Tlx1 (T-cell leukemia, homeobox 1)

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Gene: Tlx1 (T-cell leukemia, homeobox 1) Rattus norvegicus

Analyze

Symbol:

Tlx1

Name:

T-cell leukemia, homeobox 1

RGD ID:

1563655

Description:

Predicted to have DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including nervous system development; positive regulation of transcription by RNA polymerase II; and spleen development. Predicted to localize to nucleus. Human ortholog(s) of this gene implicated in adult T-cell leukemia. Orthologous to human TLX1 (T cell leukemia homeobox 1); INTERACTS WITH 17beta-estradiol; bisphenol A; progesterone.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC499361; RGD1563655; similar to transcription factor; T-cell leukemia homeobox protein 1

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):	TLX1 (T cell leukemia homeobox 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Tlx1 (T cell leukemia, homeobox 1)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Tlx1 (T cell leukemia homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	TLX1 (T cell leukemia homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	TLX1 (T cell leukemia homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Tlx1 (T cell leukemia homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	TLX1 (T cell leukemia homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	TLX1 (T cell leukemia homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Tlx1 (T cell leukemia homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	TLX1 (T cell leukemia homeobox 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Tlx1 (T cell leukemia, homeobox 1)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	tlx1 (T cell leukemia homeobox 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	C15	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

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	1	244,005,057 - 244,011,318 (+)	NCBI
Rnor_6.0 Ensembl	1	264,893,162 - 264,899,423 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	264,893,033 - 264,899,424 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	272,335,445 - 272,341,792 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	250,255,343 - 250,261,604 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	1	239,816,138 - 239,822,399 (+)	NCBI		Celera
Cytogenetic Map	1	q54	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

adult T-cell leukemia (ISO)

Aneuploidy (ISO)

Neoplastic Cell Transformation (ISO)

splenic disease (ISO)

split hand-foot malformation (ISO)

T-cell acute lymphoblastic leukemia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17beta-estradiol (EXP)

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

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (ISO)

benzo[a]pyrene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

choline (ISO)

folic acid (ISO)

genistein (ISO)

L-methionine (ISO)

lead diacetate (ISO)

N-Nitrosopyrrolidine (ISO)

O-methyleugenol (ISO)

progesterone (EXP)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

animal organ development (IBA)

animal organ formation (ISO)

biological_process (ND)

cell fate commitment (ISO)

central nervous system development (ISO)

neuron differentiation (ISO)

positive regulation of cell population proliferation (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of transcription by RNA polymerase II (IBA)

spleen development (ISO)

Cellular Component

cellular_component (ND)

nucleus (IBA)

Molecular Function

DNA-binding transcription activator activity, RNA polymerase II-specific (IEA,ISO)

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA)

molecular_function (ND)

protein binding (ISO)

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

References

References - curated


1.	Dube ID, etal., Blood. 1991 Dec 1;78(11):2996-3003.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	OMIM Disease Annotation Pipeline
4.	RGD automated data pipeline
5.	RGD automated import pipeline for gene-chemical interactions
6.	RGD comprehensive gene curation

Additional References at PubMed

PMID:11356032	PMID:12023301	PMID:15944191

Genomics

Comparative Map Data

Tlx1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	244,005,057 - 244,011,318 (+)	NCBI
Rnor_6.0 Ensembl	1	264,893,162 - 264,899,423 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	264,893,033 - 264,899,424 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	272,335,445 - 272,341,792 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	250,255,343 - 250,261,604 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	1	239,816,138 - 239,822,399 (+)	NCBI		Celera
Cytogenetic Map	1	q54	NCBI

TLX1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	10	101,131,300 - 101,137,789 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	10	101,130,773 - 101,137,789 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	10	102,891,057 - 102,897,546 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	10	102,891,061 - 102,897,546 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	10	102,880,252 - 102,887,536 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	10	102,880,251 - 102,887,526	NCBI
Celera	10	96,628,773 - 96,635,241 (+)	NCBI
Cytogenetic Map	10	q24.31	NCBI
HuRef	10	96,520,316 - 96,526,784 (+)	NCBI		HuRef
CHM1_1	10	103,175,307 - 103,181,792 (+)	NCBI		CHM1_1

