2	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	12	1	30749723	Rat
1598855	Bp294	Blood pressure QTL 294	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	1	36919844	Rat
7387292	Kidm42	Kidney mass QTL 42	3.03	0.0004	kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	12	1	38334225	Rat
9590086	Insglur6	Insulin/glucose ratio QTL 6	18.97	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	12	150810	45150810	Rat
9590147	Scort7	Serum corticosterone level QTL 7	13.61	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	12	150810	45150810	Rat
7411545	Bw128	Body weight QTL 128	5.2	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	150810	45150810	Rat
7411586	Foco5	Food consumption QTL 5	5.4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
7411660	Foco28	Food consumption QTL 28	10.9	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
7411595	Foco9	Food consumption QTL 9	4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
8694179	Bw150	Body weight QTL 150	2.9	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	150810	45150810	Rat
2303575	Insul14	Insulin level QTL 14	4		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	12	492578	45492578	Rat
737979	Pia22	Pristane induced arthritis QTL 22	53.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	2475687	47475687	Rat
634351	Apr5	Acute phase response QTL 5	6.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	12	2513442	47513442	Rat
2302042	Pia38	Pristane induced arthritis QTL 38	3.5	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	2513442	47513442	Rat
634350	Apr4	Acute phase response QTL 4	6		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	4210051	49210051	Rat
1302792	Scl21	Serum cholesterol level QTL 21	3.8	0.0011	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	12	8954593	27911196	Rat
7411547	Bw129	Body weight QTL 129		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	9223626	52716770	Rat
7411588	Foco6	Food consumption QTL 6		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
7411597	Foco10	Food consumption QTL 10		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
7411641	Foco19	Food consumption QTL 19	27.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
8552918	Pigfal7	Plasma insulin-like growth factor 1 level QTL 7			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223626	52716770	Rat
8552964	Pigfal17	Plasma insulin-like growth factor 1 level QTL 17	3.5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223626	52716770	Rat
8552912	Pigfal6	Plasma insulin-like growth factor 1 level QTL 6	5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223630	52716770	Rat
10059594	Kidm46	Kidney mass QTL 46	3.79	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	12	9789834	52716770	Rat
2293086	Iddm30	Insulin dependent diabetes mellitus QTL 30	3.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	10175889	31975590	Rat
61331	Eau2	Experimental allergic uveoretinitis QTL 2		0.0005	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	12	10256890	31723732	Rat
1300157	Rf21	Renal function QTL 21	4.4		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	12	11764995	37522089	Rat
1331786	Kidm11	Kidney mass QTL 11	3.571		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	12	13127211	27285590	Rat
1331755	Bp219	Blood pressure QTL 219	3.041		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	13127211	31723688	Rat
1331761	Bp218	Blood pressure QTL 218	2.973		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	13127211	50320041	Rat
61404	Bw120	Body weight QTL 120	5.1		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	12	14419775	52716770	Rat
1549829	Scl48	Serum cholesterol level QTL 48	5		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	12	15021986	52716770	Rat
7204484	Bp358	Blood pressure QTL 358		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	15085585	22283507	Rat
61416	Pia4	Pristane induced arthritis QTL 4	8.4		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	12	15714609	35964508	Rat
61421	Cia12	Collagen induced arthritis QTL 12	4.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	15714609	41291738	Rat
2300186	Bmd59	Bone mineral density QTL 59	7.1	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	12	15908900	52716770	Rat
2293699	Bss49	Bone structure and strength QTL 49	5.61	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	12	15908900	52716770	Rat
61443	Btemp2	Thermal response to stress QTL 2	3.3	0.000094	body temperature trait (VT:0005535)	core body temperature (CMO:0001036)	12	17114770	23839390	Rat
631543	Bp83	Blood pressure QTL 83	5.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	17185580	44098244	Rat
2293684	Bmd26	Bone mineral density QTL 26	4.4	0.0002	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	12	17960865	38409001	Rat
1641928	Alcrsp5	Alcohol response QTL 5			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	12	18342477	52716770	Rat
2303569	Gluco44	Glucose level QTL 44	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	18342477	52716770	Rat
2302060	Pia37	Pristane induced arthritis QTL 37	6.1	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	18729043	52716770	Rat
1549902	Bp269	Blood pressure QTL 269			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	18752593	52716770	Rat
1549912	Bp268	Blood pressure QTL 268			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	18752593	52716770	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	84
Count of miRNA genes:	63
Interacting mature miRNAs:	74
Transcripts:	ENSRNOT00000059592
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

