Cstf2t (cleavage stimulation factor subunit 2, tau variant)

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Gene: Cstf2t (cleavage stimulation factor subunit 2, tau variant) Rattus norvegicus

Analyze

Symbol:

Cstf2t

Name:

cleavage stimulation factor subunit 2, tau variant

RGD ID:

1310026

Description:

Predicted to have RNA binding activity. Predicted to localize to nucleoplasm. Orthologous to human CSTF2T (cleavage stimulation factor subunit 2 tau variant); PARTICIPATES IN 3'-end pre-mRNA processing pathway; RNA polymerase II transcription termination pathway; mRNA decay pathway; INTERACTS WITH 1,3-dinitrobenzene; bisphenol A; C60 fullerene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

cleavage stimulation factor subunit 2 tau; cleavage stimulation factor subunit 2 tau variant; cleavage stimulation factor, 3' pre-RNA subunit 2, tau; cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau; cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant; cleavage stimulation factor, 3' pre-RNA, subunit 2, tau; cleavage stimulation factor, 3' pre-RNA, subunit 2, tau variant; LOC309338

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	228,952,617 - 228,956,183 (+)	NCBI
Rnor_6.0 Ensembl	1	249,574,954 - 249,578,520 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	249,574,954 - 249,578,520 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	256,813,751 - 256,817,317 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	235,060,489 - 235,064,055 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	235,224,192 - 235,226,470 (+)	NCBI
Celera	1	226,077,478 - 226,081,044 (+)	NCBI		Celera
Cytogenetic Map	1	q52	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

1,3-dinitrobenzene (EXP)

17alpha-ethynylestradiol (ISO)

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

all-trans-retinoic acid (ISO)

bisphenol A (EXP)

C60 fullerene (EXP)

cadmium atom (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

enzyme inhibitor (ISO)

fipronil (EXP)

folic acid (ISO)

gentamycin (EXP)

iron atom (ISO)

iron(0) (ISO)

methapyrilene (EXP)

methotrexate (ISO)

methylmercury chloride (ISO)

paracetamol (ISO)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sunitinib (ISO)

thioacetamide (EXP)

topotecan (ISO)

trichostatin A (ISO)

troglitazone (ISO)

urethane (ISO)

valproic acid (ISO)

vitamin D (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

pre-mRNA cleavage required for polyadenylation (IBA)

Cellular Component

cellular_component (ND)

intracellular membrane-bounded organelle (ISO)

mRNA cleavage and polyadenylation specificity factor complex (IBA)

nucleoplasm (IEA,ISO)

Molecular Function

molecular_function (ND)

mRNA binding (IBA)

protein binding (ISO)

RNA binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

3'-end pre-mRNA processing pathway (ISO)

mRNA decay pathway (IEA)

RNA polymerase II transcription termination pathway (ISO)

References

References - curated


1.	Chan S, etal., Wiley Interdiscip Rev RNA. 2011 May-Jun;2(3):321-35. doi: 10.1002/wrna.54. Epub 2010 Oct 18.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Gruber AR, etal., Wiley Interdiscip Rev RNA. 2014 Mar-Apr;5(2):183-96. doi: 10.1002/wrna.1206. Epub 2013 Nov 14.
4.	MGD data from the GO Consortium
5.	Pipeline to import KEGG annotations from KEGG into RGD
6.	RGD automated import pipeline for gene-chemical interactions
7.	RGD comprehensive gene curation

Additional References at PubMed

PMID:11113135	PMID:12477932	PMID:22658674	PMID:22681889

Genomics

Comparative Map Data

Cstf2t
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	228,952,617 - 228,956,183 (+)	NCBI
Rnor_6.0 Ensembl	1	249,574,954 - 249,578,520 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	249,574,954 - 249,578,520 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	256,813,751 - 256,817,317 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	235,060,489 - 235,064,055 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	235,224,192 - 235,226,470 (+)	NCBI
Celera	1	226,077,478 - 226,081,044 (+)	NCBI		Celera
Cytogenetic Map	1	q52	NCBI

CSTF2T
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	10	51,695,486 - 51,699,595 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	10	51,695,486 - 51,699,595 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	10	53,455,246 - 53,459,355 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	10	53,125,252 - 53,129,361 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	10	53,125,251 - 53,129,361	NCBI
Celera	10	46,718,008 - 46,722,117 (-)	NCBI
Cytogenetic Map	10	q21.1	NCBI
HuRef	10	47,433,327 - 47,437,436 (-)	NCBI		HuRef
CHM1_1	10	53,737,028 - 53,741,141 (-)	NCBI		CHM1_1

Cstf2t
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	31,060,241 - 31,063,992 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	19	31,060,237 - 31,064,469 (+)	Ensembl
GRCm38	19	31,082,841 - 31,086,592 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	31,082,837 - 31,087,069 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	19	31,157,331 - 31,161,082 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	19	31,149,001 - 31,152,589 (+)	NCBI			mm8
Celera	19	31,867,444 - 31,871,195 (+)	NCBI		Celera
Cytogenetic Map	19	C1	NCBI

Cstf2t
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955425	6,832,580 - 6,834,499 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955425	6,830,775 - 6,834,799 (-)	NCBI	ChiLan1.0	ChiLan1.0

CSTF2T
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	10	50,477,193 - 50,481,591 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
Mhudiblu_PPA_v0	10	48,342,491 - 48,346,810 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

CSTF2T
(Canis lupus familiaris - dog)

No map positions available.

Cstf2t
(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_004936787	838,153 - 842,118 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CSTF2T
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	98,105,772 - 98,110,358 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	98,104,957 - 98,109,479 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	106,806,097 - 106,809,854 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

Cstf2t
(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_004624791	11,924,945 - 11,929,106 (+)	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
2292216	Bw80	Body weight QTL 80	3.23	0.0019	body mass (VT:0001259)	body weight (CMO:0000012)	1	233490105	264802994	Rat
70211	Niddm24	Non-insulin dependent diabetes mellitus QTL 24	3.79		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	236795785	281795785	Rat
631215	Stl8	Serum triglyceride level QTL 8	9.27	0.0001	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	1	245529606	282763074	Rat
2302040	Pia35	Pristane induced arthritis QTL 35	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	236265430	281265430	Rat
2302375	Bw83	Body weight QTL 83	4.87	0.0002	body mass (VT:0001259)	body weight (CMO:0000012)	1	215711860	260711860	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	156446196	274977688	Rat
61455	Niddm7	Non-insulin dependent diabetes mellitus QTL 7	5.5		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	236763415	258766873	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	161321152	273792054	Rat
724533	Rf51	Renal function QTL 51	5.3	0.0002	kidney plasma flow trait (VT:0005524)	renal plasma flow (CMO:0001914)	1	238830534	278228767	Rat
724538	Kidm1	Kidney mass QTL 1	3.2		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	233663100	273792054	Rat
724552	Glom2	Glomerulus QTL 2	3.3	0.0001	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)	1	243272341	282763074	Rat
734767	Niddm57	Non-insulin dependent diabetes mellitus QTL 57			body mass (VT:0001259)	body weight (CMO:0000012)	1	244401175	282365384	Rat
734768	Niddm59	Non-insulin dependent diabetes mellitus QTL 59			body mass (VT:0001259)	body weight (CMO:0000012)	1	235850810	280850810	Rat
734769	Niddm58	Non-insulin dependent diabetes mellitus QTL 58			body mass (VT:0001259)	body weight (CMO:0000012)	1	244992467	282365384	Rat
1298084	Thym4	Thymus enlargement QTL 4	10.68		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	215828102	260828102	Rat
631658	Cm7	Cardiac mass QTL 7	5.32	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	1	216324817	261324817	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	167394665	278228889	Rat
731175	Uae20	Urinary albumin excretion QTL 20	3.5	0.0018	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	241482188	281795785	Rat
738032	Hcas5	Hepatocarcinoma susceptibility QTL 5	3.12		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	191825895	279986079	Rat
1641926	Teswt2	Testicular weight QTL 2	2.82		testis mass (VT:1000644)	both testes wet weight (CMO:0000175)	1	215711860	258765521	Rat
1598821	Rf55	Renal function QTL 55	6.3		renal blood flow trait (VT:2000006)	ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)	1	238824734	279986079	Rat
2300175	Bmd40	Bone mineral density QTL 40	15.4	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	1	221901238	266901238	Rat
2293655	Bss36	Bone structure and strength QTL 36	10.66	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	1	221901238	266901238	Rat
2293674	Bss39	Bone structure and strength QTL 39	7.1	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	1	221901238	266901238	Rat
2293694	Bss38	Bone structure and strength QTL 38	7.05	0.0001	femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	1	221901238	266901238	Rat
2293700	Bmd27	Bone mineral density QTL 27	6.6	0.0001	femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	244401175	264636028	Rat
2293701	Bmd34	Bone mineral density QTL 34	8.3	0.0001	femur strength trait (VT:0010010)	femoral neck ultimate force (CMO:0001703)	1	244401175	264636028	Rat
631838	Niddm36	Non-insulin dependent diabetes mellitus QTL 36		0.01	insulin secretion trait (VT:0003564)	calculated pancreatic islet insulin release measurement (CMO:0001217)	1	205195290	250195290	Rat
631843	Bw116	Body weight QTL 116	4.1	0.016	abdominal adipose amount (VT:1000220)	abdominal fat pad weight (CMO:0000088)	1	244401175	282365384	Rat
634313	Niddm43	Non-insulin dependent diabetes mellitus QTL 43			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	217054291	281795785	Rat
634321	Hc1	Hypercalciuria QTL 1	2.91		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	193968438	261264776	Rat
1357335	Bw39	Body weight QTL 39	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	1	215828102	260828102	Rat
1357399	Bw45	Body weight QTL 45	3.05		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	1	225689973	270689973	Rat
1357404	Bw42	Body weight QTL 42	4.49	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	1	225689973	270689973	Rat
1600363	Hc6	Hypercalciuria QTL 6	2.7		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	195598053	265002735	Rat
1600374	Mcs17	Mammary carcinoma susceptibility QTL 17	3		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	1	215684498	260684498	Rat
1600388	Niddm67	Non-insulin dependent diabetes mellitus QTL 67	5.84	0.000004	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	213476630	278978026	Rat
1600392	Bw123	Body weight QTL 123		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	244087148	282763074	Rat
1600395	Niddm69	Non-insulin dependent diabetes mellitus QTL 69	4.14	0.0002	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	213476630	278978026	Rat
1600396	Niddm68	Non-insulin dependent diabetes mellitus QTL 68	4.97	0.0003	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	213476630	278978026	Rat
1600397	Edcs4	Endometrial carcinoma susceptibility QTL 4	2.2		uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	1	226706329	271706329	Rat
1578759	Uae30	Urinary albumin excretion QTL 30	3.3	0.003	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	161321256	273791893	Rat
1578763	Kidm29	Kidney mass QTL 29	3.3	0.0001	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	1	196395041	282763074	Rat
1578778	Pur4	Proteinuria QTL 4	3.3	0.003	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	1	161321256	273791893	Rat
1300108	Rf8	Renal function QTL 8	3.75		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	1	249206242	281795785	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1354624	Cm35	Cardiac mass QTL35	5.7		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	192639698	278228889	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	161784169	278228889	Rat
1354652	Kidm20	Kidney mass QTL 20	4.3		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	192639698	278228889	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1549910	Bw54	Body weight QTL 54		0.05	body mass (VT:0001259)	body weight (CMO:0000012)	1	236795785	281795785	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	163796316	282763074	Rat
1358191	Ept10	Estrogen-induced pituitary tumorigenesis QTL 10	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	210360774	264802828	Rat
2292220	Bp306	Blood pressure QTL 306	3.47	0.00087	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	174905700	264802994	Rat
2312564	Glom18	Glomerulus QTL 18	2.4	0.003	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	1	201358068	252480016	Rat
1358890	Bp259	Blood pressure QTL 259	3.06		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	230420627	282645769	Rat
1358898	Bp255	Blood pressure QTL 255	3.6		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	208517798	266948272	Rat
1358916	Kidm22	Kidney mass QTL 22	3.32		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	230420627	262031693	Rat
1358292	Cm37	Cardiac mass QTL 37	6.2	0.00000081	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	1	216324817	261324817	Rat
61327	Eae7	Experimental allergic encephalomyelitis QTL 7	5.6		body mass (VT:0001259)	change in body weight (CMO:0002045)	1	236265430	281265430	Rat
61376	Bp42	Blood pressure QTL 42	23.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	215828102	260828102	Rat
61400	Niddm1	Non-insulin dependent diabetes mellitus QTL 1	11		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	238830408	266793958	Rat
8655655	Arrd2	Age-related retinal degeneration QTL 2	7.79		retinal layer morphology trait (VT:0003727)	percentage of study population developing retinopathy during a period of time (CMO:0002453)	1	202571665	264802994	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
8693637	Alc29	Alcohol consumption QTL 29	2.7	0.258	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	1	227509470	255131140	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
8552891	Epfw5	Epididymal fat weight QTL 5	4.4		epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	1	210652654	255652654	Rat
7394701	Uae46	Urinary albumin excretion QTL 46	3.6	0.0056	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	221901238	266901238	Rat
7387289	Uae45	Urinary albumin excretion QTL 45	2.86	0.0021	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	244148899	282763074	Rat
8655855	Arrd3	Age-related retinal degeneration QTL 3	3.07		lens clarity trait (VT:0001304)	cataract incidence/prevalence measurement (CMO:0001585)	1	202571665	264802994	Rat
10053715	Scort24	Serum corticosterone level QTL 24	2.13	0.0088	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	1	242302911	282763074	Rat
10059587	Bw173	Body weight QTL 173	3.23	0.025	body mass (VT:0001259)	body weight (CMO:0000012)	1	222492538	267492538	Rat
10059590	Kidm44	Kidney mass QTL 44	3.42	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	210990171	255990171	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	746
Count of miRNA genes:	299
Interacting mature miRNAs:	378
Transcripts:	ENSRNOT00000074100
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	32	56	41	19	41	2	2	74	35	39	11	2
Low		11	1				6	9			2		6
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001107586	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC169065	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473953	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000047	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000074100 ⟹ ENSRNOP00000064966

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	249,574,954 - 249,578,520 (+)	Ensembl

RefSeq Acc Id:

NM_001107586 ⟹ NP_001101056

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	228,952,617 - 228,956,183 (+)	NCBI
Rnor_6.0	1	249,574,954 - 249,578,520 (+)	NCBI
Rnor_5.0	1	256,813,751 - 256,817,317 (+)	NCBI
RGSC_v3.4	1	235,060,489 - 235,064,055 (+)	RGD
Celera	1	226,077,478 - 226,081,044 (+)	RGD

Sequence:

show sequence

CGGAAGTGTGGTTCACCAGAGGACGACCCTTGGACGAATTTACTCTCCGCTAAACGCTCGGCAG
GAATCATGTCGAGTTTGGCGGTCAGAGACCCAGCCATGGATCGATCACTGCGTTCGGTGTTCGT
GGGGAACATTCCGTATGAGGCGACGGAGGAGCAGTTAAAGGACATTTTCTCGGAGGTTGGTTCA
GTTGTCAGTTTCCGTCTCGTCTACGATAGAGAGACAGGAAAGCCCAAGGGTTATGGCTTCTGCG
AGTACCAAGACCAGGAGACTGCGCTTAGTGCCATGCGGAACCTCAATGGGCGAGAATTTAGTGG
GAGAGCGCTTCGGGTGGACAATGCTGCCAGTGAAAAGAACAAGGAGGAGTTAAAAAGCTTAGGC
CCGGCAGCCCCCATCATTGACTCACCCTATGGGGACCCTATTGATCCAGAAGATGCTCCAGAAT
CGATTACTAGGGCAGTCGCCAGCCTGCCCCCAGAGCAAATGTTTGAGCTGATGAAGCAAATGAA
GTTGTGTGTCCAAAACAGTCACCAGGAAGCTCGAAACATGCTACTTCAGAACCCACAATTGGCG
TACGCTCTGCTGCAGGCACAAGTGGTGATGAGAATCATGGATCCAGAGATTGCACTGAAAATTT
TGCATCGTAAGATCCATGTCACACCACTGATCCCAGGCAAATCACAGCCTGTCTCTGGGCCTGG
CCCTGGTGGGCCTGGTGGCCCTGGTGGCCCTGGCGGCCCTGGCCCCGGCCCTGCCCCTGGCCTC
TGCCCAGGACCTAACGTCATGTTGAACCAACAGAATCCTGCCCCTCAGCCTCAGCATTTACCAA
GAAGACCTGTGAAGGACATTCCTCCTCTGATGCAGACCTCGATCCAGGGCGGAATTCCAGCTCC
GGGGCCAATACCAGCTGCAGTTCCTGGACCTGGACCTGGTTCCTTAACCCCGGGAGGAACCATG
CAGCCACAGGTTGGCATGCCAGTGGTTGGTCCAGTGCCCTTAGAGCGAGGACAGATGCAGATAT
CAGATCCTAGACCTCCAATGCCTCGTGGACCCATGCCTTCTGGTGGCATCCCTCCTCGAGGACT
ACTGGGAGATGCTCCAAATGACCCGCGTGGAGGAACTTTGCTCTCAGTGACTGGAGAAGTAGAG
CCCAGAGGCTATATGGGACCACCCCATCAGGGTCCTCCAATGCATCATGGTCATGACAACCGTG
GCCCTGCCTCACATGATATGAGAGGAGGACCGTTGGCAGCAGATCCCAGAATGCTGATTGGAGA
ACCCAGAGGTCCCATGATGGATCAAAGAGGTCTACCTATGGATGGTAGAGGAGGAAGAGACTCT
CGAGGGATGGAGGCCCGGCCCATGGAAACGGAGGTCTTGGAGCCACGAGGAATGGAGAGAAGAA
TGGAGACCTGTGCAATGGAAACCAGAGGGATGGAAGCAAGAGGCATAGACGCAAGAGGACTGGA
GATGAGGGGCCCTGGCCCTAGTTCCCGAGGTCCGATGACTGGTGGGATCCAGGGTCCTGGCCCC
ATTAATATGGGGGCAGGTGGCCCTCAGGGACCTCGACAGGTTCCAAACATTGCAGGAGTGGGAA
ATCCTGGAGGTGCCATGCAGGGGGCAGGTATACAAGGAGCAGGAATGCAGGGGGCAGGTATGCA
GGGAGGAGGGATGCAGGGGGCAGGCATGCAGGGAGGAGGGATGCAGGGGGCAGGCATGCAGGGA
GGAGGGATGCAGGGGGCTGGCATGCAAGGAGCCAGTAAGCAAGGTGCGGGCCAGCCTAGTAGTT
TTAGCCCGGGGCAAAGCCAGGTAACTCCTCAAGATCAAGAAAAAGCAGCTTTGATCATGCAGGT
TCTTCAGCTGACTGCAGATCAGATTGCCATGCTGCCTCCTGAGCAAAGGCAGAGCATTTTGATT
TTAAAGGAACAAATCCAGAAATCTACGGGTGCTTCTTGAAAGGTTTTCAGCTAAGAAGTACTTA
GTTATTCCTTCAGGGTTTACTCTGTGGCATGAAGTGGGTGCAAAAAGCTGTCTTCTGTGTTCGC
ACACTTTAACCATTTAAGGTTTCCTTCTCCCCAGACCTTAAATCTTATTTCTAGTTTTGTTACT
TTCTGTTTTCCTTTTTATTTTTTGATTGAGGGGAGGGGGTGGAGGGGGGGGGCCTGTTTACTTT
GTCACTGTTGACTCTACTGGGTACCCTAAAAATGACTACATCATACAAAATAAGGTTATGAGGA
AAATGCGGCAATAATTTGCACTTTTGTTAACTGTGTTTTAAAAATACTGAGTAAACTGGGAACT
ACATAAAAATTGAAAGTGGCTTGTTACAGTATTGATATACTAAGATAGTTTAAAGTTCTTTGGT
TGTATATTGAACTGAATGTCAGAATGTTAAGGTACACTTTTTGGTAAAAGAAATTACTATATTT
TGGAGGCAGCAGAGTACTGTAGTAAGGTTAATGTTTAGTTATTTTGGAATTATTTTGAAATATT
GGAGCTAACAGTTTGTGGTGTAGATGTGTGTTTTTTTAAAGCATTGTTATCTGTAAAAAGATAA
TTTTCATTTATCTGACTTTTTTTTTTTTGAGACCATTAATATTCTTGCCTGATCCCAACTGGTA
ATTTTGCAGGATAGTTGTAGTGTCAGCTGAATTACATAAAACCTCCTTCTTATACATTTCTCTA
AAAAATTCTTAAGGCCCAAGTCTGGTTGTAAGTAGTTTTTTCACATCCTTTTAAAGAATCAGAC
ATGAGGTTTGACTTTCTTGAGTAATGGAGGTTTTTGGGGTTTTTTTGTTTTTGTTTTTCAGTAA
AGCTCCCAAGTTCTTGATAACCTACTATCCATTCACAGATGGAATCCATTAGGTCAGCAAGAAC
CAGAAGTTAAAATCTTACTCTATGCCTTTTGATATGTCTTACAGTTTGATAACTTTCACAAACT
ACTTTTCTATCATCACCTTGCTAGAACTGGGGCCCAAGTGAACTGACAACTCTGCTCAGTTAAC
TTAATATGTTATTTCTCACAACTCACAAAAGCTCTTTGGTCATAACGTAGTTCCCATGAAGTGT
GTTTGAGAATAAGGAATGTGGAACTTAATCCATTTCTTTTAGAGCTACTGTATCATTTTCAATC
AATGTGGCACCTGGACACGGTGTCATATTTAGATAATGAGCAGAAACAAGCACAAGCTCCCACT
TGACCAAGTGGCATTCCTCTGTGGAAAAATAAATACCCACCTACAGAGGGATGAGCAGCCTTAG
GGAGGGAGCTGACCCAAGGTTGTTTTCCCTTGCAAAGTTTGAGCATTTTTGAGTGTACAGAGTT
TTCATTCCTAGGCTATTTTCCAGCCATTTAGTTTTTGTGCTAGTGTTAGACTCCTGTGGTTTCC
TCTGCCTCCTATGCTGAGGTGGGTTTGTGGTCTGTACCTTTGTGCTAGTTCTGACTAATTCCAA
TTGCTTGCTTCTTTCGAGACTGCAGTTGCTAGCCCAAAACTTCTTACAGTCTTTGTTATAAGAA
AATCTCTGCATTGTTTCATGAAAATTAAATAAAAAGGTTATATAATT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001101056	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI69065	(Get FASTA)	NCBI Sequence Viewer
	EDM13124	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001101056 ⟸ NM_001107586

- UniProtKB:

M0R6B9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSSLAVRDPAMDRSLRSVFVGNIPYEATEEQLKDIFSEVGSVVSFRLVYDRETGKPKGYGFCEY
QDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGPAAPIIDSPYGDPIDPEDAPESI
TRAVASLPPEQMFELMKQMKLCVQNSHQEARNMLLQNPQLAYALLQAQVVMRIMDPEIALKILH
RKIHVTPLIPGKSQPVSGPGPGGPGGPGGPGGPGPGPAPGLCPGPNVMLNQQNPAPQPQHLPRR
PVKDIPPLMQTSIQGGIPAPGPIPAAVPGPGPGSLTPGGTMQPQVGMPVVGPVPLERGQMQISD
PRPPMPRGPMPSGGIPPRGLLGDAPNDPRGGTLLSVTGEVEPRGYMGPPHQGPPMHHGHDNRGP
ASHDMRGGPLAADPRMLIGEPRGPMMDQRGLPMDGRGGRDSRGMEARPMETEVLEPRGMERRME
TCAMETRGMEARGIDARGLEMRGPGPSSRGPMTGGIQGPGPINMGAGGPQGPRQVPNIAGVGNP
GGAMQGAGIQGAGMQGAGMQGGGMQGAGMQGGGMQGAGMQGGGMQGAGMQGASKQGAGQPSSFS
PGQSQVTPQDQEKAALIMQVLQLTADQIAMLPPEQRQSILILKEQIQKSTGAS

hide sequence

RefSeq Acc Id:

ENSRNOP00000064966 ⟸ ENSRNOT00000074100

Protein Domains

RRM

Transcriptome

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

Promoters

RGD ID:

13690854

Promoter ID:

EPDNEW_R1379

Type:

initiation region

Name:

Cstf2t_1

Description:

cleavage stimulation factor subunit 2, tau variant

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	249,574,968 - 249,575,028	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN/SsN (MCW)

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

F344/NCrl (RGD)

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

F344/NRrrc (MCW)

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

FHH/EurMcwi (MCW)

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

FHH/EurMcwi (RGD)

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

FHL/EurMcwi (MCW)

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

FHL/EurMcwi (RGD)

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

GH/OmrMcwi (MCW)

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

GK/Ox (RGD)

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

LE/Stm (RGD)

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LH/MavRrrc (RGD)

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

LL/MavRrrc (RGD)

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

LN/MavRrrc (RGD)

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

M520/N (MCW)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (MCW)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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

Damaging Variants

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
1	235061954	235061955	G	T	snv	HCR/2Mco (UMich)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1310026	AgrOrtholog
Ensembl Genes	ENSRNOG00000050289	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000064966	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000074100	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	1.10.20.70	UniProtKB/TrEMBL
	3.30.70.330	UniProtKB/TrEMBL
InterPro	CSTF2_C_sf	UniProtKB/TrEMBL
	CSTF2_hinge	UniProtKB/TrEMBL
	CSTF_C	UniProtKB/TrEMBL
	Nucleotide-bd_a/b_plait_sf	UniProtKB/TrEMBL
	RBD_domain_sf	UniProtKB/TrEMBL
	RRM_dom	UniProtKB/TrEMBL
KEGG Report	rno:309338	UniProtKB/TrEMBL
NCBI Gene	309338	ENTREZGENE
Pfam	CSTF2_hinge	UniProtKB/TrEMBL
	CSTF_C	UniProtKB/TrEMBL
	RRM_1	UniProtKB/TrEMBL
PhenoGen	Cstf2t	PhenoGen
PROSITE	RRM	UniProtKB/TrEMBL
SMART	RRM	UniProtKB/TrEMBL
Superfamily-SCOP	SSF54928	UniProtKB/TrEMBL
UniProt	B5DFH8_RAT	UniProtKB/TrEMBL
	M0R6B9	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-04-13	Cstf2t	cleavage stimulation factor subunit 2, tau variant	Cstf2t	cleavage stimulation factor, 3' pre-RNA, subunit 2, tau variant	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2015-11-19	Cstf2t	cleavage stimulation factor, 3' pre-RNA, subunit 2, tau variant	Cstf2t	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2012-01-10	Cstf2t	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	Cstf2t	cleavage stimulation factor, 3' pre-RNA subunit 2, tau	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Cstf2t	cleavage stimulation factor, 3' pre-RNA subunit 2, tau	Cstf2t_predicted	cleavage stimulation factor, 3' pre-RNA subunit 2, tau (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Cstf2t_predicted	cleavage stimulation factor, 3' pre-RNA subunit 2, tau (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)

RGD Manual Annotations

Imported Annotations - KEGG (archival)