Tlx1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	45,138,531 - 45,145,382 (+)	NCBI	GRCm39		mm39
GRCm38	19	45,150,092 - 45,156,943 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	45,150,680 - 45,156,943 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	19	45,225,205 - 45,231,433 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	19	45,204,026 - 45,210,254 (+)	NCBI			mm8
Celera	19	45,915,431 - 45,921,662 (+)	NCBI		Celera
Cytogenetic Map	19	C3	NCBI
cM Map	19	38.45	NCBI

Tlx1
(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	NW_004955485	9,070,601 - 9,076,063 (-)	NCBI	ChiLan1.0	ChiLan1.0

TLX1
(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	10	101,207,374 - 101,214,625 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	10	101,207,374 - 101,214,625 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	10	97,731,715 - 97,738,978 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

TLX1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	28	13,807,720 - 13,813,849 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	28	13,807,428 - 13,813,875 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Tlx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936600	4,564,246 - 4,569,774 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TLX1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	112,207,360 - 112,213,955 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	112,206,964 - 112,213,957 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	121,950,524 - 121,953,763 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

TLX1
(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	9	94,147,410 - 94,155,388 (+)	NCBI
ChlSab1.1 Ensembl	9	94,149,126 - 94,154,520 (+)	Ensembl

Tlx1
(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_004624831	710,787 - 717,367 (+)	NCBI

