Tnfsf13 (TNF superfamily member 13)

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Gene: Tnfsf13 (TNF superfamily member 13) Rattus norvegicus

Analyze

Symbol:

Tnfsf13

Name:

TNF superfamily member 13

RGD ID:

1305871

Description:

Predicted to have signaling receptor binding activity. Predicted to be involved in immunoglobulin production in mucosal tissue; positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains; and positive regulation of cell population proliferation. Predicted to localize to cytoplasm; external side of plasma membrane; and extracellular space. Human ortholog(s) of this gene implicated in B-lymphoblastic leukemia/lymphoma. Orthologous to human TNFSF13 (TNF superfamily member 13); PARTICIPATES IN adaptive immune response pathway; cytokine mediated signaling pathway; rheumatoid arthritis pathway; INTERACTS WITH (+)-pilocarpine; 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

April; LOC287437; MGC95053; Tnlg7b; tumor necrosis factor (ligand) superfamily, member 13; tumor necrosis factor ligand 7b; tumor necrosis factor ligand superfamily member 13; tumor necrosis factor superfamily member 13

RGD Orthologs

Human

Mouse

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
Rnor_6.0	10	56,286,964 - 56,290,680 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	56,286,887 - 56,289,952 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	56,032,602 - 56,036,336 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	56,499,945 - 56,502,928 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	56,513,568 - 56,516,551 (-)	NCBI
Celera	10	53,554,575 - 53,557,558 (-)	NCBI		Celera
Cytogenetic Map	10	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

B-Cell Chronic Lymphocytic Leukemia (ISO)

B-lymphoblastic leukemia/lymphoma (ISO)

Colorectal Neoplasms (ISO)

dyskeratosis congenita (ISO)

IgA glomerulonephritis (ISO)

Spontaneous Abortions (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-pilocarpine (EXP)

1,1-dichloroethene (ISO)

1-chloro-2,4-dinitrobenzene (ISO)

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

3,3',4,4',5-pentachlorobiphenyl (EXP)

3-chloropropane-1,2-diol (EXP)

3H-1,2-dithiole-3-thione (EXP)

4-(ethoxymethylene)-2-phenyloxazol-5-one (ISO)

5-aza-2'-deoxycytidine (ISO)

5-fluorouracil (ISO)

6-propyl-2-thiouracil (EXP)

acrylamide (EXP)

antirheumatic drug (ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

butanal (ISO)

cadmium atom (ISO)

calcitriol (ISO)

cetrorelix (ISO)

choline (ISO)

cisplatin (ISO)

cobalt dichloride (ISO)

decabromodiphenyl ether (EXP)

diarsenic trioxide (ISO)

diuron (EXP)

endosulfan (EXP)

folic acid (ISO)

furan (EXP)

furosemide (EXP)

glycidol (EXP)

isoflurane (EXP)

L-methionine (ISO)

lead(0) (ISO)

lead(2+) (ISO)

leflunomide (ISO)

lipopolysaccharide (ISO)

methapyrilene (EXP)

oxaliplatin (EXP)

p-menthan-3-ol (ISO)

paclitaxel (ISO)

paracetamol (ISO)

pentobarbital (EXP)

phenformin (EXP)

rotenone (EXP)

silicon dioxide (EXP,ISO)

Soman (EXP)

testosterone (ISO)

tetrachloromethane (ISO)

toluene 2,4-diisocyanate (ISO)

topotecan (EXP)

Tributyltin oxide (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

immunoglobulin mediated immune response (ISO)

positive regulation of cell population proliferation (ISO)

positive regulation of germinal center formation (ISO)

positive regulation of isotype switching to IgA isotypes (IBA,ISO)

regulation of immune response (ISO)

signal transduction (IEA)

Cellular Component

cellular_component (ND)

cytoplasm (ISO)

external side of plasma membrane (ISO)

extracellular space (IBA)

integral component of membrane (IEA)

plasma membrane (IBA)

Molecular Function

cytokine activity (IEA)

molecular_function (ND)

protein binding (ISO)

signaling receptor binding (IBA)

tumor necrosis factor receptor binding (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

adaptive immune response pathway (ISO)

cytokine mediated signaling pathway (IEA)

rheumatoid arthritis pathway (IEA)

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.	MGD data from the GO Consortium
4.	Pipeline to import KEGG annotations from KEGG into RGD
5.	Planelles L, etal., Cancer Cell 2004 Oct;6(4):399-408.
6.	RGD automated data pipeline
7.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8.	RGD automated import pipeline for gene-chemical interactions
9.	RGD comprehensive gene curation
10.	Yu G, etal., Nat Immunol 2000 Sep;1(3):252-6.