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001044284	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC107410	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC105911	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473973	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FM034641	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FM049873	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ214513	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ230841	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000227	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000001869 ⟹ ENSRNOP00000001869

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	12	21,740,057 - 21,746,236 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000039280 ⟹ ENSRNOP00000033658

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	12	22,009,011 - 22,021,851 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000059592 ⟹ ENSRNOP00000056350

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	12	21,748,633 - 21,760,292 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000082910 ⟹ ENSRNOP00000071995

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	12	21,722,075 - 21,761,487 (-)	Ensembl

RefSeq Acc Id:

NM_001044284 ⟹ NP_001037749

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	18,939,150 - 18,952,008 (-)	NCBI
Rnor_6.0	12	22,008,956 - 22,021,814 (-)	NCBI
Rnor_5.0	12	24,017,638 - 24,039,147 (-)	NCBI
RGSC_v3.4	12	19,814,586 - 19,826,254 (+)	RGD
Celera	12	20,744,972 - 20,757,750 (-)	NCBI

Sequence:

show sequence

GAGCAGGCCCGAGAAGGCAGGACTTCCTGGTGTGGGGGTTGTCAACAGCCCAGAAAGAGAGAGC
CCGAGACCCAGACTGAGACGGAGCGGAGCGGAGCTGAGGAGCCGAGAGATACATCCAGTGGGGC
CACGTGGGAGGAGCCTTGAGAGAGAGCGAGCCACTCAAGGGACTGGAGTCAGCGGGGGGCTGAG
CCGCCCCCTCCCACAGCAACAGAGAAGACCCGTGGAGTGTTAACGGAGGCTGCGCCTGGGCTCC
ACCGTGGAAGCGCTGGTTTCTTCTCGTCTCAACTGCAAACTTTCCACCGAGATGCCTCGCAGAG
TGAGATGCGGACGCCAGAGAACACTGGGCAGCCCTTGACTGCTGCCTGCCGTGGCCTGCGCTAG
GCCGCCTTAGGATTAAAAAAAAAAAAAAAAAAAAAGGCATCTTTAGTCCCCAGGTCCTCTCTCC
AGCTCAGCTCGGTGGCCGAGGCCCGAGAGTTTGCAAGCTCAGCTCTGGGGTTTCAGCAGCGACA
GCAGCAGGAAAAACCTGCCTCTGCTCCCCCCCCCCCCCCTCCTGCCACCTCCCCTCTCCAGTCA
