Trim5 (tripartite motif-containing 5)

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Gene: Trim5 (tripartite motif-containing 5) Rattus norvegicus

Analyze

Symbol:

Trim5

Name:

tripartite motif-containing 5

RGD ID:

1304579

Description:

Predicted to have several functions, including pattern recognition receptor activity; protein homodimerization activity; and ubiquitin protein ligase activity. Predicted to be involved in several processes, including negative regulation of viral life cycle; positive regulation of NF-kappaB transcription factor activity; and regulation of signal transduction. Predicted to colocalize with omegasome. Orthologous to human TRIM5 (tripartite motif containing 5); INTERACTS WITH (+)-schisandrin B; 3-chloropropane-1,2-diol; 6-propyl-2-thiouracil.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

hypothetical protein LOC308906; LOC308906; RGD1304579; similar to 9230105E10Rik protein; tripartite motif-containing protein 5

RGD Orthologs

Human

Mouse

Bonobo

Pig

Green Monkey

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	1	169,446,774 - 169,463,760 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	169,446,805 - 169,534,896 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	175,586,814 - 175,603,800 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	162,096,439 - 162,113,409 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	162,190,323 - 162,207,293 (-)	NCBI
Celera	1	156,710,957 - 156,727,926 (-)	NCBI		Celera
Cytogenetic Map	1	q32	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

human immunodeficiency virus infectious disease (ISO)

prostate cancer (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

(-)-epigallocatechin 3-gallate (ISO)

1,2-dichloroethane (ISO)

17beta-hydroxy-5alpha-androstan-3-one (ISO)

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

6-propyl-2-thiouracil (EXP)

acetamide (EXP)

acrolein (ISO)

alpha-pinene (ISO)

bisphenol A (EXP)

buspirone (EXP)

cobalt dichloride (ISO)

cyclosporin A (ISO)

cytarabine (ISO)

dorsomorphin (ISO)

genistein (ISO)

glafenine (EXP)

mercury dichloride (ISO)

methapyrilene (EXP)

nefazodone (EXP)

nimesulide (EXP)

ozone (ISO)

paracetamol (ISO)

phenylmercury acetate (ISO)

potassium chromate (ISO)

rotenone (EXP)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

Soman (EXP)

succimer (ISO)

sulforaphane (ISO)

sunitinib (ISO)

tetrachloromethane (EXP)

valdecoxib (EXP)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

activation of innate immune response (ISO)

autophagy (ISO)

innate immune response (IBA,ISO)

negative regulation of viral entry into host cell (ISO)

negative regulation of viral release from host cell (ISO)

positive regulation of autophagy (IBA)

positive regulation of DNA-binding transcription factor activity (ISO)

positive regulation of I-kappaB kinase/NF-kappaB signaling (IBA,ISO)

positive regulation of MAPK cascade (ISO)

positive regulation of NF-kappaB transcription factor activity (IBA,ISO)

protein K63-linked ubiquitination (ISO)

protein polyubiquitination (IBA)

protein ubiquitination (IBA)

regulation of gene expression (IBA)

regulation of lipopolysaccharide-mediated signaling pathway (ISO)

regulation of protein localization (IBA,ISO)

regulation of viral entry into host cell (IBA)

Cellular Component

cytoplasm (IBA,ISO)

cytosol (IBA)

nucleoplasm (IBA)

omegasome (ISO)

P-body (ISO)

Molecular Function

identical protein binding (ISO)

pattern recognition receptor activity (ISO)

protein binding (ISO)

protein homodimerization activity (IBA,ISO)

protein kinase binding (IBA,ISO)

protein-macromolecule adaptor activity (ISO)

transcription coactivator activity (ISO)

ubiquitin protein ligase activity (IBA)

ubiquitin-protein transferase activity (ISO)

zinc ion binding (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.	RGD automated data pipeline
3.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4.	RGD automated import pipeline for gene-chemical interactions
5.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Additional References at PubMed

PMID:11331580	PMID:12878161	PMID:17156811	PMID:18248090	PMID:20357094	PMID:21512573	PMID:22493164	PMID:22829933	PMID:23077300	PMID:25127057