Position Markers

Tlx1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	264,898,574 - 264,899,306	NCBI	Rnor6.0
Rnor_5.0	1	272,340,942 - 272,341,674	UniSTS	Rnor5.0
Celera	1	239,821,550 - 239,822,282	UniSTS
Cytogenetic Map	1	q54	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
70211	Niddm24	Non-insulin dependent diabetes mellitus QTL 24	3.79		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	236795785	281795785	Rat
631215	Stl8	Serum triglyceride level QTL 8	9.27	0.0001	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	1	245529606	282763074	Rat
2302040	Pia35	Pristane induced arthritis QTL 35	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	236265430	281265430	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	156446196	274977688	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	161321152	273792054	Rat
724533	Rf51	Renal function QTL 51	5.3	0.0002	kidney plasma flow trait (VT:0005524)	renal plasma flow (CMO:0001914)	1	238830534	278228767	Rat
724538	Kidm1	Kidney mass QTL 1	3.2		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	233663100	273792054	Rat
724552	Glom2	Glomerulus QTL 2	3.3	0.0001	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)	1	243272341	282763074	Rat
734767	Niddm57	Non-insulin dependent diabetes mellitus QTL 57			body mass (VT:0001259)	body weight (CMO:0000012)	1	244401175	282365384	Rat
734768	Niddm59	Non-insulin dependent diabetes mellitus QTL 59			body mass (VT:0001259)	body weight (CMO:0000012)	1	235850810	280850810	Rat
734769	Niddm58	Non-insulin dependent diabetes mellitus QTL 58			body mass (VT:0001259)	body weight (CMO:0000012)	1	244992467	282365384	Rat
631669	Iddm9	Insulin dependent diabetes mellitus QTL 9	2.8	0.039	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	252955158	280632620	Rat
631690	Scl5	Serum cholesterol level QTL 5	2.1		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	258132568	282763074	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	167394665	278228889	Rat
1581544	Rf52	Renal function QTL 52		0.05	total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	1	252948438	281795785	Rat
731175	Uae20	Urinary albumin excretion QTL 20	3.5	0.0018	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	241482188	281795785	Rat
738032	Hcas5	Hepatocarcinoma susceptibility QTL 5	3.12		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	191825895	279986079	Rat
631536	Lnnr2	Liver neoplastic nodule remodeling QTL 2	2.9	0.0005	liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)	1	255728828	282763074	Rat
1598821	Rf55	Renal function QTL 55	6.3		renal blood flow trait (VT:2000006)	ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)	1	238824734	279986079	Rat
2300175	Bmd40	Bone mineral density QTL 40	15.4	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	1	221901238	266901238	Rat
2293655	Bss36	Bone structure and strength QTL 36	10.66	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	1	221901238	266901238	Rat
2293674	Bss39	Bone structure and strength QTL 39	7.1	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	1	221901238	266901238	Rat
2293694	Bss38	Bone structure and strength QTL 38	7.05	0.0001	femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	1	221901238	266901238	Rat
631836	Stl31	Serum triglyceride level QTL 31	4.64	0.00000487	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	1	259295704	282763074	Rat
631837	Niddm35	Non-insulin dependent diabetes mellitus QTL 35		0.01	blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	258709726	281795785	Rat
631843	Bw116	Body weight QTL 116	4.1	0.016	abdominal adipose amount (VT:1000220)	abdominal fat pad weight (CMO:0000088)	1	244401175	282365384	Rat
634313	Niddm43	Non-insulin dependent diabetes mellitus QTL 43			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	217054291	281795785	Rat
1357399	Bw45	Body weight QTL 45	3.05		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	1	225689973	270689973	Rat
1357404	Bw42	Body weight QTL 42	4.49	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	1	225689973	270689973	Rat
1600363	Hc6	Hypercalciuria QTL 6	2.7		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	195598053	265002735	Rat
1600388	Niddm67	Non-insulin dependent diabetes mellitus QTL 67	5.84	0.000004	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	213476630	278978026	Rat
1600392	Bw123	Body weight QTL 123		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	244087148	282763074	Rat
1600395	Niddm69	Non-insulin dependent diabetes mellitus QTL 69	4.14	0.0002	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	213476630	278978026	Rat
1600396	Niddm68	Non-insulin dependent diabetes mellitus QTL 68	4.97	0.0003	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	213476630	278978026	Rat
1600397	Edcs4	Endometrial carcinoma susceptibility QTL 4	2.2		uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	1	226706329	271706329	Rat
1578759	Uae30	Urinary albumin excretion QTL 30	3.3	0.003	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	161321256	273791893	Rat
1578763	Kidm29	Kidney mass QTL 29	3.3	0.0001	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	1	196395041	282763074	Rat
1578778	Pur4	Proteinuria QTL 4	3.3	0.003	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	1	161321256	273791893	Rat
1300108	Rf8	Renal function QTL 8	3.75		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	1	249206242	281795785	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1354624	Cm35	Cardiac mass QTL35	5.7		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	192639698	278228889	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	161784169	278228889	Rat
1354652	Kidm20	Kidney mass QTL 20	4.3		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	192639698	278228889	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1549910	Bw54	Body weight QTL 54		0.05	body mass (VT:0001259)	body weight (CMO:0000012)	1	236795785	281795785	Rat
2316896	Gluco57	Glucose level QTL 57	7.2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	249607907	266793958	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	163796316	282763074	Rat
1358890	Bp259	Blood pressure QTL 259	3.06		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	230420627	282645769	Rat
1358898	Bp255	Blood pressure QTL 255	3.6		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	208517798	266948272	Rat
61327	Eae7	Experimental allergic encephalomyelitis QTL 7	5.6		body mass (VT:0001259)	change in body weight (CMO:0002045)	1	236265430	281265430	Rat
61400	Niddm1	Non-insulin dependent diabetes mellitus QTL 1	11		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	238830408	266793958	Rat
7394701	Uae46	Urinary albumin excretion QTL 46	3.6	0.0056	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	221901238	266901238	Rat
7387289	Uae45	Urinary albumin excretion QTL 45	2.86	0.0021	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	244148899	282763074	Rat
10053715	Scort24	Serum corticosterone level QTL 24	2.13	0.0088	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	1	242302911	282763074	Rat
10059587	Bw173	Body weight QTL 173	3.23	0.025	body mass (VT:0001259)	body weight (CMO:0000012)	1	222492538	267492538	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	66
Count of miRNA genes:	55
Interacting mature miRNAs:	60
Transcripts:	ENSRNOT00000021714
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	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium					11
Low		19							7		9
Below cutoff	2	24	12	4	7	4	1	1	29	8	20	1	1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001109166	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC105485	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473986	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000054	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000021714 ⟹ ENSRNOP00000021714

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	264,893,162 - 264,899,423 (+)	Ensembl

RefSeq Acc Id:

NM_001109166 ⟹ NP_001102636

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	244,005,057 - 244,011,318 (+)	NCBI
Rnor_6.0	1	264,893,162 - 264,899,423 (+)	NCBI
Rnor_5.0	1	272,335,445 - 272,341,792 (+)	NCBI
RGSC_v3.4	1	250,255,343 - 250,261,604 (+)	RGD
Celera	1	239,816,138 - 239,822,399 (+)	RGD