CTAACCAGGCACCCCCAAGTTCCCACAAGGCCCTCCTGCCATGACGGACCCAGACGTCCCCAGG
GGCCCTGATGTCCCTGCCATGTGGCCCCCTTGTTCCAGAGGTGCCTGAGCCCCTCTTCAGGAGC
CCAGCCCCTCCCCCACCCCAGCCCAGTCCGGAGCCCTAGGGACCATGAGTGGTGGTAAGAAGAA
AAGTAGTTTTCAGATCACCAGCGTCACCACGGACTATGAGGGCCCAGGAAGCCCAGGGGCTTCG
GACCCCCCTGCCCCTCCGGCTCCCGCTGGGCCCCCGCCCCGCCTCCCCAACGGGGAACCCAACC
CTGATCCAGGGGGCAGGGGCACCCCCCGGAATGGCTCTCCGCCACCTGGAGCCCCTGCCTCCCG
TTTCCGGGTGGTGAAGCTGCCCCAAGGTTTAGGAGAGCCTTATCGACGAGGTCGGTGGACGTGT
GTGGATGTTTACGAGAGAGACCTGGAGCCCCCGAGCTTCGGTCGGCTTCTGGAGGGAATTCGAG
GGGCCTCAGGAGGCACCGGAGGCAGATCATTGGATTCTAGGTTGGAGCTGGCTAGCTTGGGCAT
AAGCACCCCTATCCCTCAGCCAGGCCTGTCTCAGGGCCCCACCTCTTGGCTCCGCCCGCCCCCT
ACTTCTCCTGGACCACAGGCTCGATCCTTCACAGGGGGGCTGGGCCAGCTGGCAGGACCTGGCA
AGGCTAAGGTGGAGACGCCCCCGCTGTCAGCCTCTCCACCCCAGCAGCGCCCCCCAGGGCCTGG
GACTGGAGATAGTGCTCAAACCCTGCCCTCCCTGAGGGTAGAAGTGGAGTCTGGGGGTTTAGCA
GCCGGAACCCCTCCTCTGTCACGGAGAAGAGATGGAGCAGTTCGGCTGAGGATGGAGTTAGTTG
CTCCAGAGGAGACAGGGAAGGTACCTCCCATCGACTCTCGCCCCAACTCCCCAGCCCTCTACTT
CGATGCCAGCCTGGTTCACAAGTCTCCAGACCCATTCGGAGCTGCAGCAGCCCAGAGCCTCAGC
CTGGCTCGGTCCATGTTGGCCATCAGCGGTCACCTGGACAGTGATGACGACAGTGGTTCCGGAA
GCCTGGTTGGCATTGACAACAAGATTGAACAAGCCATGGACTTGGTGAAGTCCCACCTCATGTT
TGCCGTGCGAGAGGAGGTGGAGGTGCTGAAGGAGCAGATCCGGGACCTGGCAGAGCGGAATGCT
GCACTGGAGCAGGAAAATGGATTGCTGCGTGCCCTGGCCAGCCCGGAGCAGCTGGCCCAGCTGC
CATCCTCGGGGCTCCCAAGGCTCGGGCCCTCTGCACCCAATGGGCCTTCCATCTGAGCCTTCTT
TCCCTCACAATGTGCCTTTGGGGGCTGCCACTGGCCGCCGGGCCTTGTGCCAGCAGCCTGCCCC
CTCTTCCTATGTAGCTTTAATGCCCACGCCCGACCCCAATGCCCAGGGATGGGAGTTGAGGCTA
AATATTGGCCTGTCCCTTCCCACCTGGTCTCCCCAGAAGCCTCAGGCCTTGCCGGAAGAGAAAG
AACCCAGGAGGGGATGTTTATCTGAAGCCCCTCATCCATGAAAGAACCCAGCCCCACCTCCTTC
CCTGGGAATCAGTGTTCTGGGGAGCCCCTCAGCAGCAGATGGCTCAGAAAGATTTGGAGGTTCC
CTGGCAGGCCCCCTCACCATCCCACCTTGTTCTCTTCAAGTGCCCCCTCTCCTCTGCCCAGGGA
GGGGGTATGGACAGTATCTTCAACTTCTTGGATTCAGGTTGTTATTAAAATAATAATTATAATT
AAAAAAAAATCTGAAGAAACTTGAATATGGA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001037749	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI05912	(Get FASTA)	NCBI Sequence Viewer
	EDM13242	(Get FASTA)	NCBI Sequence Viewer
	Q3B8N7	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001037749 ⟸ NM_001044284

- UniProtKB:

Q3B8N7 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MSGGKKKSSFQITSVTTDYEGPGSPGASDPPAPPAPAGPPPRLPNGEPNPDPGGRGTPRNGSPP
PGAPASRFRVVKLPQGLGEPYRRGRWTCVDVYERDLEPPSFGRLLEGIRGASGGTGGRSLDSRL
ELASLGISTPIPQPGLSQGPTSWLRPPPTSPGPQARSFTGGLGQLAGPGKAKVETPPLSASPPQ
QRPPGPGTGDSAQTLPSLRVEVESGGLAAGTPPLSRRRDGAVRLRMELVAPEETGKVPPIDSRP
NSPALYFDASLVHKSPDPFGAAAAQSLSLARSMLAISGHLDSDDDSGSGSLVGIDNKIEQAMDL
VKSHLMFAVREEVEVLKEQIRDLAERNAALEQENGLLRALASPEQLAQLPSSGLPRLGPSAPNG
PSI

hide sequence

RefSeq Acc Id:

ENSRNOP00000033658 ⟸ ENSRNOT00000039280

RefSeq Acc Id:

ENSRNOP00000056350 ⟸ ENSRNOT00000059592

RefSeq Acc Id:

ENSRNOP00000071995 ⟸ ENSRNOT00000082910

RefSeq Acc Id:

ENSRNOP00000001869 ⟸ ENSRNOT00000001869

Transcriptome

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

Promoters

RGD ID:

13698508

Promoter ID:

EPDNEW_R9033

Type:

multiple initiation site

Name:

Tsc22d4_2

Description:

TSC22 domain family, member 4

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Alternative Promoters:

null; see alsoEPDNEW_R9034

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	12	22,021,602 - 22,021,662	EPDNEW

RGD ID:

13698509

Promoter ID:

EPDNEW_R9034

Type:

initiation region

Name:

Tsc22d4_1

Description:

TSC22 domain family, member 4

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Alternative Promoters:

null; see alsoEPDNEW_R9033

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	12	22,021,763 - 22,021,823	EPDNEW

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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CSV

TAB

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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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TAB

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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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TAB

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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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CSV

TAB

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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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1584380	AgrOrtholog
	RGD:7605479	AgrOrtholog
Ensembl Genes	ENSRNOG00000024616	Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ENSRNOG00000050805	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000033658	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOP00000056350	UniProtKB/Swiss-Prot
	ENSRNOP00000071995	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000039280	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOT00000059592	UniProtKB/Swiss-Prot
	ENSRNOT00000082910	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7387593	IMAGE-MGC_LOAD
InterPro	DUF4703	UniProtKB/TrEMBL
	TSC-22_Dip_Bun	UniProtKB/Swiss-Prot
	TSC22D4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:102550456	UniProtKB/Swiss-Prot
	rno:684980	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:125073	IMAGE-MGC_LOAD
NCBI Gene	684980	ENTREZGENE
PANTHER	PTHR47610	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	DUF4703	UniProtKB/TrEMBL
	TSC22	UniProtKB/Swiss-Prot
PhenoGen	Tsc22d4	PhenoGen
PROSITE	TSC22	UniProtKB/Swiss-Prot
UniProt	A0A0G2K1V1_RAT	UniProtKB/TrEMBL
	Q3B8N7	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2021-03-09	Tsc22d4	TSC22 domain family, member 4	LOC102550456	TSC22 domain family protein 4-like	Data Merged	737654	PROVISIONAL
2013-12-18	LOC102550456	TSC22 domain family protein 4-like			Symbol and Name status set to provisional	70820	PROVISIONAL
2008-07-08	Tsc22d4	TSC22 domain family, member 4	LOC686226	similar to TSC22 domain family protein 4 (TSC22-related-inducible leucine zipper protein 2)	Data Merged	1643240	APPROVED
2008-03-06	Tsc22d4	TSC22 domain family, member 4	MGC125073	similar to TSC22 domain family protein 4 (TSC22-related-inducible leucine zipper protein 2)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-11-19	MGC125073	similar to TSC22 domain family protein 4 (TSC22-related-inducible leucine zipper protein 2)			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-11-19	LOC686226	similar to TSC22 domain family protein 4 (TSC22-related-inducible leucine zipper protein 2)			Symbol and Name status set to provisional	70820	PROVISIONAL

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)

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

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Imported Disease Annotations - ClinVar