Genomics

Comparative Map Data

Trim5
(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	1	169,446,774 - 169,463,760 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	169,446,805 - 169,534,896 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	175,586,814 - 175,603,800 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	162,096,439 - 162,113,409 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	162,190,323 - 162,207,293 (-)	NCBI
Celera	1	156,710,957 - 156,727,926 (-)	NCBI		Celera
Cytogenetic Map	1	q32	NCBI

TRIM5
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	11	5,663,195 - 5,938,619 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	11	5,590,906 - 5,685,108 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	11	5,676,740 - 5,706,339 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	5,641,364 - 5,662,869 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	11	5,641,368 - 5,662,869	NCBI
Celera	11	5,803,483 - 5,825,436 (-)	NCBI
Cytogenetic Map	11	p15.4	NCBI
HuRef	11	5,344,050 - 5,365,972 (-)	NCBI		HuRef
CHM1_1	11	5,683,377 - 5,705,274 (-)	NCBI		CHM1_1

Trim5
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	103,912,593 - 103,937,448 (-)	NCBI	GRCm39		mm39
GRCm38	7	104,263,386 - 104,288,254 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	104,263,386 - 104,288,094 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	111,413,000 - 111,436,646 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	7	104,137,205 - 104,162,054 (-)	NCBI			mm8
Celera	7	104,635,824 - 104,653,489 (-)	NCBI		Celera
Cytogenetic Map	7	E3	NCBI

TRIM5
(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	11	5,479,033 - 5,754,014 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	11	5,479,033 - 5,500,758 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	11	5,798,336 - 5,819,876 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

LOC733579
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	9	4,157,290 - 4,170,204 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	9	4,157,290 - 4,170,233 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	9	4,724,246 - 4,737,190 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

TRIM5
(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	1	61,040,908 - 61,067,815 (+)	NCBI

Position Markers

RH129380

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	169,446,841 - 169,447,056	NCBI	Rnor6.0
Rnor_5.0	1	175,586,881 - 175,587,096	UniSTS	Rnor5.0
RGSC_v3.4	1	162,096,490 - 162,096,705	UniSTS	RGSC3.4
Celera	1	156,711,008 - 156,711,223	UniSTS
Cytogenetic Map	1	q32	UniSTS
RH 3.4 Map	1	1300.2	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
70209	Niddm23	Non-insulin dependent diabetes mellitus QTL 23	2.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	99983293	216325819	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34993530	173445086	Rat
71118	Thym1	Thymus enlargement QTL 1	10.17	0.001	thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	153655976	198655976	Rat
631199	Cm23	Cardiac mass QTL 23	4.6	0.0004	heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	1	124603592	188289386	Rat
631202	Gluco13	Glucose level QTL 13		0.0001	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	139523928	170246858	Rat
631205	Bp196	Blood pressure QTL 196	4	0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	126240667	217054291	Rat
631206	Niddm40	Non-insulin dependent diabetes mellitus QTL 40			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	144723107	174343537	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	156446196	274977688	Rat
61442	Strs1	Sensitivity to stroke QTL 1	7.4		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	1	133946489	178946489	Rat
70160	Bw18	Body weight QTL 18	5.7		body mass (VT:0001259)	body weight (CMO:0000012)	1	156446196	214277437	Rat
724521	Uae1	Urinary albumin excretion QTL 1	3.8	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	94201400	184846632	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	161321152	273792054	Rat
724550	Thym3	Thymus enlargement QTL 3	7.82	0.001	thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	153655976	198655976	Rat
724562	Rends1	Renal damage susceptibility QTL 1		0.05	kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	1	137787261	236763528	Rat
1331749	Hrtrt11	Heart rate QTL 11	2.973		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	99983293	216213510	Rat
1331751	Bp199	Blood pressure QTL 199	3.60022		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	99983293	198656062	Rat
737828	Hcas3	Hepatocarcinoma susceptibility QTL 3	4.9		liver integrity trait (VT:0010547)	liver tumorous lesion volume to total liver volume ratio (CMO:0001082)	1	156446196	243311614	Rat
631654	Bp107	Blood pressure QTL 107			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	133076978	178076978	Rat
1331793	Bp200	Blood pressure QTL 200	3.71601		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	99983293	188289386	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	167394665	278228889	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	49578577	169852184	Rat
731168	Bp154	Blood pressure QTL 154	3.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	100131562	236763528	Rat
738006	Anxrr14	Anxiety related response QTL 14	4	0.00035	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	141296374	186296374	Rat
738028	Anxrr12	Anxiety related response QTL 12	4.9	0.00001	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	141296374	186296374	Rat
631519	Pia11	Pristane induced arthritis QTL 11	5.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	153656062	198656062	Rat
631544	Bp84	Blood pressure QTL 84	5.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	130779148	198585664	Rat
631548	Bp88	Blood pressure QTL 88	5	0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	167394665	191883991	Rat
631549	Bp89	Blood pressure QTL 89	5.7		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	130779320	219238476	Rat
1641895	Bp298	Blood pressure QTL 298			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	130779148	199254774	Rat
1598850	Bp297	Blood pressure QTL 297	2.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	131334152	176334152	Rat
1598853	Memor3	Memory QTL 3	4.5		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	1	153834077	232297227	Rat
1598866	Bp287	Blood pressure QTL 287	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	131334152	176334152	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49578693	217054291	Rat
634315	Niddm45	Non-insulin dependent diabetes mellitus QTL 45	7.16		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	156446783	188289244	Rat
634348	Bp138	Blood pressure QTL 138			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	133076978	184188922	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
1578770	Stresp23	Stress response QTL 23			kidney sympathetic nerve activity (VT:0004050)	stimulated renal sympathetic nerve activity to basal renal sympathetic nerve activity ratio (CMO:0001786)	1	130779148	199254774	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
1578780	Cm52	Cardiac mass QTL 52	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	1	82788437	239853971	Rat
1300158	Bp173	Blood pressure QTL 173	3.48		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	1	122614824	201146953	Rat
1354591	Cm36	Cardiac mass QTL 36	4.1		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	108986301	219232156	Rat
1354602	Bw35	Body weight QTL 35	12.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	219232156	Rat
1354606	Bp246	Blood pressure QTL 246	3.6		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	108986301	238830534	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1354615	Cm32	Cardiac mass QTL 32	5.2		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	1	108986301	219232156	Rat
1354618	Kidm15	Kidney mass QTL 15	5		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	1	167394665	219232156	Rat
1354620	Kidm19	Kidney mass QTL 19	4		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	161784169	219232156	Rat
1354634	Kidm12	Kidney mass QTL 12	3.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	1	161784169	219232156	Rat
1354636	Lmblg1	Limb length QTL 1	6.4		tibia length (VT:0004357)	tibia length (CMO:0000450)	1	161784169	219232156	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	161784169	278228889	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1558645	Bw55	Body weight QTL 55	3.2	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	1	144395993	189395993	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	163796316	282763074	Rat
1358189	Cstrr1	Cold stress response QTL 1		0.0001	catecholamine amount (VT:0010543)	urine norepinephrine level (CMO:0001629)	1	130779148	199254774	Rat
2312420	Pur17	Proteinuria QTL 17	7.1	0.0001	urine protein amount (VT:0005160)	urine total protein excretion rate (CMO:0000756)	1	167394665	238830534	Rat
1358886	Bp260	Blood pressure QTL 260	3.67		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	161784422	246226103	Rat
1358902	Bw47	Body weight QTL 47	1.67		body mass (VT:0001259)	body weight (CMO:0000012)	1	94201400	197187904	Rat
1582204	Livw1	Liver weight QTL 1	3.6	0.0003	liver mass (VT:0003402)	liver weight as percentage of body weight (CMO:0000141)	1	166100317	188289386	Rat
2293140	Bp313	Blood pressure QTL 313			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	129208943	174208943	Rat
61341	Bp26	Blood pressure QTL 26			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	137787261	236763528	Rat
61343	Bp28	Blood pressure QTL 28			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	167027868	212027868	Rat
61348	Bp30	Blood pressure QTL 30	2.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	154337847	215828102	Rat
61379	Bp44	Blood pressure QTL 44	19.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	156446783	189514504	Rat
4889428	Stresp24	Stress response QTL 24		0.05	heart pumping trait (VT:2000009)	absolute change in electrocardiographic low frequency R-R spectral component to high frequency R-R spectral component ratio (CMO:0002162)	1	166577232	211577232	Rat
6893347	Bw98	Body weight QTL 98	0.2	0.53	body mass (VT:0001259)	body weight (CMO:0000012)	1	144395993	189395993	Rat
6893361	Bw104	Body weight QTL 104	0.59	0.27	body mass (VT:0001259)	body weight (CMO:0000012)	1	144395993	189395993	Rat
8655649	Arrd1	Age-related retinal degeneration QTL 1	4.89		retinal layer morphology trait (VT:0003727)	percentage of study population developing retinopathy during a period of time (CMO:0002453)	1	106002252	202571904	Rat
7794788	Mcs32	Mammary carcinoma susceptibility QTL 32	2.61		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	1	122614824	262664716	Rat
9685799	Bp375	Blood pressure QTL 375			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	133076978	178076978	Rat
9685802	Bp376	Blood pressure QTL 376			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	134089429	179089429	Rat
8693608	Alc24	Alcohol consumption QTL 24	2.3	0.74	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	1	161072673	178935582	Rat
7771612	Cm80	Cardiac mass QTL 80	8.4		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	1	144634295	241482368	Rat
7421630	Bp362	Blood pressure QTL 362		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	125875758	262433692	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	35377692	217372257	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	417
Count of miRNA genes:	234
Interacting mature miRNAs:	268
Transcripts:	ENSRNOT00000023100
Prediction methods:	Microtar, Miranda, Rnahybrid
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	43	57	41	19	41	4	6		31	30	11	4
Low							4	5	74	4	11		4
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001014023	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006229912	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AAHX01007633	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC112864	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC113720	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC078926	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473956	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ225508	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ230638	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ232280	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ235112	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000023100 ⟹ ENSRNOP00000023099