Sequence:

show sequence

GGAAGGAGAAGCCGGAGAGGGGAAGAATACAGCTCTCCCTCTCTCCTCCCCCTCCCCCCTACTT
TGGCCCTTCTGCGCACTTCGCCTTCAAGTCTCACCGCAGCCTGGAGCGGCGATTGCCTCCGCGC
CCCTACTCGCTGCCCGGGTAGTCCAGCGCAGCGAGCGCCCGCGCCCGGGCCCCCGCGTGGGGCC
GGGGCCAGCATGGAGCACCTGGGTCCGCACCATCTCCACCCGGGCCACGCGGAGCCCATCAGCT
TCGGCATCGACCAGATCCTCAACAGCCCGGACCAGGGCGGCTGCATGGGGCCCGCCTCGCGCCT
CCAGGACGGAGAATACGGCCTTGGCTGTTTGGTCGGAGGCGCCTACACTTATGGCGGAGGGGGT
TCCGCCGCTGGAGCGGGGGCCGGGGGCACAGGCGCTTACGGCACCGGTGGCCCGGGTGGTCCCG
GAGGCCCGGCGGGCGGTGGCGGAGGTGCCTGCAGCATGGGCCCACTGGCCGGCTCCTACAACGT
GAACATGGCCTTGGCGGGCGGCCCGGGTCCGGGAGGCGGCGGCGGTGGCGCGGGTGCCGGTGGC
GCCGGTGCGCTGAGCGCTGCAGGGGTGATCCGGGTGCCCGCGCACAGGCCGCTAGCTGGAGCTG
TGGCCCATCCCCAGCCCCTGGCCACCGGCTTGCCTACTGTGCCCTCTGTGCCTGCGGTGCCGGG
TGTCAACAACCTCACCGGCCTCACCTTCCCCTGGATGGAGAGTAACCGCAGATACACAAAGGAC
AGGTTCACAGGTCACCCCTATCAGAACCGGACGCCCCCTAAGAAGAAGAAGCCGCGTACATCCT
TCACACGCCTGCAGATCTGTGAGCTGGAAAAGCGCTTCCACCGCCAGAAGTACTTGGCTTCGGC
GGAGCGCGCTGCTCTGGCCAAAGCGCTCAAAATGACCGATGCGCAAGTCAAAACCTGGTTCCAG
AACAGGAGGACGAAATGGAGGCGACAGACAGCAGAGGAGCGTGAGGCCGAGAGGCAGCAGGCGA
ACCGCATCCTCTTGCAGCTGCAGCAGGAGGCCTTCCAGAAGAGCCTGGCCCAGCCGCTGCCTGC
AGACCCACTGTGCGTGCACAACTCGTCGCTCTTTGCCCTGCAGAACCTGCAGCCGTGGTCTGAC
GACTCCACCAAAATCACTAGCGTCACGTCCGTGGCTTCGGCCTGTGAGTGAGGACCCAAGCCCA
ATTGAGGGCTATCCGGAGAACCAGAACTCTCGATACCTTTTCTGAGTGCACGCAGGAAGGGAAC
GGGCTTCTCAGCAAGGCTCCCAGCACCGCCTCACACCCCTGAGGACACTGTCCGGTCTTCGGTG
GAAGAGGGTGGAGATAGAGGCAGAAGCCTGCGTGATCCTGTCTCACTCTGGAACTGTTCAGAAT
CTCCTCTTTTTCTCTATTTCATAAAATTTACTCTGATTTTAACATGGGACAGAGAGACCCAAGG
GATGTAGGGTCCTGAAGGCTTCTGGGATCCCCAGGCAGCCATCCGTACTAAGGCTGGAAACCTC
TCTATTCCTTTCCTCCTACATCCACACAGAGGTGATACCACTGTCCCTCCTGGCGTCACCTTAG
AGCCACATGCAGGGGCCGATGGCAGAGCATCACAGCACATACAGGATCACAACAAATGACCCTT
GCCGTTGGGCACAGTCTAGGGTGACACTTGGACTCGCCCAAACAGCACGGACCTCCTCTTACTC
GAACACAAGGCCATAGTCACATAGTGACACACCAGCCCACACACAACAGCTAAACCTGGCCTGT
CAGGTCCCTCGCCACACATCCCAGCGGCACCCAGGTATGCACAGACAGGCTTTCACACAAATGC
AGCCCATTTCTCCAGATCCTGTTTGGGGAGGGGGGTAAGTTATGCACTTATAAGTTATGCACTT
ATAAGGTGTTTTCTGTGTAACCATTTTATAAAGTGCTTGTGTAATTTATGTGGAAAAATAATAA
AACCCTCCCGATCAGG

hide sequence

RefSeq Acc Id:

XM_006231554 ⟹ XP_006231616

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	264,893,033 - 264,899,424 (+)	NCBI
Rnor_5.0	1	272,335,445 - 272,341,792 (+)	NCBI

Sequence:

show sequence

TTCACCCCGCTCCTCTCCACGCACAGCCAATGGAGAGACCCGGCCGAAACAGCTAGGCTCGCTC
GCTCAGGGCTTTTTCGCCCGGTGATTGATGTCCCAGAGTCAACAGCGAGCGAGCAGCCGGAGAA
GGGAAGGAGAAGCCGGAGAGGGGAAGAATACAGCTCTCCCTCTCTCCTCCCCCTCCCCCCTACT
TTGGCCCTTCTGCGCACTTCGCCTTCAAGTCTCACCGCAGCCTGGAGCGGCGATTGCCTCCGCG
CCCCTACTCGCTGCCCGGGTAGTCCAGCGCAGCGAGCGCCCGCGCCCGGGCCCCCGCGTGGGGC
CGGGGCCAGCATGGAGCACCTGGGTCCGCACCATCTCCACCCGGGCCACGCGGAGCCCATCAGC
TTCGGCATCGACCAGATCCTCAACAGCCCGGACCAGGGCGGCTGCATGGGGCCCGCCTCGCGCC
TCCAGGACGGAGAATACGGCCTTGGCTGTTTGGTCGGAGGCGCCTACACTTATGGCGGAGGGGG
TTCCGCCGCTGGAGCGGGGGCCGGGGGCACAGGCGCTTACGGCACCGGTGGCCCGGGTGGTCCC
GGAGGCCCGGCGGGCGGTGGCGGAGGTGCCTGCAGCATGGGCCCACTGGCCGGCTCCTACAACG
TGAACATGGCCTTGGCGGGCGGCCCGGGTCCGGGAGGCGGCGGCGGTGGCGCGGGTGCCGGTGG
CGCCGGTGCGCTGAGCGCTGCAGGGGTGATCCGGGTGCCCGCGCACAGGCCGCTAGCTGGAGCT
GTGGCCCATCCCCAGCCCCTGGCCACCGGCTTGCCTACTGTGCCCTCTGTGCCTGCGGTGCCGG
GTGTCAACAACCTCACCGGCCTCACCTTCCCCTGGATGGAGAGTAACCGCAGATACACAAAGGA
CAGGTTCACAGTGGCCCTCTCACCCTTCACTGTAACACGCCGTATAGGTCACCCCTATCAGAAC
CGGACGCCCCCTAAGAAGAAGAAGCCGCGTACATCCTTCACACGCCTGCAGATCTGTGAGCTGG
AAAAGCGCTTCCACCGCCAGAAGTACTTGGCTTCGGCGGAGCGCGCTGCTCTGGCCAAAGCGCT
CAAAATGACCGATGCGCAAGTCAAAACCTGGTTCCAGAACAGGAGGACGAAATGGAGGCGACAG
ACAGCAGAGGAGCGTGAGGCCGAGAGGCAGCAGGCGAACCGCATCCTCTTGCAGCTGCAGCAGG
AGGCCTTCCAGAAGAGCCTGGCCCAGCCGCTGCCTGCAGACCCACTGTGCGTGCACAACTCGTC
GCTCTTTGCCCTGCAGAACCTGCAGCCGTGGTCTGACGACTCCACCAAAATCACTAGCGTCACG
TCCGTGGCTTCGGCCTGTGAGTGAGGACCCAAGCCCAATTGAGGGCTATCCGGAGAACCAGAAC
TCTCGATACCTTTTCTGAGTGCACGCAGGAAGGGAACGGGCTTCTCAGCAAGGCTCCCAGCACC
GCCTCACACCCCTGAGGACACTGTCCGGTCTTCGGTGGAAGAGGGTGGAGATAGAGGCAGAAGC
CTGCGTGATCCTGTCTCACTCTGGAACTGTTCAGAATCTCCTCTTTTTCTCTATTTCATAAAAT
TTACTCTGATTTTAACATGGGACAGAGAGACCCAAGGGATGTAGGGTCCTGAAGGCTTCTGGGA
TCCCCAGGCAGCCATCCGTACTAAGGCTGGAAACCTCTCTATTCCTTTCCTCCTACATCCACAC
AGAGGTGATACCACTGTCCCTCCTGGCGTCACCTTAGAGCCACATGCAGGGGCCGATGGCAGAG
CATCACAGCACATACAGGATCACAACAAATGACCCTTGCCGTTGGGCACAGTCTAGGGTGACAC
TTGGACTCGCCCAAACAGCACGGACCTCCTCTTACTCGAACACAAGGCCATAGTCACATAGTGA
CACACCAGCCCACACACAACAGCTAAACCTGGCCTGTCAGGTCCCTCGCCACACATCCCAGCGG
CACCCAGGTATGCACAGACAGGCTTTCACACAAATGCAGCCCATTTCTCCAGATCCTGTTTGGG
GAGGGGGGTAAGTTATGCACTTATAAGTTATGCACTTATAAGGTGTTTTCTGTGTAACCATTTT
ATAAAGTGCTTGTGTAATTTATGTGGAAAAATAATAAAACCCTCCCGATCAGGA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001102636	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL94303	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001102636 ⟸ NM_001109166