Additional References at PubMed

PMID:12477932	PMID:14729948	PMID:14988498	PMID:19199708	PMID:19828625	PMID:25466610	PMID:26646413

Genomics

Comparative Map Data

Tnfsf13
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	10	56,286,964 - 56,290,680 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	56,286,887 - 56,289,952 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	56,032,602 - 56,036,336 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	56,499,945 - 56,502,928 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	56,513,568 - 56,516,551 (-)	NCBI
Celera	10	53,554,575 - 53,557,558 (-)	NCBI		Celera
Cytogenetic Map	10	q24	NCBI

TNFSF13
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	17	7,558,292 - 7,561,608 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	17	7,558,282 - 7,561,601 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	17	7,461,609 - 7,464,925 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	7,402,340 - 7,405,642 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	17	7,402,339 - 7,405,641	NCBI
Celera	17	7,487,932 - 7,491,248 (+)	NCBI
Cytogenetic Map	17	p13.1	NCBI
HuRef	17	7,355,794 - 7,359,110 (+)	NCBI		HuRef
CHM1_1	17	7,470,571 - 7,473,887 (+)	NCBI		CHM1_1

Tnfsf13
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	69,573,403 - 69,576,380 (-)	NCBI	GRCm39		mm39
GRCm38	11	69,682,577 - 69,685,554 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	69,682,846 - 69,685,784 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	69,496,079 - 69,499,056 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	11	69,498,772 - 69,501,749 (-)	NCBI			mm8
MGSCv36	11	70,266,684 - 70,269,661 (-)	NCBI			mm8
Cytogenetic Map	11	B3	NCBI

TNFSF13
(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	17	7,576,518 - 7,579,834 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	7,576,465 - 7,579,834 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	17	7,589,931 - 7,593,527 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

TNFSF13
(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	5	32,482,723 - 32,484,789 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	5	32,482,723 - 32,484,790 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Tnfsf13
(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_004936595	839,877 - 842,962 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TNFSF13
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	52,853,665 - 52,857,033 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	52,853,646 - 52,857,033 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

LOC103242307
(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	16	6,935,073 - 6,938,792 (+)	NCBI
ChlSab1.1 Ensembl	16	6,926,584 - 6,938,019 (+)	Ensembl

Tnfsf13
(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_004624786	10,175,534 - 10,179,233 (+)	NCBI

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
631554	Bp133	Blood pressure QTL 133		0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	764421	66221621	Rat
2298544	Neuinf9	Neuroinflammation QTL 9	4.6		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	10	5877536	64401490	Rat
8662860	Vetf10	Vascular elastic tissue fragility QTL 10			artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	10	6229095	75983805	Rat
61427	Cia16	Collagen induced arthritis QTL 16	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	6429075	99492409	Rat
2303118	Mamtr7	Mammary tumor resistance QTL 7		0.003	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	9841807	108540162	Rat
9590310	Scort19	Serum corticosterone level QTL 19	6.3	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	12639513	57639513	Rat
9590268	Scort13	Serum corticosterone level QTL 13	3.26	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	12639513	57639513	Rat
9589136	Insul27	Insulin level QTL 27	10.46	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	10	12639513	57639513	Rat
2301967	Cm73	Cardiac mass QTL 73	4.55		heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	10	14827894	92423564	Rat
631268	Cia21	Collagen induced arthritis QTL 21	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	14827894	107857673	Rat
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14827894	110992275	Rat
1354587	Kidm21	Kidney mass QTL 21	3.3		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	10	15375474	62469074	Rat
631564	Apr3	Acute phase response QTL 3	3.9		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	10	16468736	61468736	Rat
6893350	Bw99	Body weight QTL 99	0.87	0.16	body mass (VT:0001259)	body weight (CMO:0000012)	1	17121542	62121542	Rat
6893352	Bw100	Body weight QTL 100	0.33	0.6	body mass (VT:0001259)	body weight (CMO:0000012)	1	17121542	62121542	Rat
1598852	Anxrr19	Anxiety related response QTL 19	5.07		body movement coordination trait (VT:0005424)	number of rearing movements in an experimental apparatus (CMO:0001752)	10	19402814	64402814	Rat
1554317	Bmd4	Bone mineral density QTL 4	9.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	20170031	102897474	Rat
70223	Bp57	Blood pressure QTL 57	5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	21523906	83549467	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	21523906	90312401	Rat
70198	BpQTLcluster9	Blood pressure QTL cluster 9	2.94		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	21523906	90312401	Rat
1581497	Esta1	Estrogen-induced thymic atrophy QTL 1			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	21707766	64648311	Rat
724556	Pur2	Proteinuria QTL 2	5.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	22901497	93886300	Rat
1331762	Rf40	Renal function QTL 40	3.873		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	10	23861015	66539843	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	23861015	112626471	Rat
631267	Cia20	Collagen induced arthritis QTL 20	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61325	Aia5	Adjuvant induced arthritis QTL 5		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61354	Pia10	Pristane induced arthritis QTL 10		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
70224	Eae3	Experimental allergic encephalomyelitis QTL 3	4.1		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	10	27237530	64648311	Rat
1298069	Bp168	Blood pressure QTL 168	5.5		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	10	27237530	101482600	Rat
631542	Bp82	Blood pressure QTL 82	6.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	27237530	102427718	Rat
2300171	Bmd58	Bone mineral density QTL 58	4.9	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	28789280	73789280	Rat
2292441	Bp308	Blood pressure QTL 308			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30099909	75099909	Rat
10402859	Bp381	Blood pressure QTL 381		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30099909	75099909	Rat
724527	Bp148	Blood pressure QTL 148		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30983805	75983805	Rat
1576311	Pia26	Pristane induced arthritis QTL 26			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	31919397	78343192	Rat
1578779	Tcas10	Tongue tumor susceptibility QTL 10	3.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	10	33179030	78179030	Rat
631557	Bp136	Blood pressure QTL 136		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	33343192	78343192	Rat
1576319	Cia29	Collagen induced arthritis QTL 29			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	35139424	80139424	Rat
6893342	Cm78	Cardiac mass QTL 78	0.1	0.88	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	10	36185929	82675365	Rat
631552	Vetf2	Vascular elastic tissue fragility QTL 2	4.5	0.0002	aorta elastic tissue integrity trait (VT:0010556)	artery internal elastic lamina non-tumorous lesion count (CMO:0001913)	10	36185929	95845311	Rat
1358897	Stresp6	Stress response QTL 6	4.17	0.022	blood norepinephrine amount (VT:0005663)	plasma norepinephrine level (CMO:0001010)	10	36584373	66539843	Rat
61441	Btemp1	Thermal response to stress QTL 1	4		body temperature trait (VT:0005535)	core body temperature (CMO:0001036)	10	36584560	66015527	Rat
2317042	Aia20	Adjuvant induced arthritis QTL 20	3.38		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	40514044	85514044	Rat
2317043	Aia7	Adjuvant induced arthritis QTL 7	3.82		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	40514044	85514044	Rat
1576308	Schws1	Schwannoma susceptibility QTL 1		0.0041	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	10	41260363	106105607	Rat
631269	Cia22	Collagen induced arthritis QTL 22	8.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	41260363	107857673	Rat
631270	Cia23	Collagen induced arthritis QTL 23	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	41260363	107857673	Rat
8552805	Bw145	Body weight QTL 145	2.2		body mass (VT:0001259)	change in body weight to body weight ratio (CMO:0002216)	10	43188659	81042642	Rat
1298078	Stresp5	Stress response QTL 5	2.99	0.00025	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	43289657	108540162	Rat
61463	Bp12	Blood pressure QTL 12	6.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	43704955	88704955	Rat
2300218	Hpcl2	Hepatic cholesterol level QTL 2			liver cholesterol amount (VT:0010498)	liver cholesterol level (CMO:0001597)	10	46593021	98939209	Rat
9589030	Epfw9	Epididymal fat weight QTL 9	19.24	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	10	46848346	91848346	Rat
7411614	Foco18	Food consumption QTL 18		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	10	46848346	91848346	Rat
8694173	Bw149	Body weight QTL 149	4.38	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	10	46848346	91848346	Rat
631547	Bp87	Blood pressure QTL 87	4.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	50638337	95638337	Rat
2293652	Bmd22	Bone mineral density QTL 22	4.9	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	10	51289203	84596393	Rat
2293669	Bmd33	Bone mineral density QTL 33	4.5	0.0001	femur strength trait (VT:0010010)	femoral neck polar moment of inertia (CMO:0001670)	10	51289203	84596393	Rat
2293679	Bmd30	Bone mineral density QTL 30	3.5	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	10	51289203	84596393	Rat
2293705	Bmd25	Bone mineral density QTL 25	7.1	0.0001	femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	10	51289203	84596393	Rat
7207811	Bmd90	Bone mineral density QTL 90	5.2		femur size trait (VT:1000369)	femoral neck cross-sectional area (CMO:0001697)	10	51289203	84596393	Rat
1549846	Scl47	Serum cholesterol level QTL 47	3.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	10	53104718	98104718	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	53621375	112626471	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	53621375	112626471	Rat
631530	Tls3	T-lymphoma susceptibility QTL 3	0	0.0001	thymus integrity trait (VT:0010555)	percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)	10	53625815	98939209	Rat
631535	Cm51	Cardiac mass QTL 51	3		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	10	53637485	94807701	Rat
1578762	Toxo1	Toxoplasma gondii resistance QTL 1			brain integrity trait (VT:0010579)	percentage of study population displaying Toxoplasma gondii brain cysts at a point in time (CMO:0002028)	10	54057616	61300905	Rat
1359017	Hrtrt21	Heart rate QTL 21	2.4		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	10	55224855	100224855	Rat
1354585	Eae18a	Experimental allergic encephalomyelitis QTL 18a	7.5	0.0004	nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	10	55678976	60404791	Rat
2306787	Ean3	Experimental allergic neuritis QTL 3	3.1		nervous system integrity trait (VT:0010566)	body weight loss (CMO:0001399)	10	55678976	69385767	Rat
70171	Cari1	Carrageenan-induced inflammation QTL 1	4.9	0.0005	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	10	55678976	112626471	Rat
70164	Bw21	Body weight QTL 21	4.36	0.00005	body mass (VT:0001259)	body weight (CMO:0000012)	10	55679084	102427604	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	108
Count of miRNA genes:	88
Interacting mature miRNAs:	104
Transcripts:	ENSRNOT00000056903
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	3		2		13				17	24	13	11
Low		43	55	41	6	41	8	11	53	11	28		8
Below cutoff									4

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001009623	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008767796	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008767802	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017597090	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AAHX01064586	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC136563	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC087135	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ215356	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	LN874415	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000056903 ⟹ ENSRNOP00000053740

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	56,286,973 - 56,289,952 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000090762 ⟹ ENSRNOP00000073136

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	56,286,887 - 56,289,882 (-)	Ensembl

RefSeq Acc Id:

NM_001009623 ⟹ NP_001009623

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	56,286,969 - 56,289,952 (-)	NCBI
Rnor_5.0	10	56,032,602 - 56,036,336 (-)	NCBI
RGSC_v3.4	10	56,499,945 - 56,502,928 (-)	RGD
Celera	10	53,554,575 - 53,557,558 (-)	RGD

Sequence:

show sequence

CGGCTGCCCTGCCCTTCCTAGATAATTGGCACCAAATTCTCCTGAGGCTTGGGGGGGAGGGGGC
CAGGGGTGTCAGAGGGACACTAGCTGGGGATCAGGGGACTAATAGGACCCTAGCTTGATTTCTT
CCTATTCTCAAGTTCCTTTTTATTTCTCCCTTGCGTAACTCGCTCTTCCCTTCTGCGCCTTTGC
CTGTATTCCCACCCTCCCTGCTACCTCCTGGCCACCTCACTTGCAGCCCACAGCTGTCAGCAGG
GTCCCTAGCTCATGCCAGCCTCATCTCCAGGCAACATGGGAGGCTCAGTCAGAGAGCCAGCCCT
TTCGGTCACTCTTTGGTTGAGTTGGGGGGCAGTTCTGGGGGCTGTGACTTGTGCTGTCGCACTA
CTGATCCAACAAGCAGAGTTGCAGAGCCTAAGGCGGGAGGTGAGCCGGCTGCAGCGGAGTGGAG
GAGCTTCCCAGAAGCGGGGAGAGCCTCCATGGCAGAGCCTCTGGGAACAGAGTCCTGATGTCCT
GGGAGCCTGGAAGGATGGGGCCAAATCTCGGAGAAGGAGAGCAGTACTCACCCAGAAGCACAAG
AAGAAGCAGTCCGTTCTGCATCTTGTTCCAATTAACATTACCTCCAAGGACTCTGACATGACAG
AGGTGATGTGGCAACCAGCTCTTAGGCGTGGGAGAGGCCTGGAGGCCCAAGGAGACACTGTTCG
AGTCCGGGACACTGGAATTTATCTGCTATATAGTCAGGTCCTGTTTCATGATGTGACTTTCACC
ATGGGTCAGGTGGTATCTCGGGAAGGCCAAGGGAGAAGGGAGACTCTATTCCGGTGTATCAAAA
GTATGCCTTCTGATCCTGACCGTGCCTACAACAGCTGCTACAGTGCAGGTGTCTTTCACTTACA
TCAAGGGGATATTATCACTGTCAAAATTCCTCGGGCAAACGCAAAACTTAGCCTTTCTCCACAT
GGAACATTCCTGGGGTTTGTGAAACTATGACTGTGCTATAAAGGTGGGGTTCCCATTCCAAGAA
CTGGCTAGACAAAGGACAGCAAGTGGTCAAGAACCGTTCTCCTTGGTTTTGACGTCTTGACTGT
TGTTCCCCGCTTTGCCTTTCCCGATCCCACTATCTGGGTTCTGATTCCATAGATATTAAAGAAG
TAGAATATTTTGTGTCTATCTCCCACATGGCCCCAAATTCTTTTGTTGTGTGTGTTAAAGGGGT
TTTGTGCACTGTGCCAAGCCTTATCCACTGGACTGCATCCAGAACAGCACCACCATCTAGAGGC
AGTTTGAGGAAAGAACACGGTCTCTGCTAGGGAAAACGTGTCCCTCGGCCACAACTCTTCAAGC
CCCCTGCTTCAATGTACAAGAAGCCCGATTTTCACTATCTCACTATTGCGTCCAAATTCTTGTT
ACTGTCTAGAAAAAAAATGTATTTTAGGTGCCTCGACATCCATTCCATTCATGCTCCCCATTCC
CCTAGCAAACTTCCGAGCTGAACATTGTGCTTCACCGCTTTAATCCCAGTACTCGGAGGCCTAT
TTCTATGTTAGCGGTCAACTTGGTCTAAATAGTGAGTTCCAGGCCATCCAGGGGTTACAGTGGT
TGAGACCCTGTTTCAAACAAACAAATAAAAGACTCTACAAGAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_008767796 ⟹ XP_008766018

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	56,286,964 - 56,289,708 (-)	NCBI

Sequence:

show sequence

GCTGTCAGCAGGGTCCCTAGCTCATGCCAGCCTCATCTCCAGGCAACATGGGAGGCTCAGTCAG
AGAGCCAGCCCTTTCGGTCACTCTTTGGTTGAGTTGGGGGGCAGTTCTGGGGGCTGTGACTTGT
GCTGTCGCACTACTGATCCAACAAGCAGAGTTGCAGAGCCTAAGGCGGGAGGTGAGCCGGCTGC
AGCGGAGTGGAGGAGCTTCCCAGAAGCGGGGAGAGCCTCCATGGCAGAGCCTCTGGGAACAGAG
TCCTGATGTCCTGGGAGCCTGGAAGGATGGGGCCAAATCTCGGAGAAGGAGAGCAGTACTCACC
CAGAAGCACAAGAAGAAGCAGTCCGTTCTGCATCTTGTTCCAATTAACATTACCTCCAAGGCAG
ACTCTGACATGACAGAGGTGATGTGGCAACCAGCTCTTAGGCGTGGGAGAGGCCTGGAGGCCCA
AGGAGACACTGTTCGAGTCCGGGACACTGGAATTTATCTGCTATATAGTCAGGTCCTGTTTCAT
GATGTGACTTTCACCATGGGTCAGGTGGTATCTCGGGAAGGCCAAGGGAGAAGGGAGACTCTAT
TCCGGTGTATCAAAAGTATGCCTTCTGATCCTGACCGTGCCTACAACAGCTGCTACAGTGCAGG
TGTCTTTCACTTACATCAAGGGGATATTATCACTGTCAAAATTCCTCGGGCAAACGCAAAACTT
AGCCTTTCTCCACATGGAACATTCCTGGGGGGTTTTGTGCACTGTGCCAAGCCTTATCCACTGG
ACTGCATCCAGAACAGCACCACCATCTAGAGGCAGTTTGAGGAAAGAACACGGTCTCTGCTAGG
GAAAACGTGTCCCTCGGCCACAACTCTTCAAGCCCCCTGCTTCAATGTACAAGAAGCCCGATTT
TCACTATCTCACTATTGCGTCCAAATTCTTGTTACTGTCTAGAAAAAAAATGTATTTTAGGTGC
CTCGACATCCATTCCATTCATGCTCCCCATTCCCCTAGCAAACTTCCGAGCTGAACATTGTGCT
TCACCGCTTTAATCCCAGTACTCGGAGGCCTATTTCTATGTTAGCGGTCAACTTGGTCTAAATA
GTGAGTTCCAGGCCATCCAGGGGTTACAGTGGTTGAGACCCTGTTTCAAACAAACAAATAAAAG
ACTCTACAAGATCGGA

hide sequence

RefSeq Acc Id:

XM_008767802 ⟹ XP_008766024

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	56,286,971 - 56,289,708 (-)	NCBI

Sequence:

show sequence

GCTGTCAGCAGGGTCCCTAGCTCATGCCAGCCTCATCTCCAGGCAACATGGGAGGCTCAGTCAG
AGAGCCAGCCCTTTCGGTCACTCTTTGGTTGAGTTGGGGGGCAGTTCTGGGGGCTGTGACTTGT
GCTGTCGCACTACTGATCCAACAAGCAGAGTTGCAGAGCCTAAGGCGGGAGGTGAGCCGGCTGC
AGCGGAGTGGAGGAGCTTCCCAGAAGCGGGGAGAGCCTCCATGGCAGAGCCTCTGGGAACAGAG
TCCTGATGTCCTGGGAGCCTGGAAGGATGGGGCCAAATCTCGGAGAAGGAGAGCAGTACTCACC
CAGAAGCACAAGACAGACTCTGACATGACAGAGGTGATGTGGCAACCAGCTCTTAGGCGTGGGA
GAGGCCTGGAGGCCCAAGGAGACACTGTTCGAGTCCGGGACACTGGAATTTATCTGCTATATAG
TCAGGTCCTGTTTCATGATGTGACTTTCACCATGGGTCAGGTGGTATCTCGGGAAGGCCAAGGG
AGAAGGGAGACTCTATTCCGGTGTATCAAAAGTATGCCTTCTGATCCTGACCGTGCCTACAACA
GCTGCTACAGTGCAGGTGTCTTTCACTTACATCAAGGGGATATTATCACTGTCAAAATTCCTCG
GGCAAACGCAAAACTTAGCCTTTCTCCACATGGAACATTCCTGGGGTTTGTGAAACTATGACTG
TGCTATAAAGGTGGGGTTCCCATTCCAAGAACTGGCTAGACAAAGGACAGCAAGTGGTCAAGAA
CCGTTCTCCTTGGTTTTGACGTCTTGACTGTTGTTCCCCGCTTTGCCTTTCCCGATCCCACTAT
CTGGGTTCTGATTCCATAGATATTAAAGAAGTAGAATATTTTGTGTCTATCTCCCACATGGCCC
CAAATTCTTTTGTTGTGTGTGTTAAAGGGGTTTTGTGCACTGTGCCAAGCCTTATCCACTGGAC
TGCATCCAGAACAGCACCACCATCTAGAGGCAGTTTGAGGAAAGAACACGGTCTCTGCTAGGGA
AAACGTGTCCCTCGGCCACAACTCTTCAAGCCCCCTGCTTCAATGTACAAGAAGCCCGATTTTC
ACTATCTCACTATTGCGTCCAAATTCTTGTTACTGTCTAGAAAAAAAATGTATTTTAGGTGCCT
CGACATCCATTCCATTCATGCTCCCCATTCCCCTAGCAAACTTCCGAGCTGAACATTGTGCTTC
ACCGCTTTAATCCCAGTACTCGGAGGCCTATTTCTATGTTAGCGGTCAACTTGGTCTAAATAGT
GAGTTCCAGGCCATCCAGGGGTTACAGTGGTTGAGACCCTGTTTCAAACAAACAAATAAAAGAC
TCTACAA

hide sequence

RefSeq Acc Id:

XM_017597090 ⟹ XP_017452579

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	56,286,969 - 56,290,680 (-)	NCBI

Sequence:

show sequence

CAAAGATACCAGAAAAAAAAAAACCATGCAAACAACAACAAAACCACCTGGTCCTCTGCACAAG
GCGCTGCAGAAGCAGCCTCATTTTCCTAGCAGCGGACTTCCTCCTGCAGGGGAATCCCTGGCTG
GGAGGAGCAGGGTCCTTCCTCTTGGCGGCCTCAGGACATTCAGCAGTTGAGCAGAGAACCTTAT
GTAAGAACTCTTCTTGGGAAACAGGAAGTCCGGCTTGCCAAGTTCAGCACAGGGAGTAGTGCAG
GCCTGGTTCCAACACACCCGGCCCAGCCTTAACCCCAGCACCCTGCCAGTTTCTTGTCCTTGGT
TCTCCTCCCTGCTGGCCCCTAGCCCCCCTTTTTTTTTCATTTCCAGTCACCCCTAACAAGCCTC
CTCAAAGCTGTCATTTGTGCCTCAGGCAGAGAGAGAGTCCACCACACTCACCTTCTAAGGCTCA
TGCTGCTGAGCTTGTCCCCATTCCCTGCCCCTGGCACCATGCCCCATAACCAACCGACCTTCCC
TCCTCCAACTTAGGGGCCGCCCCTGGGCTCCTGAACGCTGACCGCTCCTTCTGGGTGTCACGGC
TGCCCTGCCCTTCCTAGATAATTGGCACCAAATTCTCCTGAGGCTTGGGGGGGAGGGGGCCAGG
GGTGTCAGAGGGACACTAGCTGGGGATCAGGGGACTAATAGGACCCTAGCTTGATTTCTTCCTA
TTCTCAAGTTCCTTTTTATTTCTCCCTTGCGTAACTCGCTCTTCCCTTCTGCGCCTTTGCCTGT
ATTCCCACCCTCCCTGCTACCTCCTGGCCACCTCACTTGCAGCCCACAGCTGTCAGCAGGGTCC
CTAGCTCATGCCAGCCTCATCTCCAGGCAACATGGGAGGCTCAGTCAGAGAGCCAGCCCTTTCG
GTCACTCTTTGGTTGAGTTGGGGGGCAGTTCTGGGGGCTGTGACTTGTGCTGTCGCACTACTGA
TCCAACAAGCAGAGTTGCAGAGCCTAAGGCGGGAGGTGAGCCGGCTGCAGCGGAGTGGAGGAGC
TTCCCAGAAGCGGGGAGAGCCTCCATGGCAGAGCCTCTGGGAACAGAGTCCTGATGTCCTGGGA
GCCTGGAAGGATGGGGCCAAATCTCGGAGAAGGAGAGCAGTACTCACCCAGAAGCACAAGAAGA
AGCAGTCCGTTCTGCATCTTGTTCCAATTAACATTACCTCCAAGGACTCTGACATGACAGAGGT
GATGTGGCAACCAGCTCTTAGGCGTGGGAGAGGCCTGGAGGCCCAAGGAGACACTGTTCGAGTC
CGGGACACTGGAATTTATCTGCTATATAGTCAGGTCCTGTTTCATGATGTGACTTTCACCATGG
GTCAGGTGGTATCTCGGGAAGGCCAAGGGAGAAGGGAGACTCTATTCCGGTGTATCAAAAGTAT
GCCTTCTGATCCTGACCGTGCCTACAACAGCTGCTACAGTGCAGGTGTCTTTCACTTACATCAA
GGGGATATTATCACTGTCAAAATTCCTCGGGCAAACGCAAAACTTAGCCTTTCTCCACATGGAA
CATTCCTGGGGTTTGTGAAACTATGACTGTGCTATAAAGGTGGGGTTCCCATTCCAAGAACTGG
CTAGACAAAGGACAGCAAGTGGTCAAGAACCGTTCTCCTTGGTTTTGACGTCTTGACTGTTGTT
CCCCGCTTTGCCTTTCCCGATCCCACTATCTGGGTTCTGATTCCATAGATATTAAAGAAGTAGA
ATATTTTGTGTCTATCTCCCACATGGCCCCAAATTCTTTTGTTGTGTGTGTTAAAGGGGTTTTG
TGCACTGTGCCAAGCCTTATCCACTGGACTGCATCCAGAACAGCACCACCATCTAGAGGCAGTT
TGAGGAAAGAACACGGTCTCTGCTAGGGAAAACGTGTCCCTCGGCCACAACTCTTCAAGCCCCC
TGCTTCAATGTACAAGAAGCCCGATTTTCACTATCTCACTATTGCGTCCAAATTCTTGTTACTG
TCTAGAAAAAAAATGTATTTTAGGTGCCTCGACATCCATTCCATTCATGCTCCCCATTCCCCTA
GCAAACTTCCGAGCTGAACATTGTGCTTCACCGCTTTAATCCCAGTACTCGGAGGCCTATTTCT
ATGTTAGCGGTCAACTTGGTCTAAATAGTGAGTTCCAGGCCATCCAGGGGTTACAGTGGTTGAG
ACCCTGTTTCAAACAAACAAATAAAAGACTCTACAAGA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001009623	(Get FASTA)	NCBI Sequence Viewer
	XP_008766018	(Get FASTA)	NCBI Sequence Viewer
	XP_008766024	(Get FASTA)	NCBI Sequence Viewer
	XP_017452579	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH87135	(Get FASTA)	NCBI Sequence Viewer
	CTQ86180	(Get FASTA)	NCBI Sequence Viewer
	EDM04888	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001009623 ⟸ NM_001009623

- UniProtKB:

Q5PQL1 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MPASSPGNMGGSVREPALSVTLWLSWGAVLGAVTCAVALLIQQAELQSLRREVSRLQRSGGASQ
KRGEPPWQSLWEQSPDVLGAWKDGAKSRRRRAVLTQKHKKKQSVLHLVPINITSKDSDMTEVMW
QPALRRGRGLEAQGDTVRVRDTGIYLLYSQVLFHDVTFTMGQVVSREGQGRRETLFRCIKSMPS
DPDRAYNSCYSAGVFHLHQGDIITVKIPRANAKLSLSPHGTFLGFVKL

hide sequence

RefSeq Acc Id:

XP_008766018 ⟸ XM_008767796

- Peptide Label:

isoform X1

- Sequence:

show sequence

MPASSPGNMGGSVREPALSVTLWLSWGAVLGAVTCAVALLIQQAELQSLRREVSRLQRSGGASQ
KRGEPPWQSLWEQSPDVLGAWKDGAKSRRRRAVLTQKHKKKQSVLHLVPINITSKADSDMTEVM
WQPALRRGRGLEAQGDTVRVRDTGIYLLYSQVLFHDVTFTMGQVVSREGQGRRETLFRCIKSMP
SDPDRAYNSCYSAGVFHLHQGDIITVKIPRANAKLSLSPHGTFLGGFVHCAKPYPLDCIQNSTT
I

hide sequence

RefSeq Acc Id:

XP_008766024 ⟸ XM_008767802

- Peptide Label:

isoform X3

- Sequence:

show sequence

MPASSPGNMGGSVREPALSVTLWLSWGAVLGAVTCAVALLIQQAELQSLRREVSRLQRSGGASQ
KRGEPPWQSLWEQSPDVLGAWKDGAKSRRRRAVLTQKHKTDSDMTEVMWQPALRRGRGLEAQGD
TVRVRDTGIYLLYSQVLFHDVTFTMGQVVSREGQGRRETLFRCIKSMPSDPDRAYNSCYSAGVF
HLHQGDIITVKIPRANAKLSLSPHGTFLGFVKL

hide sequence

RefSeq Acc Id:	XP_017452579 ⟸ XM_017597090
- Peptide Label:	isoform X2
- UniProtKB:	Q5PQL1 (UniProtKB/TrEMBL)
- Sequence:	show sequence MPASSPGNMGGSVREPALSVTLWLSWGAVLGAVTCAVALLIQQAELQSLRREVSRLQRSGGASQ KRGEPPWQSLWEQSPDVLGAWKDGAKSRRRRAVLTQKHKKKQSVLHLVPINITSKDSDMTEVMW QPALRRGRGLEAQGDTVRVRDTGIYLLYSQVLFHDVTFTMGQVVSREGQGRRETLFRCIKSMPS DPDRAYNSCYSAGVFHLHQGDIITVKIPRANAKLSLSPHGTFLGFVKL hide sequence

RefSeq Acc Id:

ENSRNOP00000073136 ⟸ ENSRNOT00000090762

RefSeq Acc Id:

ENSRNOP00000053740 ⟸ ENSRNOT00000056903

Protein Domains

TNF_2

Transcriptome

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

Promoters

RGD ID:

13697322

Promoter ID:

EPDNEW_R7847

Type:

single initiation site

Name:

Tnfsf13_1

Description:

TNF superfamily member 13

SO ACC ID:

SO:0000170

Source:

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

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	56,289,980 - 56,290,040	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

Visual

CSV

TAB

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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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1305871	AgrOrtholog
Ensembl Genes	ENSRNOG00000014171	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000053740	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOP00000073136	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000056903	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOT00000090762	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	2.60.120.40	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7123934	IMAGE-MGC_LOAD
InterPro	TNF_CS	UniProtKB/TrEMBL
	TNF_family	UniProtKB/TrEMBL
	Tumour_necrosis_fac-like	UniProtKB/TrEMBL
KEGG Report	rno:287437	UniProtKB/TrEMBL
MGC_CLONE	MGC:95053	IMAGE-MGC_LOAD
NCBI Gene	287437	ENTREZGENE
Pfam	TNF	UniProtKB/TrEMBL
PhenoGen	Tnfsf13	PhenoGen
PROSITE	TNF_1	UniProtKB/TrEMBL
	TNF_2	UniProtKB/TrEMBL
SMART	TNF	UniProtKB/TrEMBL
Superfamily-SCOP	TNF_like	UniProtKB/TrEMBL
UniGene	Rn.19955	ENTREZGENE
UniProt	A0A0G2K4Q8_RAT	UniProtKB/TrEMBL
	Q5PQL1	ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary	E9PSM9	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2017-03-21	Tnfsf13	TNF superfamily member 13	Tnfsf13	tumor necrosis factor superfamily member 13	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2015-11-25	Tnfsf13	tumor necrosis factor superfamily member 13	Tnfsf13	tumor necrosis factor (ligand) superfamily, member 13	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	Tnfsf13	tumor necrosis factor (ligand) superfamily, member 13	Tnfsf13_predicted	tumor necrosis factor (ligand) superfamily, member 13 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Tnfsf13_predicted	tumor necrosis factor (ligand) superfamily, member 13 (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)

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

RGD Manual Annotations

Imported Annotations - KEGG (archival)