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	169,446,805 - 169,463,760 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000030827 ⟹ ENSRNOP00000038739

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	169,447,585 - 169,456,098 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000082645 ⟹ ENSRNOP00000073760

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	169,447,386 - 169,534,896 (-)	Ensembl

RefSeq Acc Id:

NM_001014023 ⟹ NP_001014045

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	169,446,790 - 169,463,760 (-)	NCBI
Rnor_5.0	1	175,586,814 - 175,603,800 (-)	NCBI
RGSC_v3.4	1	162,096,439 - 162,113,409 (-)	RGD
Celera	1	156,710,957 - 156,727,926 (-)	RGD

Sequence:

show sequence

TGCTGGTGTGGCAGCTGCCCTGAACTACATCATCCTTTCGGTTCTCATCCTGCACCTGAGCAGA
CGTGTGAGGAGTCAGTAGAGTCAGACACAGGATCACAGCAACTATGGCTTCAGAATTCGTGATG
AATTTAAAAGAGGAGGTGACCTGTCCTATCTGCCTGGACCTGATGGTAGAACCTGTGAGTGGAG
ATTGTGGTCACAGCTTCTGCCAAGCCTGCATCACGCTGAACTATGAATCCAGCAAATGCAATCA
GGATGAGTTCATTTGCCCTGTGTGCCGAGTTAGTTACCTGTTTAAGAACCTGAGGCCCAATCGA
CATGTGGCCAACATAGTGCAGAGGCTCAAAGAGTTCAAGTCCAGCCCAGAAGAGGAGCCGAAGG
TGCTTTCTTGTGCAAGGCATGGAGAGAAACTCCAGCTCTTCTGTAAGAAGGACATGATGCCCAT
CTGCTGGCTTTGTGAGCGATCTCAGGAGCACCGTGGACACCAAACAGTTCTCATTGAAGAGGTG
GTCCAGGAGTATAAGGAGAAGCTGCAGGCAGCTCTGCAAAAGCTGATGGCAGACAAGAAAGAAT
TTGAGAACTGGAAAGATGACCTTCAAAAGGAGAGAACTTACTGGCAGAATCAAATACAGAAAGA
TGTGGAAAATGTCCAGTCAGAGTTTAAAGGAATGAGAGATATCATGGACTCTGAGGAGAAGAAG
GAATTGCAGAAGCTGATGCAAGAGAAGGAAGACATTATGAGCAGCCTGGAAGAGTCTGAAAATG
AGTATTCTCAGCAGAGTAAGTTGCTAGGAGACCTCATCTTAGATGTGGAACATCAGTTACAATG
CTCAGCCACGGAAATGCTGCAGGGTGTAGAGAACACCATAAAACGGAGTCATACTTTTTCGATG
AGGAAGCCCAAAACCATCCCCAAGGAACAAAGAAGAGTGTTCCGAGCCCCTGATCTGCAAGGCA
TGCTGCAAGTGTTACAAGAGGTCACAGAGGCCCAACGCTACTGGGTTCAAGTGACGCTGGTTGA
AAGCAACAATCCAAACATTTTCATTACCGCCGACAAAAGACAGATACGATATGAAGACCACCAA
GCAAGACATTTTGCCCGTCCGACTGAAAACTGTCATGCAGGTGTCCTGGGATACCCAGCTATCC
AATCAGGAAAACACTACTGGGAAGTAGATGTGTCTGGAAAAGGTTCTTGGGTTCTGGGATTAAG
TGATGGAAGCTACCTCTTTAATCCAATATTTCGTTCAAATGCAGAAAGACCCCCAAACCCCCCC
TTATTTCGTTTGAATCTTAGTAATGATTCACATTCTCGTTTGAGTCTTAGTAATGATTCACATT
ATCAACCTAAATATGGCTTCTGGGTTATAGGGCTGTGGGGAAATTCTGTGTATAATGCTTTTGA
GGAGTGTACGTTCACAGGCAAGCCCAGTGTGTTGACCCTCTCTCTGATGGTCCGACCCTGTCGT
GTCGGTATTTTCCTCGACTGTGCAGCTGGCACCCTCTCGTTTTACAATATTTCCAACCATGGCA
CTCTTATCTACAGATTCTGTGCAGGTTCCTTTCCTGATAGGGTTTTTCCATATTTTAACCCCAT
GGGAAGTTCAGAGCCATTGACAATATGCTGGCCAGACTCTTAATCTTCACTGTCTCTGTGCATG
GTCTCTGGTCCTGATGTGTATGTCATGTGCCTGAGCTCATCAGCACTATTTTATCGTTTTGTTC
ATGTCTCTAATCTTTCATTGGAAAATATATTCATTTCTCTAGGCCATATTCTCAGTTTCTTGGG
GTATTTTTTGTCTTTGTTTTGTTTTGTTTTTAGGTGAGACTAACAAATCACTTCCCATATAGTC
AAGGACAAATGTCTAGTGCTCACTGCGTAAGATAACACCGATGCAAAATTCCTCTTATTCTTCA
TGCCAGAGATGGAAGGCAAGGCCTTGTGCACGGTGAGGATGTGCTCCACCGCTGAGCTGTTTGC
TTCAGCTGTCATGTCCCTATAACCTCATTCGGCCCATCAATGAAAGATTAAAGAAGGTTCTTCG
ACAACTTGTCTATTCATGCTGAAAATTATATATAGGAGTCTCTGCTTAAGAAATGCACCCTGAG
CTGTAGGCCAAAGAATGAAGGAGAAGCATCACAAGAAGCCTTATCACTGTGACTAAATTAAGTG
ATCATTAAGACTGTGCATCAGTCTTGCCTGGGAGCTCATACCTGCCATCCTGCATCTGGGAAGT
TGTGGCAGGAAGATTGCTGTGTATTTGAAGCCACCCTTGTATAGAGTTAAGAGCCTGCTTAAAA
AAAATAATCAAGAATATGTATAAAAACCACTACTCTATTTTGTTCTAAGAAATAGAATAACTAG
ATTTCAGAATTGCAGGGTTTGGGTCGTTTTCACAATTTGTAAATAAATGTTTACTAAAAATAAA
TGTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006229912 ⟹ XP_006229974

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	169,446,774 - 169,463,700 (-)	NCBI
Rnor_5.0	1	175,586,814 - 175,603,800 (-)	NCBI

Sequence:

show sequence

CAGCTCCAACCTCAGGGGAACACTACAACTTTCTGTCCCTAACCTTTTTCCTTCCCTTTGGGCC
ACACTTGCCACCAAGGCAAAACCCAGTCTGGAGCTCTGGTGCAAGAGAAACCATGGGGAAGGCT
TTCTTTCCATCACAGGCAGGTTTCCAGAGGATCAGGAACTTGTTTAGTGATTCTGCCCTAAGCC
TGAACAACTGTCTTAGGGAATTCTAGAAACCTCTAAAAAAAACCAGTTAAGTGTGGGAGAGTTT
ATCATACTAGCTCCCCGGAGACAGCCAATGCTGGCCTGAAGAAAACGTCCTCAGCGAGTGGGGG
AGGCAGCTCATTGGTCGGTCGAGTTGTGGTTTCTCTTTCATTTCCAGCGCTCAAACTTTGGTTC
CTCTTAGAGTGGGGTCTTAAGTATCTTGAAATTCTGGATTAGCGAGTTAATTTTCTGTGATTTA
CGAATTCTCGGTGTCTGAAAGCCGGTGGAACAATTTTAGGGAGCAAAGTTTTGAGGACTTTGGA
AGGAAAACATTGCTTTTGCTTGGGCACCTGAGCAGACGTGTGAGGAGTCAGTAGAGTCAGACAC
AGGATCACAGCAACTATGGCTTCAGAATTCGTGATGAATTTAAAAGAGGAGGTGACCTGTCCTA
TCTGCCTGGACCTGATGGTAGAACCTGTGAGTGGAGATTGTGGTCACAGCTTCTGCCAAGCCTG
CATCACGCTGAACTATGAATCCAGCAAATGCAATCAGGATGAGTTCATTTGCCCTGTGTGCCGA
GTTAGTTACCTGTTTAAGAACCTGAGGCCCAATCGACATGTGGCCAACATAGTGCAGAGGCTCA
AAGAGTTCAAGTCCAGCCCAGAAGAGGAGCCGAAGGTGCTTTCTTGTGCAAGGCATGGAGAGAA
ACTCCAGCTCTTCTGTAAGAAGGACATGATGCCCATCTGCTGGCTTTGTGAGCGATCTCAGGAG
CACCGTGGACACCAAACAGTTCTCATTGAAGAGGTGGTCCAGGAGTATAAGGAGAAGCTGCAGG
CAGCTCTGCAAAAGCTGATGGCAGACAAGAAAGAATTTGAGAACTGGAAAGATGACCTTCAAAA
GGAGAGAACTTACTGGCAGAATCAAATACAGAAAGATGTGGAAAATGTCCAGTCAGAGTTTAAA
GGAATGAGAGATATCATGGACTCTGAGGAGAAGAAGGAATTGCAGAAGCTGATGCAAGAGAAGG
AAGACATTATGAGCAGCCTGGAAGAGTCTGAAAATGAGTATTCTCAGCAGAGTAAGTTGCTAGG
AGACCTCATCTTAGATGTGGAACATCAGTTACAATGCTCAGCCACGGAAATGCTGCAGGGTGTA
GAGAACACCATAAAACGGAGTCATACTTTTTCGATGAGGAAGCCCAAAACCATCCCCAAGGAAC
AAAGAAGAGTGTTCCGAGCCCCTGATCTGCAAGGCATGCTGCAAGTGTTACAAGAGGTCACAGA
GGCCCAACGCTACTGGGTTCAAGTGACGCTGGTTGAAAGCAACAATCCAAACATTTTCATTACC
GCCGACAAAAGACAGATACGATATGAAGACCACCAAGCAAGACATTTTGCCCGTCCGACTGAAA
ACTGTCATGCAGGTGTCCTGGGATACCCAGCTATCCAATCAGGAAAACACTACTGGGAAGTAGA
TGTGTCTGGAAAAGGTTCTTGGGTTCTGGGATTAAGTGATGGAAGCTACCTCTTTAATCCAATA
TTTCGTTCAAATGCAGAAAGACCCCCAAACCCCCCCTTATTTCGTTTGAATCTTAGTAATGATT
CACATTCTCGTTTGAGTCTTAGTAATGATTCACATTATCAACCTAAATATGGCTTCTGGGTTAT
AGGGCTGTGGGGAAATTCTGTGTATAATGCTTTTGAGGAGTGTACGTTCACAGGCAAGCCCAGT
GTGTTGACCCTCTCTCTGATGGTCCGACCCTGTCGTGTCGGTATTTTCCTCGACTGTGCAGCTG
GCACCCTCTCGTTTTACAATATTTCCAACCATGGCACTCTTATCTACAGATTCTGTGCAGGTTC
CTTTCCTGATAGGGTTTTTCCATATTTTAACCCCATGGGAAGTTCAGAGCCATTGACAATATGC
TGGCCAGACTCTTAATCTTCACTGTCTCTGTGCATGGTCTCTGGTCCTGATGTGTATGTCATGT
GCCTGAGCTCATCAGCACTATTTTATCGTTTTGTTCATGTCTCTAATCTTTCATTGGAAAATAT
ATTCATTTCTCTAGGCCATATTCTCAGTTTCTTGGGGTATTTTTTGTCTTTGTTTTGTTTTGTT
TTTAGGTGAGACTAACAAATCACTTCCCATATAGTCAAGGACAAATGTCTAGTGCTCACTGCGT
AAGATAACACCGATGCAAAATTCCTCTTATTCTTCATGCCAGAGATGGAAGGCAAGGCCTTGTG
CACGGTGAGGATGTGCTCCACCGCTGAGCTGTTTGCTTCAGCTGTCATGTCCCTATAACCTCAT
TCGGCCCATCAATGAAAGATTAAAGAAGGTTCTTCGACAACTTGTCTATTCATGCTGAAAATTA
TATATAGGAGTCTCTGCTTAAGAAATGCACCCTGAGCTGTAGGCCAAAGAATGAAGGAGAAGCA
TCACAAGAAGCCTTATCACTGTGACTAAATTAAGTGATCATTAAGACTGTGCATCAGTCTTGCC
TGGGAGCTCATACCTGCCATCCTGCATCTGGGAAGTTGTGGCAGGAAGATTGCTGTGTATTTGA
AGCCACCCTTGTATAGAGTTAAGAGCCTGCTTAAAAAAAATAATCAAGAATATGTATAAAAACC
ACTACTCTATTTTGTTCTAAGAAATAGAATAACTAGATTTCAGAATTGCAGGGTTTGGGTCGTT
TTCACAATTTGTAAATAAATGTTTACTAAAAATAAATGTTAACTTCATAGCTGTCCAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001014045	(Get FASTA)	NCBI Sequence Viewer
	XP_006229974	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH78926	(Get FASTA)	NCBI Sequence Viewer
	EDM18081	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001014045 ⟸ NM_001014023

- UniProtKB:

Q6AYT1 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MASEFVMNLKEEVTCPICLDLMVEPVSGDCGHSFCQACITLNYESSKCNQDEFICPVCRVSYLF
KNLRPNRHVANIVQRLKEFKSSPEEEPKVLSCARHGEKLQLFCKKDMMPICWLCERSQEHRGHQ
TVLIEEVVQEYKEKLQAALQKLMADKKEFENWKDDLQKERTYWQNQIQKDVENVQSEFKGMRDI
MDSEEKKELQKLMQEKEDIMSSLEESENEYSQQSKLLGDLILDVEHQLQCSATEMLQGVENTIK
RSHTFSMRKPKTIPKEQRRVFRAPDLQGMLQVLQEVTEAQRYWVQVTLVESNNPNIFITADKRQ
IRYEDHQARHFARPTENCHAGVLGYPAIQSGKHYWEVDVSGKGSWVLGLSDGSYLFNPIFRSNA
ERPPNPPLFRLNLSNDSHSRLSLSNDSHYQPKYGFWVIGLWGNSVYNAFEECTFTGKPSVLTLS
LMVRPCRVGIFLDCAAGTLSFYNISNHGTLIYRFCAGSFPDRVFPYFNPMGSSEPLTICWPDS

hide sequence

RefSeq Acc Id:	XP_006229974 ⟸ XM_006229912
- Peptide Label:	isoform X1
- UniProtKB:	Q6AYT1 (UniProtKB/TrEMBL)
- Sequence:	show sequence MASEFVMNLKEEVTCPICLDLMVEPVSGDCGHSFCQACITLNYESSKCNQDEFICPVCRVSYLF KNLRPNRHVANIVQRLKEFKSSPEEEPKVLSCARHGEKLQLFCKKDMMPICWLCERSQEHRGHQ TVLIEEVVQEYKEKLQAALQKLMADKKEFENWKDDLQKERTYWQNQIQKDVENVQSEFKGMRDI MDSEEKKELQKLMQEKEDIMSSLEESENEYSQQSKLLGDLILDVEHQLQCSATEMLQGVENTIK RSHTFSMRKPKTIPKEQRRVFRAPDLQGMLQVLQEVTEAQRYWVQVTLVESNNPNIFITADKRQ IRYEDHQARHFARPTENCHAGVLGYPAIQSGKHYWEVDVSGKGSWVLGLSDGSYLFNPIFRSNA ERPPNPPLFRLNLSNDSHSRLSLSNDSHYQPKYGFWVIGLWGNSVYNAFEECTFTGKPSVLTLS LMVRPCRVGIFLDCAAGTLSFYNISNHGTLIYRFCAGSFPDRVFPYFNPMGSSEPLTICWPDS hide sequence

RefSeq Acc Id:

ENSRNOP00000073760 ⟸ ENSRNOT00000082645

RefSeq Acc Id:

ENSRNOP00000023099 ⟸ ENSRNOT00000023100

RefSeq Acc Id:

ENSRNOP00000038739 ⟸ ENSRNOT00000030827

Protein Domains

B box-type B30.2/SPRY RING-type

Transcriptome

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

Promoters

RGD ID:

13690280

Promoter ID:

EPDNEW_R805

Type:

multiple initiation site

Name:

Trim5_1

Description:

tripartite motif-containing 5

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	1	169,463,759 - 169,463,819	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN/SsN (MCW)

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

F344/NCrl (RGD)

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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

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

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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)

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

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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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

LE/Stm (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

LEW/Crl (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

LEW/NCrlBR (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

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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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

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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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

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

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

SBN/Ygl (MCW)

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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:	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:1304579	AgrOrtholog
Ensembl Genes	ENSRNOG00000017191	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000023099	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOP00000038739	UniProtKB/TrEMBL
	ENSRNOP00000073760	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000023100	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOT00000030827	UniProtKB/TrEMBL
	ENSRNOT00000082645	UniProtKB/TrEMBL
Gene3D-CATH	2.60.120.920	UniProtKB/TrEMBL
	3.30.40.10	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7106563	IMAGE-MGC_LOAD
InterPro	B30.2/SPRY_sf	UniProtKB/TrEMBL
	B302	UniProtKB/TrEMBL
	Butyrophylin	UniProtKB/TrEMBL
	ConA-like_dom	UniProtKB/TrEMBL
	SPRY_rcpt	UniProtKB/TrEMBL
	TRIM5	UniProtKB/TrEMBL
	Znf-RING_LisH	UniProtKB/TrEMBL
	Znf_B-box	UniProtKB/TrEMBL
	Znf_RING	UniProtKB/TrEMBL
	Znf_RING/FYVE/PHD	UniProtKB/TrEMBL
	Znf_RING_CS	UniProtKB/TrEMBL
KEGG Report	rno:308906	UniProtKB/TrEMBL
MGC_CLONE	MGC:93716	IMAGE-MGC_LOAD
NCBI Gene	308906	ENTREZGENE
PANTHER	PTHR24103:SF416	UniProtKB/TrEMBL
Pfam	SPRY	UniProtKB/TrEMBL
	zf-B_box	UniProtKB/TrEMBL
	zf-RING_UBOX	UniProtKB/TrEMBL
PhenoGen	Trim5	PhenoGen
PRINTS	BUTYPHLNCDUF	UniProtKB/TrEMBL
PROSITE	B302_SPRY	UniProtKB/TrEMBL
	ZF_BBOX	UniProtKB/TrEMBL
	ZF_RING_1	UniProtKB/TrEMBL
	ZF_RING_2	UniProtKB/TrEMBL
SMART	BBOX	UniProtKB/TrEMBL
	RING	UniProtKB/TrEMBL
	SPRY	UniProtKB/TrEMBL
Superfamily-SCOP	ConA_like_lec_gl	UniProtKB/TrEMBL
UniGene	Rn.12117	ENTREZGENE
UniProt	A0A0G2K6C7_RAT	UniProtKB/TrEMBL
	D4A0Y0_RAT	UniProtKB/TrEMBL
	Q6AYT1	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2010-04-23	Trim5	tripartite motif-containing 5	RGD1304579	similar to 9230105E10Rik protein	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	RGD1304579	similar to 9230105E10Rik protein	RGD1304579_predicted	similar to 9230105E10Rik protein (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1304579_predicted	similar to 9230105E10Rik protein (predicted)	LOC308906_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC308906_predicted	similar to 9230105E10Rik protein (predicted)			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