- UniProtKB:

D4A270 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MEHLGPHHLHPGHAEPISFGIDQILNSPDQGGCMGPASRLQDGEYGLGCLVGGAYTYGGGGSAA
GAGAGGTGAYGTGGPGGPGGPAGGGGGACSMGPLAGSYNVNMALAGGPGPGGGGGGAGAGGAGA
LSAAGVIRVPAHRPLAGAVAHPQPLATGLPTVPSVPAVPGVNNLTGLTFPWMESNRRYTKDRFT
GHPYQNRTPPKKKKPRTSFTRLQICELEKRFHRQKYLASAERAALAKALKMTDAQVKTWFQNRR
TKWRRQTAEEREAERQQANRILLQLQQEAFQKSLAQPLPADPLCVHNSSLFALQNLQPWSDDST
KITSVTSVASACE

hide sequence

RefSeq Acc Id:

XP_006231616 ⟸ XM_006231554

- Peptide Label:

isoform X1

- Sequence:

show sequence

MEHLGPHHLHPGHAEPISFGIDQILNSPDQGGCMGPASRLQDGEYGLGCLVGGAYTYGGGGSAA
GAGAGGTGAYGTGGPGGPGGPAGGGGGACSMGPLAGSYNVNMALAGGPGPGGGGGGAGAGGAGA
LSAAGVIRVPAHRPLAGAVAHPQPLATGLPTVPSVPAVPGVNNLTGLTFPWMESNRRYTKDRFT
VALSPFTVTRRIGHPYQNRTPPKKKKPRTSFTRLQICELEKRFHRQKYLASAERAALAKALKMT
DAQVKTWFQNRRTKWRRQTAEEREAERQQANRILLQLQQEAFQKSLAQPLPADPLCVHNSSLFA
LQNLQPWSDDSTKITSVTSVASACE

hide sequence

RefSeq Acc Id:

ENSRNOP00000021714 ⟸ ENSRNOT00000021714

Protein Domains

Homeobox

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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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

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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CSV

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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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CSV

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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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CSV

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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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CSV

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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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CSV

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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

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
1	272335821	272335822	G	A	snv	DOB/Oda (KyushuU)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1563655	AgrOrtholog
Ensembl Genes	ENSRNOG00000016120	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000021714	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000021714	ENTREZGENE, UniProtKB/TrEMBL
InterPro	Homeobox	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_region	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
	TLX1/2/3	UniProtKB/TrEMBL
KEGG Report	rno:499361	UniProtKB/TrEMBL
NCBI Gene	499361	ENTREZGENE
PANTHER	PTHR45921	UniProtKB/TrEMBL
Pfam	Homeobox	UniProtKB/TrEMBL
PhenoGen	Tlx1	PhenoGen
PRINTS	HOMEOBOX	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	Homeodomain_like	UniProtKB/TrEMBL
UniProt	D4A270	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-04	Tlx1	T-cell leukemia, homeobox 1	Tlx1_predicted	T-cell leukemia homeobox protein 1 (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2007-02-05	Tlx1_predicted	T-cell leukemia homeobox protein 1 (predicted)	RGD1563655_predicted	similar to transcription factor (predicted)	Symbol and Name updated to reflect Human and Mouse nomenclature	1299863	PROVISIONAL
2006-03-07	RGD1563655_predicted	similar to transcription factor (predicted)	LOC499361	similar to transcription factor	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC499361	similar to transcription factor			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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD