Zc3h15 (zinc finger CCCH-type containing 15)

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner VCMap Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

Gene: Zc3h15 (zinc finger CCCH-type containing 15) Rattus norvegicus

Analyze

Symbol:

Zc3h15

Name:

zinc finger CCCH-type containing 15

RGD ID:

1359234

Description:

Predicted to have metal ion binding activity. Predicted to be involved in cytokine-mediated signaling pathway; cytoplasmic translation; and positive regulation of GTPase activity. Predicted to localize to cytosol. Orthologous to human ZC3H15 (zinc finger CCCH-type containing 15); INTERACTS WITH bisphenol A; finasteride; flutamide.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

brain zinc finger protein; LOC362154; MGC95079; p48ZnF; zinc finger CCCH domain-containing protein 15

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	ZC3H15 (zinc finger CCCH-type containing 15)	HGNC	EggNOG, Ensembl, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Zc3h15 (zinc finger CCCH-type containing 15)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Zc3h15 (zinc finger CCCH-type containing 15)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	ZC3H15 (zinc finger CCCH-type containing 15)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	ZC3H15 (zinc finger CCCH-type containing 15)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Zc3h15 (zinc finger CCCH-type containing 15)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	ZC3H15 (zinc finger CCCH-type containing 15)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	ZC3H15 (zinc finger CCCH-type containing 15)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Zc3h15 (zinc finger CCCH-type containing 15)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Zc3h15 (zinc finger CCCH-type containing 15)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Homo sapiens (human):	ZC3H15 (zinc finger CCCH-type containing 15)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	zc3h15 (zinc finger CCCH-type containing 15)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	F27D4.4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	CG8635	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Saccharomyces cerevisiae (baker's yeast):	TMA46	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	68,744,591 - 68,764,335 (+)	NCBI
Rnor_6.0 Ensembl	3	71,020,534 - 71,040,157 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	71,020,420 - 71,040,159 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	77,550,822 - 77,570,544 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	66,821,085 - 66,840,710 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	66,717,456 - 66,737,080 (+)	NCBI
Celera	3	68,123,487 - 68,143,111 (+)	NCBI		Celera
Cytogenetic Map	3	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Neurodevelopmental Disorders (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

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

2-methylcholine (ISO)

aflatoxin B1 (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

cadmium dichloride (ISO)

cyclosporin A (ISO)

dicrotophos (ISO)

disodium selenite (ISO)

doxorubicin (ISO)

elemental selenium (ISO)

enzyme inhibitor (ISO)

ethanol (ISO)

finasteride (EXP)

flutamide (EXP)

folic acid (ISO)

glafenine (EXP)

gold atom (ISO)

gold(0) (ISO)

hypochlorous acid (ISO)

kojic acid (ISO)

methyl methanesulfonate (ISO)

methylparaben (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

selenium atom (ISO)

succimer (ISO)

tetrachloromethane (ISO)

triphenyl phosphate (EXP)

triptonide (ISO)

vinclozolin (EXP)

vitamin E (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cytokine-mediated signaling pathway (ISO)

cytoplasmic translation (IBA)

positive regulation of GTPase activity (ISO)

Cellular Component

cytosol (IBA,ISO)

nucleus (IEA)

Molecular Function

metal ion binding (IEA)

protein binding (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Heese K, etal., Exp Mol Med 2004 Apr 30;36(2):130-4.
3.	MGD data from the GO Consortium
4.	RGD automated data pipeline
5.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6.	RGD automated import pipeline for gene-chemical interactions
7.	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:10880228	PMID:22658674	PMID:22681889	PMID:23470633	PMID:23711155	PMID:25468996

Genomics

Comparative Map Data

Zc3h15
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	68,744,591 - 68,764,335 (+)	NCBI
Rnor_6.0 Ensembl	3	71,020,534 - 71,040,157 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	71,020,420 - 71,040,159 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	77,550,822 - 77,570,544 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	66,821,085 - 66,840,710 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	66,717,456 - 66,737,080 (+)	NCBI
Celera	3	68,123,487 - 68,143,111 (+)	NCBI		Celera
Cytogenetic Map	3	q24	NCBI

ZC3H15
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	2	186,486,253 - 186,509,361 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	2	186,486,253 - 186,509,361 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	2	187,350,987 - 187,374,088 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	187,059,130 - 187,082,333 (+)	NCBI	NCBI36		hg18	NCBI36
Celera	2	180,946,684 - 180,969,891 (+)	NCBI
Cytogenetic Map	2	q32.1	NCBI
HuRef	2	179,210,476 - 179,234,063 (+)	NCBI		HuRef
CHM1_1	2	187,357,183 - 187,380,391 (+)	NCBI		CHM1_1

Zc3h15
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	83,474,922 - 83,494,961 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	2	83,474,779 - 83,494,966 (+)	Ensembl
GRCm38	2	83,644,578 - 83,664,617 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	83,644,435 - 83,664,622 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	83,484,735 - 83,504,774 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	83,445,417 - 83,465,456 (+)	NCBI			mm8
Celera	2	85,284,428 - 85,304,248 (+)	NCBI		Celera
Cytogenetic Map	2	D	NCBI

Zc3h15
(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_004955403	11,740,107 - 11,761,005 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955403	11,740,107 - 11,761,005 (-)	NCBI	ChiLan1.0	ChiLan1.0

ZC3H15
(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	2B	191,576,403 - 191,599,609 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2B	191,576,403 - 191,599,609 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	2B	73,774,955 - 73,798,061 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

ZC3H15
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	36	28,730,213 - 28,743,884 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	36	28,725,079 - 28,743,884 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	36	28,627,635 - 28,641,296 (+)	NCBI
ROS_Cfam_1.0	36	28,950,239 - 29,009,303 (+)	NCBI
UMICH_Zoey_3.1	36	29,014,656 - 29,028,335 (+)	NCBI
UNSW_CanFamBas_1.0	36	28,946,032 - 28,959,704 (+)	NCBI
UU_Cfam_GSD_1.0	36	29,116,356 - 29,130,029 (+)	NCBI

Zc3h15
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405303	145,903,340 - 145,929,725 (+)	NCBI
SpeTri2.0	NW_004936506	10,908,347 - 10,934,785 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ZC3H15
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	15	91,493,657 - 91,529,696 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	15	91,493,591 - 91,517,362 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	15	101,503,541 - 101,527,322 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ZC3H15
(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	10	72,020,594 - 72,044,050 (+)	NCBI
ChlSab1.1 Ensembl	10	72,020,808 - 72,043,420 (+)	Ensembl

Zc3h15
(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_004624899	3,394,009 - 3,415,446 (-)	NCBI

Position Markers

RH140856

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Cytogenetic Map	3	q24	UniSTS

DXS9848

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	68,753,435 - 68,754,836 (+)	MAPPER
Rnor_6.0	3	71,029,262 - 71,030,662	NCBI	Rnor6.0
Rnor_5.0	3	77,559,647 - 77,561,047	UniSTS	Rnor5.0
RGSC_v3.4	3	66,829,813 - 66,831,213	UniSTS	RGSC3.4
Celera	3	68,132,215 - 68,133,615	UniSTS
Cytogenetic Map	3	q24	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
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	95176874	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10094081	93415837	Rat
2298542	Neuinf11	Neuroinflammation QTL 11	3.9		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	3	10119318	79772001	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
2302055	Pia30	Pristane induced arthritis QTL 30	3.5	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)	3	29321714	74321714	Rat
9590286	Uminl1	Urine mineral level QTL 1	3.5	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	3	29682732	74682732	Rat
9590136	Scort3	Serum corticosterone level QTL 3	23.37	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	29682732	74682732	Rat
8552950	Pigfal12	Plasma insulin-like growth factor 1 level QTL 12	7.3		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	3	29682732	74682732	Rat
8694196	Abfw2	Abdominal fat weight QTL 2	16.58	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	3	29682732	74682732	Rat
8694386	Bw159	Body weight QTL 159	4.52	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	3	29682732	74682732	Rat
1354590	Despr11	Despair related QTL 11		0.000031	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	3	29908255	74908255	Rat
2303593	Gluco46	Glucose level QTL 46	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	29908255	74908255	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	30114912	123700444	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	30846101	172879276	Rat
2301400	Cm68	Cardiac mass QTL 68		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	3	31103589	72989078	Rat
11565451	Bw177	Body weight QTL 177		0.002	body mass (VT:0001259)	body weight (CMO:0000012)	3	31103589	72989078	Rat
11565452	Kidm57	Kidney mass QTL 57		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	31103589	72989078	Rat
12879866	Cm94	Cardiac mass QTL 94		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	31103589	72989078	Rat
12879867	Cm95	Cardiac mass QTL 95		0.047	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	3	31103589	72989078	Rat
12879868	Am6	Aortic mass QTL 6		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	3	31103589	72989078	Rat
61356	Bp37	Blood pressure QTL 37	3		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	32130997	77130997	Rat
631647	Bp122	Blood pressure QTL 122	6.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	32130997	77130997	Rat
1354589	Bw31	Body weight QTL 31	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	3	33477354	81136227	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	33477354	108914061	Rat
61419	Cia11	Collagen induced arthritis QTL 11	5.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	3	34394121	103141944	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	39248391	140271184	Rat
738019	Anxrr10	Anxiety related response QTL 10	3.9		exploratory behavior trait (VT:0010471)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	3	40422921	85422921	Rat
1331777	Bw24	Body weight QTL 24	3.503		body mass (VT:0001259)	body weight (CMO:0000012)	3	40523593	92654473	Rat
1331795	Rf30	Renal function QTL 30	3.708		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	3	40523593	92654473	Rat
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	43295930	108914061	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	43295930	163640485	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	43295930	163640485	Rat
1300178	Hrtrt4	Heart rate QTL 4	3.74		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	45406058	94467785	Rat
1581503	Cm58	Cardiac mass QTL 58	2.7	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	45406058	127023997	Rat
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	45406058	177699992	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	48561928	155263151	Rat
1358186	Ept2	Estrogen-induced pituitary tumorigenesis QTL 2	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	48562146	115249962	Rat
2292613	Ept16	Estrogen-induced pituitary tumorigenesis QTL 16	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	48562146	115249962	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	51821836	124513579	Rat
724523	Tsu1	Thymus enlargement suppressive QTL 1	3.84		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	3	51822008	120917851	Rat
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	54630948	119830094	Rat
1582238	Bw68	Body weight QTL 68	3.2	0.0064	body mass (VT:0001259)	body weight (CMO:0000012)	3	54630948	119830094	Rat
1582239	Epfw1	Epididymal fat weight QTL 1	4.5	0.0006	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	3	54630948	119830094	Rat
61377	Edpm3	Estrogen-dependent pituitary mass QTL 3	7.05	0.038	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	54631046	93415673	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	55245276	95176874	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	55245276	95176874	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	55245276	95176874	Rat
1358293	Bw38	Body weight QTL 38	6	0.0000031	body mass (VT:0001259)	body weight (CMO:0000012)	3	56735995	101735995	Rat
1581568	Rf53	Renal function QTL 53			total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	58204463	170534769	Rat
8662816	Vetf4	Vascular elastic tissue fragility QTL 4	4		renal artery integrity trait (VT:0010642)	number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)	3	61241033	165369047	Rat
1300111	Rf12	Renal function QTL 12	3.78		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	3	62922868	127023997	Rat
631200	Cm25	Cardiac mass QTL 25	4.8	0.0001	heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	3	63049050	92654302	Rat
1582221	Kidm30	Kidney mass QTL 30	3.5	0.0008	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	3	66711607	119830094	Rat
1582210	Bw71	Body weight QTL 71	3.3	0.0012	body mass (VT:0001259)	body weight (CMO:0000012)	3	66711607	119830094	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	459
Count of miRNA genes:	231
Interacting mature miRNAs:	279
Transcripts:	ENSRNOT00000007276
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	8	11	74	35	41	11	8
Low
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001010963	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_352425	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AY377983	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC088438	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473949	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ212631	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ232115	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ233565	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000115	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000007276 ⟹ ENSRNOP00000007276

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	71,020,534 - 71,040,157 (+)	Ensembl

RefSeq Acc Id:

NM_001010963 ⟹ NP_001010963

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	68,744,708 - 68,764,335 (+)	NCBI
Rnor_6.0	3	71,020,534 - 71,040,159 (+)	NCBI
Rnor_5.0	3	77,550,822 - 77,570,544 (+)	NCBI
RGSC_v3.4	3	66,821,085 - 66,840,710 (+)	RGD
Celera	3	68,123,487 - 68,143,111 (+)	RGD

Sequence:

show sequence

GTAGCCATCTGCGTCGCAGACGGCTCGGCGCCCCCGCCTCCGCAATGCCCCCCAAGAAACAGGC
TCAGGCCGGGGGCAGCAAGAAGGCGGAGCAGAAGAAGAAGGAGAAGATCATCGAGGACAAAACT
TTTGGACTAAAGAATAAGAAGGGAGCAAAACAACAGAAATTTATTAAGGCTGTCACTCATCAAG
TGAAATTTGGACAACAGAATCCTCGTCAGGTAGCACAAAGTGAAGCTGAAAAGAAATTGAAGAA
AGATGACAAGAAGAAAGAGCTACAAGAACTAAATGAGTTGTTCAAACCGGTAGTTGCTGCACAA
AAAATAAGTAAAGGTGCGGACCCCAAATCTGTGGTGTGCGCATTCTTCAAACAGGGACAGTGTA
CTAAAGGAGATAAATGTAAGTTCTCTCATGACCTCACTTTGGAGAGAAAATGTGAAAAACGAAG
TGTTTACATTGATGCAAGAGATGAAGAACTTGAAAAAGATACCATGGATAACTGGGATGAGAAA
AAGCTGGAAGAAGTAGTAAACAAGAAGCACGGTGAGGCGGAAAAGAAAAAACCAAAAACTCAAA
TAGTGTGCAGACATTTTCTTGAAGCTATTGAAAATAACAAGTATGGCTGGTTTTGGGTGTGTCC
TGGAGGTGGGGACAATTGCATGTATCGCCATGCACTTCCTCCTGGGTTTGTGCTAAAGAAAGAC
AAAAAGAAAGAAGAAAAAGAAGATGAAATATCATTAGAAGATCTAATTGAAAGAGAGCGTTCTG
CCCTAGGTCCAAATGTTACCAAAATCACTCTAGAATCTTTTCTTGCATGGAAGAAAAGGAAAAG
ACAAGAAAAGATTGATAAACTTGAACAAGATATGGAGAGGCGGAAAGCTGACTTCAAAGCAGGG
AAAGCGCTGGTGATCAGTGGTCGTGAGGTGTTTGAGTTTCGTCCAGAGCTGGTCAACGATGACG
ACGAGGAAGCAGACGACACCCGTTACATTCAGGGAACAGGAGGTGATGAGGTTGATGACTCTGT
GGGTGTAAATGACATAGATCTAAGCCTCTATGTCCCAAGAGATGTGGAAGAGACAGGGATCACT
GTGGCCAGTCTTGAAAGATTCAGCACCTATGCGTCAGATAAGGACGAGAACAAATTAAGTGAAG
CTTCTGGAGGTCTGGCTGAAAATGGTGAAAGAAGTGATTTGGATGAGGACAGCGGAGGGGGAGG
ACAGGAAAATGGGTCCATCGATGCTGTTCCTGTTGATGAAAACCTGTTCACTGGTGAAGATCTG
GATGAACTAGAAGAAGAATTAAACACACTTGATTTAGAAGAATGACGACAAGGAAGAAAATTAG
GTCGGCTCAGTACGATCAACATGAACTGAGATTGACAACGTTAATTGTTTTGCCACCCGGAATC
AACAGGATGTTTATTTCCCCGTGATGATTCTGGAGGGACTCTGTCCTCCAAAAGGAATACTCTC
CCTGCGTCTTCTCTTCTGACTCTGACTACAGCTCTTAGTAAGTTCAGAGTAGTTGGTGATAAAT
TAAAAATGCTCATTACAGAAGACGATTGTTGTTGTAACTGTCCACTCATGTAGGAAGTGTAACC
GCTTTTCCAGCTTTTGTTTTCTTTGGGCATGTGTAATTTCCAGGAACAACAAATTCACACTTAA
AATACTTGTGTTTGATGCAGTTTTTAATGAGTGGCTTCCTTTCCTTTGTATTTATGTTTTAGAG
ACGACCTGAAAAGTGAGCACTGTACTTGATAAAGGAAACTGCATATGCAGGTTCAGTATTGTAC
GTGGACATGAGAATGGGAAACTGCATATGCAGGTTCAGTATTGTACGTGGACATGAGAATGGGA
AACTGCATATGCAGGTTCAGTATTGTACGTGGACATGAGACTGGGACTTGTTCAATCCAACAGG
GTCAGCTACAGCGCCCTGTATGAAAGATGTTTGAAGTTCTCCCCTTTTTGCCAATAAAGTTGTA
AATAAAAACCATCATACATCCAAATCCAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XR_352425

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	68,744,591 - 68,764,335 (+)	NCBI
Rnor_6.0	3	71,020,420 - 71,040,159 (+)	NCBI
Rnor_5.0	3	77,550,822 - 77,570,544 (+)	NCBI

Sequence:

show sequence

CCGTCCTGTCGCAAAGGCCACATCCGGGCGGCGAATGAGCGAGTCGCTTTCCGTGCGCTGCGGC
GGCGGCGGCTGGGTCTTCCTGCTCGCGCCGCGCTGCCGGACGCCCCGACGGTAGCCATCTGCGT
CGCAGACGGCTCGGCGCCCCCGCCTCCGCAATGCCCCCCAAGAAACAGGCTCAGGCCGGGGGCA
GCAAGAAGGCGGAGCAGAAGAAGAAGGAGAAGATCATCGAGGACAAAACTTTTGGACTAAAGAA
TAAGAAGGGAGCAAAACAACAGAAATTTATTAAGGCTGTCACTCATCAAGTGAAATTTGGACAA
CAGAATCCTCGTCAGGTAGCACAAAGTGAAGCTGAAAAGAAATTGAAGAAAGATGACAAGAAGA
AAGAGCTACAAGAACTAAATGAGTTGTTCAAACCGGTAGTTGCTGCACAAAAAATAAGTAAAGG
TGCGGACCCCAAATCTGTGGTGTGCGCATTCTTCAAACAGGGACAGTGTACTAAAGGAGATAAA
TGTAAGTTCTCTCATGACCTCACTTTGGAGAGAAAATGTGAAAAACGAAGTGTTTACATTGATG
CAAGAGATGAAGAACTTGAAAAAGATACCATGGATAACTGGGATGAGAAAAAGCTGGAAGAAGT
AGTAAACAAGAAGCACGGTGAGGCGGAAAAGAAAAAACCAAAAACTCAAATAGTGTGCAGACAT
TTTCTTGAAGCTATTGAAAATAACAAGTATGGCTGGTTTTGGGTGTGTCCTGGAGGTGGGGACA
ATTGCATGTATCGCCATGCACTTCCTCCTGGGTTTGTGCTAAAGAAAGACAAAAAGAAAGAAGA
AAAAGAAGATGAAATATCATTAGAAGATCTAATTGAAAGAGAGCGTTCTGCCCTAGGTCCAAAT
GTTACCAAAATCACTCTAGAATCTTTTCTTGCATGGAAGAAAAGGAAAAGACAAGAAAAGATTG
ATAAACTTGAACAAGATATGGAGAGGCGGAAAGCTGACTTCAAAGCAGGGAAAGCGCTGGTGAT
CAGTGGTCGTGAGGTGTTTGAGTTTCGTCCAGAGCTGGTCAACGATGACGACGAGGAAGCAGAC
GACACCCGTTACATTCAGGGAACAGGAGGTGATGAGGTTGATGACTCTGTGGGTGTAAATGACA
TAGATCTAAGCCTCTATGTCCCAAGAGATGTGGAAGAGACAGGGATCACTGTGGCCAGTCTTGA
AAGATTCAGCACCTATGCGTCAGATAAGGACGAGAACAAATTAAGTGAAGCTTCTGGAGGTCTG
GCTGAAAATGGTGAAAGAAGTGATTTGGATGAGGACAGCGGAGGGGGAGGACAGGAAAATGGGT
CCATCGATGCTGTTCCTGTTGATGAAAACCTGTTCACTGGTGAAGATCTGGATGAACTAGAAGA
AGAATTAAACACACTTGATTTAGAAGAATGACGACAAGGAAGAAAATTAGGTCGGCTCAGTACG
ATCAACATGAACTGAGATTGACAACGTTAATTGTTTTGCCACCCGGAATCAACAGGATGTTTAT
TTCCCCGTGATGATTCTGGAGGGACTCTGTCCTCCAAAAGGAATACTCTCCCTGCGTCTTCTCT
TCTGACTCTGACTACAGCTCTTAGTAAGTTCAGAGTAGTTGGTGATAAATTAAAAATGCTCATT
ACAGAAGACGATTGTTGTTGTAACTGTCCACTCATGTAGGAAGTGTAACCGCTTTTCCAGCTTT
TGTTTTCTTTGGGCATGTGTAATTTCCAGGAACAACAAATTCACACTTAAAATACTTGTGTTTG
ATGCAGTTTTTAATGAGTGGCTTCCTTTCCTTTGTATTTATGTTTTAGAGACGACCTGAAAAGT
GAGCACTGTACTTGATAAAGGAAACTGCATATGCAGGTTCAGTATTGTACGTGGACATGAGAAT
GGGAAACTGCATATGCAGGTTCAGTATTGTACGTGGACATGAGACTGGGACTTGTTCAATCCAA
CAGGGTCAGCTACAGCGCCCTGTATGAAAGATGTTTGAAGTTCTCCCCTTTTTGCCAATAAAGT
TGTAAATAAAAACCATCATACATCCAAATCCAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001010963	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH88438	(Get FASTA)	NCBI Sequence Viewer
	AAR24540	(Get FASTA)	NCBI Sequence Viewer
	EDL79292	(Get FASTA)	NCBI Sequence Viewer
	Q6U6G5	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001010963 ⟸ NM_001010963

- UniProtKB:

Q6U6G5 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MPPKKQAQAGGSKKAEQKKKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSE
AEKKLKKDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQGQCTKGDKCKFSHDLTLE
RKCEKRSVYIDARDEELEKDTMDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCRHFLEAIENNKY
GWFWVCPGGGDNCMYRHALPPGFVLKKDKKKEEKEDEISLEDLIERERSALGPNVTKITLESFL
AWKKRKRQEKIDKLEQDMERRKADFKAGKALVISGREVFEFRPELVNDDDEEADDTRYIQGTGG
DEVDDSVGVNDIDLSLYVPRDVEETGITVASLERFSTYASDKDENKLSEASGGLAENGERSDLD
EDSGGGGQENGSIDAVPVDENLFTGEDLDELEEELNTLDLEE

hide sequence

RefSeq Acc Id:

ENSRNOP00000007276 ⟸ ENSRNOT00000007276

Transcriptome

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

Promoters

RGD ID:

13692175

Promoter ID:

EPDNEW_R2700

Type:

initiation region

Name:

Zc3h15_1

Description:

zinc finger CCCH-type containing 15

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	3	71,020,460 - 71,020,520	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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

ACI/EurMcwi (RGD)

Visual

CSV

TAB

Printer

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

ACI/N (MCW)

Visual

CSV

TAB

Printer

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

BBDP/Wor (RGD)

Visual

CSV

TAB

Printer

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

BN/SsN (MCW)

Visual

CSV

TAB

Printer

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

Buf/N (MCW)

Visual

CSV

TAB

Printer

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

COP/CrCrl (MCW & UW)

Visual

CSV

TAB

Printer

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

F344/NCrl (RGD)

Visual

CSV

TAB

Printer

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

F344/NRrrc (MCW)

Visual

CSV

TAB

Printer

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

FHH/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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

FHH/EurMcwi (RGD)

Visual

CSV

TAB

Printer

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

FHL/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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

FHL/EurMcwi (RGD)

Visual

CSV

TAB

Printer

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

GH/OmrMcwi (MCW)

Visual

CSV

TAB

Printer

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

GK/Ox (RGD)

Visual

CSV

TAB

Printer

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

LE/Stm (RGD)

Visual

CSV

TAB

Printer

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

LEW/Crl (RGD)

Visual

CSV

TAB

Printer

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

LEW/NCrlBR (RGD)

Visual

CSV

TAB

Printer

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

LH/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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

LL/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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

LN/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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

M520/N (MCW)

Visual

CSV

TAB

Printer

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

MHS/Gib (RGD)

Visual

CSV

TAB

Printer

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

MNS/Gib (RGD)

Visual

CSV

TAB

Printer

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

MR/N (MCW)

Visual

CSV

TAB

Printer

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

SBH/Ygl (MCW)

Visual

CSV

TAB

Printer

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

SBH/Ygl (RGD)

Visual

CSV

TAB

Printer

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

SBN/Ygl (MCW)

Visual

CSV

TAB

Printer

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

SBN/Ygl (RGD)

Visual

CSV

TAB

Printer

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

SHR/NHsd (RGD)

Visual

CSV

TAB

Printer

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

SHRSP/Gcrc (RGD)

Visual

CSV

TAB

Printer

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

SR/JrHsd (MCW)

Visual

CSV

TAB

Printer

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

SR/JrHsd (RGD)

Visual

CSV

TAB

Printer

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

SS/Jr (RGD)

Visual

CSV

TAB

Printer

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

SS/JrHsdMcwi (MCW)

Visual

CSV

TAB

Printer

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

SS/JrHsdMcwi (RGD)

Visual

CSV

TAB

Printer

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

WAG/Rij (RGD)

Visual

CSV

TAB

Printer

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

WKY/Gcrc (RGD)

Visual

CSV

TAB

Printer

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

WKY/N (MCW)

Visual

CSV

TAB

Printer

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

WKY/NCrl (RGD)

Visual

CSV

TAB

Printer

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

WKY/NHsd (RGD)

Visual

CSV

TAB

Printer

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

WN/N (MCW)

Visual

CSV

TAB

Printer

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

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
3	77563729	77563730	C	G	snv	RCS/Kyo (KyushuU), BDIX/NemOda (KyushuU)
3	77566070	77566071	T	G	snv	ACI/EurMcwi (MCW), FHH/EurMcwi (MCW)

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
3	71035685	71035686	T	G	snv	FHH/EurMcwi (MCW)
3	71035687	71035688	T	G	snv	ACI/N (MCW)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
3	66833895	66833896	C	G	snv	SHRSP/Gcrc (MDC)
3	66836238	66836239	T	G	snv	ACI/N (KNAW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1359234	AgrOrtholog
Ensembl Genes	ENSRNOG00000005256	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000007276	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000007276	ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7126102	IMAGE-MGC_LOAD
InterPro	ZC3H15/TMA46_C	UniProtKB/Swiss-Prot
	Znf-CCCH_4	UniProtKB/Swiss-Prot
	Znf_CCCH	UniProtKB/Swiss-Prot
	Znf_CCCH_sf	UniProtKB/Swiss-Prot
KEGG Report	rno:362154	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:95079	IMAGE-MGC_LOAD
NCBI Gene	362154	ENTREZGENE
Pfam	DFRP_C	UniProtKB/Swiss-Prot
	zf-CCCH_4	UniProtKB/Swiss-Prot
PhenoGen	Zc3h15	PhenoGen
PROSITE	ZF_C3H1	UniProtKB/Swiss-Prot
SMART	ZnF_C3H1	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF90229	UniProtKB/Swiss-Prot
UniProt	Q6U6G5	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-05	Zc3h15	zinc finger CCCH-type containing 15	LOC362154	brain zinc finger protein	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-07-29	LOC362154	brain zinc finger protein			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)

Send us a Message

Imported Disease Annotations - ClinVar