Zcchc7 (zinc finger CCHC-type containing 7)

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Gene: Zcchc7 (zinc finger CCHC-type containing 7) Rattus norvegicus

Analyze

Symbol:

Zcchc7

Name:

zinc finger CCHC-type containing 7

RGD ID:

1310467

Description:

Predicted to have nucleic acid binding activity and zinc ion binding activity. Predicted to localize to cytosol and nucleolus. Orthologous to human ZCCHC7 (zinc finger CCHC-type containing 7); PARTICIPATES IN RNA degradation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 2,4-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC298086; TRAMP-like complex RNA-binding factor ZCCHC7; zinc finger CCHC domain-containing protein 7; zinc finger, CCHC domain containing 7

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):	ZCCHC7 (zinc finger CCHC-type containing 7)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Zcchc7 (zinc finger, CCHC domain containing 7)	HGNC	Treefam, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Zcchc7 (zinc finger CCHC-type containing 7)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	ZCCHC7 (zinc finger CCHC-type containing 7)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	ZCCHC7 (zinc finger CCHC-type containing 7)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Zcchc7 (zinc finger CCHC-type containing 7)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	ZCCHC7 (zinc finger CCHC-type containing 7)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	ZCCHC7 (zinc finger CCHC-type containing 7)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Zcchc7 (zinc finger CCHC-type containing 7)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	ZCCHC7 (zinc finger CCHC-type containing 7)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Zcchc7 (zinc finger, CCHC domain containing 7)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	zcchc7 (zinc finger, CCHC domain containing 7)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Saccharomyces cerevisiae (baker's yeast):	AIR1	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Zcchc7	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER)
Saccharomyces cerevisiae (baker's yeast):	AIR2	Alliance	DIOPT (InParanoid\|OrthoInspector\|PANTHER\|PhylomeDB)

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	5	58,992,558 - 59,173,308 (+)	NCBI
Rnor_6.0 Ensembl	5	60,250,546 - 60,429,708 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	60,250,546 - 60,430,119 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	64,759,112 - 64,938,844 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	61,263,753 - 61,478,276 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	61,387,798 - 61,478,845 (+)	NCBI
Celera	5	57,566,173 - 57,745,122 (+)	NCBI		Celera
Cytogenetic Map	5	q22	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

(S)-nicotine (ISO)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

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

2,3,7,8-Tetrachlorodibenzofuran (EXP)

2,4-dinitrotoluene (EXP)

2-methylcholine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

acrolein (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

alpha-pinene (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bilirubin IXalpha (ISO)

bisphenol A (EXP)

bisphenol F (ISO)

carbamazepine (ISO)

carbon nanotube (ISO)

chrysene (ISO)

clofibrate (ISO)

copper atom (EXP)

copper(0) (EXP)

cyclosporin A (ISO)

dexamethasone (ISO)

diazinon (EXP)

diuron (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

ethyl methanesulfonate (ISO)

fluoranthene (ISO)

folic acid (ISO)

gentamycin (EXP)

indometacin (ISO)

kainic acid (ISO)

levonorgestrel (ISO)

methapyrilene (EXP)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

nicotine (ISO)

oxaliplatin (EXP)

ozone (ISO)

paracetamol (ISO)

phenobarbital (ISO)

potassium dichromate (ISO)

quercetin (ISO)

resveratrol (ISO)

SB 431542 (ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

succimer (ISO)

sunitinib (ISO)

testosterone undecanoate (ISO)

tetrachloromethane (EXP,ISO)

thapsigargin (ISO)

topotecan (EXP)

trichostatin A (ISO)

tungsten (ISO)

tunicamycin (ISO)

valproic acid (EXP,ISO)

vinclozolin (EXP)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Cellular Component

cytosol (IEA,ISO)

nucleolus (IEA,ISO)

Molecular Function

nucleic acid binding (IEA)

protein binding (ISO)

zinc ion binding (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

RNA degradation pathway (IEA)

References

References - curated


1.	MGD data from the GO Consortium
2.	Pipeline to import KEGG annotations from KEGG into RGD
3.	RGD automated data pipeline
4.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:22658674

Genomics

Comparative Map Data

Zcchc7
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	58,992,558 - 59,173,308 (+)	NCBI
Rnor_6.0 Ensembl	5	60,250,546 - 60,429,708 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	60,250,546 - 60,430,119 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	64,759,112 - 64,938,844 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	61,263,753 - 61,478,276 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	61,387,798 - 61,478,845 (+)	NCBI
Celera	5	57,566,173 - 57,745,122 (+)	NCBI		Celera
Cytogenetic Map	5	q22	NCBI

ZCCHC7
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	9	37,120,539 - 37,358,149 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	9	37,120,574 - 37,358,149 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	9	37,120,166 - 37,358,149 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	9	37,120,161 - 37,358,146 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	9	37,120,469 - 37,358,146 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	37,110,469 - 37,348,146 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	9	37,110,632 - 37,348,143	NCBI
Celera	9	37,053,823 - 37,291,368 (+)	NCBI
Cytogenetic Map	9	p13.2	NCBI
HuRef	9	37,071,313 - 37,309,243 (+)	NCBI		HuRef
CHM1_1	9	37,121,671 - 37,359,439 (+)	NCBI		CHM1_1

Zcchc7
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	44,756,556 - 44,932,215 (+)	NCBI	GRCm39		mm39
GRCm38	4	44,756,558 - 44,932,215 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	44,755,877 - 44,932,215 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	44,769,440 - 44,945,083 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	4	44,777,668 - 44,933,159 (+)	NCBI			mm8
Celera	4	44,776,366 - 44,951,978 (+)	NCBI		Celera
Cytogenetic Map	4	B1	NCBI
cM Map	4	23.57	NCBI

Zcchc7
(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_004955419	29,108,644 - 29,334,670 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955419	29,108,905 - 29,339,602 (-)	NCBI	ChiLan1.0	ChiLan1.0

ZCCHC7
(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	9	37,888,350 - 38,126,234 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
Mhudiblu_PPA_v0	9	36,962,689 - 37,201,092 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

ZCCHC7
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	11	53,438,985 - 53,685,855 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	11	53,434,007 - 53,686,187 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Zcchc7
(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_004936524	4,927,956 - 5,154,225 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ZCCHC7
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	237,820,401 - 238,069,534 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	237,820,675 - 238,068,505 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	265,773,621 - 266,019,861 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ZCCHC7
(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	12	43,234,800 - 43,484,893 (-)	NCBI
ChlSab1.1 Ensembl	12	43,234,590 - 43,463,364 (-)	Ensembl

Zcchc7
(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_004624930	725,808 - 968,072 (+)	NCBI

Position Markers

RH143970

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	60,417,315 - 60,417,436	NCBI	Rnor6.0
Rnor_5.0	5	64,926,432 - 64,926,553	UniSTS	Rnor5.0
RGSC_v3.4	5	61,465,864 - 61,465,985	UniSTS	RGSC3.4
Celera	5	57,732,710 - 57,732,831	UniSTS
RH 3.4 Map	5	378.1	UniSTS
Cytogenetic Map	5	q22	UniSTS

RH134930

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	60,414,346 - 60,414,551	NCBI	Rnor6.0
Rnor_6.0	5	18,827,974 - 18,828,179	NCBI	Rnor6.0
Rnor_5.0	5	64,923,463 - 64,923,668	UniSTS	Rnor5.0
Rnor_5.0	5	23,615,234 - 23,615,439	UniSTS	Rnor5.0
RGSC_v3.4	5	61,462,895 - 61,463,100	UniSTS	RGSC3.4
RGSC_v3.4	2	46,742,970 - 46,743,175	UniSTS	RGSC3.4
Celera	2	42,069,737 - 42,069,942	UniSTS
Celera	5	57,729,738 - 57,729,943	UniSTS
Cytogenetic Map	5	q22	UniSTS

RH136908

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	60,429,766 - 60,429,961	NCBI	Rnor6.0
Rnor_5.0	5	64,938,883 - 64,939,078	UniSTS	Rnor5.0
RGSC_v3.4	5	61,478,315 - 61,478,510	UniSTS	RGSC3.4
Celera	5	57,745,161 - 57,745,356	UniSTS
RH 3.4 Map	5	391.3	UniSTS
Cytogenetic Map	5	q22	UniSTS

RH137049

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	60,429,387 - 60,429,546	NCBI	Rnor6.0
Rnor_5.0	5	64,938,504 - 64,938,663	UniSTS	Rnor5.0
RGSC_v3.4	5	61,477,936 - 61,478,095	UniSTS	RGSC3.4
Celera	5	57,744,782 - 57,744,941	UniSTS
RH 3.4 Map	5	390.4	UniSTS
Cytogenetic Map	5	q22	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
1331771	Rf35	Renal function QTL 35	4.36965		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	5	1	89432042	Rat
1331756	Rf34	Renal function QTL 34	4.16275		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	5	1	93273395	Rat
70212	Niddm25	Non-insulin dependent diabetes mellitus QTL 25	3.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	1	136640934	Rat
1576314	Eutr1	Estrogen induced uterine response QTL 1			uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	1525098	78720537	Rat
8662454	Vetf3	Vascular elastic tissue fragility QTL 3	27.4		artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	5	1666587	71552720	Rat
7394712	Emca13	Estrogen-induced mammary cancer QTL 13			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	9514842	103580403	Rat
634305	Mamtr1	Mammary tumor resistance QTL 1		0.0001	mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	12651967	117554267	Rat
1600358	Mamtr5	Mammary tumor resistance QTL 5			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	18847913	63847913	Rat
1358353	Srcrtb2	Stress Responsive Cort Basal QTL 2	3.48	0.003	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	18847913	76608178	Rat
8552954	Pigfal14	Plasma insulin-like growth factor 1 level QTL 14	9		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	21904363	66904363	Rat
1578767	Stresp17	Stress response QTL 17	4.3	0.01	blood aldosterone amount (VT:0005346)	plasma aldosterone level (CMO:0000551)	5	29078899	74078899	Rat
1578776	Stresp18	Stress response QTL 18	2.9		thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	5	29078899	74078899	Rat
6903292	Stl28	Serum triglyceride level QTL 28	2.6	0.0073	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	5	29641661	74641661	Rat
6903306	Scl35	Serum cholesterol QTL 35	2.6	0.0073	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	29641661	74641661	Rat
2290448	Scl54	Serum cholesterol level QTL 54	2.93		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	31926122	136640934	Rat
1298067	Scl15	Serum cholesterol level QTL 15	4.8	0.001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	34402409	79402409	Rat
1302786	Kidm8	Kidney mass QTL 8	28.15		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	5	34402409	79402409	Rat
1598807	Glom12	Glomerulus QTL 12	2.7		kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	5	34402409	79402409	Rat
1576317	Eutr2	Estrogen induced uterine response QTL 2		0.01	uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	35225432	108092802	Rat
2316959	Gluco59	Glucose level QTL 59	4.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	35661945	117554267	Rat
1641922	Alcrsp8	Alcohol response QTL 8			alcohol metabolism trait (VT:0015089)	blood ethanol level (CMO:0000535)	5	35788756	70742105	Rat
1641912	Alcrsp18	Alcohol response QTL 18			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	5	35788756	147487820	Rat
1549845	Scl44	Serum cholesterol level QTL 44	6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	40777918	154732375	Rat
1331773	Scl26	Serum cholesterol level QTL 26	3.065		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	44404276	89432042	Rat
1331801	Rf33	Renal function QTL 33	4.149		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	5	44404276	134502294	Rat
1578766	Tcas11	Tongue tumor susceptibility QTL 11	4.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	5	47745646	167946134	Rat
1300115	Hrtrt7	Heart rate QTL 7	2.76		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	5	48722038	93587756	Rat
1576312	Emca8	Estrogen-induced mammary cancer QTL 8	4.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	51418671	147487820	Rat
9589025	Epfw7	Epididymal fat weight QTL 7	20.66	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	5	51804426	96804426	Rat
7411561	Bw134	Body weight QTL 134	24	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	51804426	96804426	Rat
2303615	Vencon7	Ventilatory control QTL 7		0.001	respiration trait (VT:0001943)	respiration rate (CMO:0000289)	5	53309568	98309568	Rat
2303574	Gluco42	Glucose level QTL 42	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	55903593	100903593	Rat
61359	Eaex	Experimental allergic encephalomyelitis QTL x	3		nervous system integrity trait (VT:0010566)	post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)	5	56902367	101902367	Rat
70189	Mcs5	Mammary carcinoma susceptibility QTL 5	10.51		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	56991667	137729065	Rat
1358895	Bp254	Blood pressure QTL 254	3.6	0.0003	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	5	60072951	133313852	Rat
1598868	Mcs12	Mammary carcinoma susceptibility QTL 12		0.0001	mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	60225095	61370302	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	38
Count of miRNA genes:	32
Interacting mature miRNAs:	37
Transcripts:	ENSRNOT00000017707
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	40	51	35	19	35	8	8	74	35	40	11	8
Low		3	6	6		6		3			1
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106658	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039109461	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039109462	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039109464	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005504379	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005504380	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005504381	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005504382	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC161967	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473962	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000161	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000017707 ⟹ ENSRNOP00000017707

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	5	60,250,546 - 60,429,708 (+)	Ensembl

RefSeq Acc Id:

NM_001106658 ⟹ NP_001100128

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	58,993,302 - 59,172,916 (+)	NCBI
Rnor_6.0	5	60,250,546 - 60,429,727 (+)	NCBI
Rnor_5.0	5	64,759,112 - 64,938,844 (+)	NCBI
RGSC_v3.4	5	61,263,753 - 61,478,276 (+)	RGD
Celera	5	57,566,173 - 57,745,122 (+)	RGD

Sequence:

show sequence

CTGGTCGCAGCCGCGGCACATTGCGGCAACTGACTTTCCATAATGTTTGGTGGCTTTGAGACTA
TAGAAGCATTCGAAGATGACCTTTATCGTGATGATTCATCTAGTGAACTTAGTGTTGATAGTGA
AGTGGAATTTCAGCTCTACAGCCAAGTCCATTATTCCCAGAATATTCATAATGCCAACGAGGAG
GAAGGGTATGAGGAAAAGAACTGTGAGAGTTCTGAAACAGTGAGTATTCAACCAGACCAGAAGA
ACTTAATCGTCCTTTCAGATAGTGAGGTCATCCAGCTGTCAGATACATCAGAGGTCATCACATT
GTCTGATGAAGATAGTATTTATAGATGTAAGAGAAAAAATATTGAAGTCCAAGCACAAGAAAAG
ACCCAAAGTCCTGCAACGCCTCGTTCTAATAAAGTGGCTAACAAATGCAAGAGGAGTAATAAGA
AGCCTGAACCTGAAGAGAGCCCAAGTACGATCCGAGAGGTCATGATCATAGAGGTCAGCTCAGA
TGAGGAGGAAGAAAGTACCATTTCAGAGAATGAAAATGTGGAAAGCTGGATGCTCCTGGGATGT
GAGGAAGATGATAAAGACAATGACATCCTTCTCAACCTGGTGGGATGCAAGGACGCTGGTGCTG
AAGGAGAAAATGATGTAAATTGGTTCATCAGTGACAAAGACATCGAGGCCAAGATAGATAACAA
CAGATCATCTGGAAGGTGGAACAACCGATACTATTCAGTCAACAAAAATGTCACGTGTAGAAAT
TGTGATAAACGTGGCCATTTGTCAAAAAACTGCCCCTTACCACAAAAAGTCCGGCCCTGCTGTC
TCTGCTCGGAAAGAGGACACCTCCAGTATGGCTGTCCAGCCCGTTACTGCTTAGACTGCTCTTT
GCCCATGTCTTCCACTCACAGATGTTTTGAAAGATCTTCCTGGAGAAAGCGATGTGACCGATGT
GATATGATAGGCCACTATGCTGATGCTTGCCCAGAAATCTGGAGGCAGTATCACCTAACGACCA
AACCTGGACCACCTAAAAAGCCAAAGACCCCTTCTGGACAATCAGCGCTGGTGTATTGCTACAA
CTGTGCACAGAAAGGCCATTATGGACATGAATGTACAGAGAGACGGATGTTTAACCAGGCGTTT
CCAACATCTCCATTCATATATTGCTATGACGACAAATACGACATCCAGCAAAGGGATCGGAGAA
TAAAACGGAAACTGAAAGATATCAAGAAAAATGGAGATTTTCCAAGGCAGTTCAAAAGACCACA
TGGAGAAGAGACAGATAGATATCACCATGATAGGAGAAAAAGCCGTTTCTCAGGAAAACGCAGT
CGGTGGCCTCGAGAAAGTAAGGAAACGCAGAAAGAGAAGACCAGGGGTAGAGAAGGCGAGAAGC
ACAGGAGGGACCGCCAGCCTCGCGATGAGGATGAAGACTTCCCTAGGGGCCTGAAACCCAACTC
CTCCAGCAGCAGTAACAGCCAGAAGCCTTCTAAGTCCCTCCACCAGGCATCCCATTACCACAGG
CTGAGGGAAGAGAAGCTTCGCAGAGAGAGCATGCGGAGCAAGCCGAAGAAAAGGAAATTCGTAG
AGGATGGCAGCCATGATGATTTATTTCTTATTAAGCAAAGGAAGAAGAAACCTAAGTCCAGTGG
TTTCTGACCTGGTCTTCCTGGTTCAGTGTTCTGGAAGTGCTTCAGTATCTGTTAAATGAAGAAA
GGCTGGGGATTTTGATCGCTGAATTCTGGCCATTCCTGAAGTGCTGTACAAAGGCCACGGAGAG
TTCAGGTCTGTGTCCACCGGGTGTCCTTAGGTAGGAAGGCAAACTTGAGGTAGAAAATTGTCAT
TTCAAGAAAACCTTTTTAAATGCTTTGAAGAAATTACAAGTTCATCAGATATAATTCATCTACA
ATGTTTGAGGACTTAAAAGCTCATTGGAAGAGAGTTTATTATTAAAGAAAAGTCACCGCTTTTT
TAGCAATCTTTAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_017593243 ⟹ XP_017448732

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	5	60,390,408 - 60,430,119 (+)	NCBI

Sequence:

show sequence

ATGGAGAAGCTCCAGGTCCAGGGAGATCCAGCAGCGTCTTCTGGAGAAAATGATGTAAATTGGT
TCATCAGTGACAAAGACATCGAGGCCAAGATAGATAACAACAGATCATCTGGAAGGTGGAACAA
CCGATACTATTCAGTCAACAAAAATGTCACGTGTAGAAATTGTGATAAACGTGGCCATTTGTCA
AAAAACTGCCCCTTACCACAAAAAGTCCGGCCCTGCTGTCTCTGCTCGGAAAGAGGACACCTCC
AGTATGGCTGTCCAGCCCGTTACTGCTTAGACTGCTCTTTGCCCATGTCTTCCACTCACAGATG
TTTTGAAAGATCTTCCTGGAGAAAGCGATGTGACCGATGTGATATGATAGGCCACTATGCTGAT
GCTTGCCCAGAAATCTGGAGGCAGTATCACCTAACGACCAAACCTGGACCACCTAAAAAGCCAA
AGACCCCTTCTGGACAATCAGCGCTGGTGTATTGCTACAACTGTGCACAGAAAGGCCATTATGG
ACATGAATGTACAGAGAGACGGATGTTTAACCAGGCGTTTCCAACATCTCCATTCATATATTGC
TATGACGACAAATACGACATCCAGCAAAGGGATCGGAGAATAAAACGGAAACTGAAAGATATCA
AGAAAAATGGAGATTTTCCAAGGCAGTTCAAAAGACCACATGGAGAAGAGACAGATAGATATCA
CCATGATAGGAGAAAAAGCCGTTTCTCAGGAAAACGCAGTCGGTGGCCTCGAGAAAGTAAGGAA
ACGCAGAAAGAGAAGACCAGGGGTAGAGAAGGCGAGAAGCACAGGAGGGACCGCCAGCCTCGCG
ATGAGGATGAAGACTTCCCTAGGGGCCTGAAACCCAACTCCTCCAGCAGCAGTAACAGCCAGAA
GCCTTCTAAGTCCCTCCACCAGGCATCCCATTACCACAGGCTGAGGGAAGAGAAGCTTCGCAGA
GAGAGCATGCGGAGCAAGCCGAAGAAAAGGAAATTCGTAGAGGATGGCAGCCATGATGATTTAT
TTCTTATTAAGCAAAGGAAGAAGAAACCTAAGTCCAGTGGTTTCTGACCTGGTCTTCCTGGTTC
AGTGTTCTGGAAGTGCTTCAGTATCTGTTAAATGAAGAAAGGCTGGGGATTTTGATCGCTGAAT
TCTGGCCATTCCTGAAGTGCTGTACAAAGGCCACGGAGAGTTCAGGTCTGTGTCCACCGGGTGT
CCTTAGGTAGGAAGGCAAACTTGAGGTAGAAAATTGTCATTTCAAGAAAACCTTTTTAAATGCT
TTGAAGAAATTACAAGTTCATCAGATATAATTCATCTACAATGTTTGAGGACTTAAAAGCTCAT
TGGAAGAGAGTTTATTATTAAAGAAAAGTCACCGCTTTTTTAGCAATCTTTAAAAAAAAAAAAA
AAAAAACACTGGAAAAATCAATGAAAATCCAAGCCCAGCTTTGCTTGTGTCAGAGGCTGTTGGA
GTCTTTCTCTGTACAGGAAGTGTGTAAAATGAAGCTGTCACCACTGAAACCTGGAGGAGGTGGA
GGGGAGGCCATAACAAAATACACATAGAGAAGGGGTGCAGTGTGGGGTACCAAGAGGCGTCCTC
AAACCTGAGTGCAATCGCAGGGACACTGTCCTTACTGGTTAACAGCCATAGATCAAGAACTAGA
GATAAATATTACCAACCTAATTGTTCTCATGGATCTTTTTAAACACTGCAAAGCTATTTAGAAT
CTTTTGTACTCATGAGCCTTTTTTACATTTGTGAAAGCCTAATGTTAGAATAAGGAAAATAAAA
TGCCTGAAACCATG

hide sequence

RefSeq Acc Id:

XM_039109461 ⟹ XP_038965389

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	58,993,193 - 59,173,308 (+)	NCBI

RefSeq Acc Id:

XM_039109462 ⟹ XP_038965390

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	58,992,597 - 59,173,308 (+)	NCBI

RefSeq Acc Id:

XM_039109464 ⟹ XP_038965392

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	58,992,558 - 59,173,308 (+)	NCBI

RefSeq Acc Id:

XR_005504379

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	58,993,182 - 59,172,452 (+)	NCBI

RefSeq Acc Id:

XR_005504380

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	58,993,182 - 59,170,275 (+)	NCBI

RefSeq Acc Id:

XR_005504381

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	58,993,178 - 59,172,452 (+)	NCBI

RefSeq Acc Id:

XR_005504382

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	58,993,178 - 59,170,275 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001100128	(Get FASTA)	NCBI Sequence Viewer
	XP_038965389	(Get FASTA)	NCBI Sequence Viewer
	XP_038965390	(Get FASTA)	NCBI Sequence Viewer
	XP_038965392	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI61967	(Get FASTA)	NCBI Sequence Viewer
	B1WC15	(Get FASTA)	NCBI Sequence Viewer
	EDL98795	(Get FASTA)	NCBI Sequence Viewer
	EDL98796	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001100128 ⟸ NM_001106658

- UniProtKB:

B1WC15 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MFGGFETIEAFEDDLYRDDSSSELSVDSEVEFQLYSQVHYSQNIHNANEEEGYEEKNCESSETV
SIQPDQKNLIVLSDSEVIQLSDTSEVITLSDEDSIYRCKRKNIEVQAQEKTQSPATPRSNKVAN
KCKRSNKKPEPEESPSTIREVMIIEVSSDEEEESTISENENVESWMLLGCEEDDKDNDILLNLV
GCKDAGAEGENDVNWFISDKDIEAKIDNNRSSGRWNNRYYSVNKNVTCRNCDKRGHLSKNCPLP
QKVRPCCLCSERGHLQYGCPARYCLDCSLPMSSTHRCFERSSWRKRCDRCDMIGHYADACPEIW
RQYHLTTKPGPPKKPKTPSGQSALVYCYNCAQKGHYGHECTERRMFNQAFPTSPFIYCYDDKYD
IQQRDRRIKRKLKDIKKNGDFPRQFKRPHGEETDRYHHDRRKSRFSGKRSRWPRESKETQKEKT
RGREGEKHRRDRQPRDEDEDFPRGLKPNSSSSSNSQKPSKSLHQASHYHRLREEKLRRESMRSK
PKKRKFVEDGSHDDLFLIKQRKKKPKSSGF

hide sequence

RefSeq Acc Id:

XP_017448732 ⟸ XM_017593243

- Peptide Label:

isoform X1

- Sequence:

show sequence

MEKLQVQGDPAASSGENDVNWFISDKDIEAKIDNNRSSGRWNNRYYSVNKNVTCRNCDKRGHLS
KNCPLPQKVRPCCLCSERGHLQYGCPARYCLDCSLPMSSTHRCFERSSWRKRCDRCDMIGHYAD
ACPEIWRQYHLTTKPGPPKKPKTPSGQSALVYCYNCAQKGHYGHECTERRMFNQAFPTSPFIYC
YDDKYDIQQRDRRIKRKLKDIKKNGDFPRQFKRPHGEETDRYHHDRRKSRFSGKRSRWPRESKE
TQKEKTRGREGEKHRRDRQPRDEDEDFPRGLKPNSSSSSNSQKPSKSLHQASHYHRLREEKLRR
ESMRSKPKKRKFVEDGSHDDLFLIKQRKKKPKSSGF

hide sequence

RefSeq Acc Id:

ENSRNOP00000017707 ⟸ ENSRNOT00000017707

RefSeq Acc Id:	XP_038965392 ⟸ XM_039109464
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038965390 ⟸ XM_039109462
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038965389 ⟸ XM_039109461
- Peptide Label:	isoform X1

Protein Domains

CCHC-type

Transcriptome

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

Promoters

RGD ID:

13693693

Promoter ID:

EPDNEW_R4218

Type:

initiation region

Name:

Zcchc7_1

Description:

zinc finger CCHC-type containing 7

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	5	60,250,527 - 60,250,587	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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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)

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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

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1310467	AgrOrtholog
Ensembl Genes	ENSRNOG00000013078	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000017707	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000017707	ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:9028474	IMAGE-MGC_LOAD
InterPro	Znf_CCHC	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Znf_CCHC_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:298086	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:187773	IMAGE-MGC_LOAD
NCBI Gene	298086	ENTREZGENE
Pfam	zf-CCHC	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Zcchc7	PhenoGen
PROSITE	ZF_CCHC	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	ZnF_C2HC	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF57756	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	B1WC15	ENTREZGENE
	F1M989_RAT	UniProtKB/TrEMBL
	ZCHC7_RAT	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-02-17	Zcchc7	zinc finger CCHC-type containing 7	Zcchc7	zinc finger, CCHC domain containing 7	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Zcchc7	zinc finger, CCHC domain containing 7	Zcchc7_predicted	zinc finger, CCHC domain containing 7 (predicted)	'predicted' is removed	2292626	APPROVED
2008-01-09	Zcchc7_predicted	zinc finger, CCHC domain containing 7 (predicted)	LOC683686	similar to zinc finger, CCHC domain containing 7	Data Merged	1643240	APPROVED
2006-11-19	LOC683686	similar to zinc finger, CCHC domain containing 7			Symbol and Name status set to provisional	70820	PROVISIONAL
2005-01-12	Zcchc7_predicted	zinc finger, CCHC domain containing 7 (predicted)			Symbol and Name status set to approved	70820	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Annotations - KEGG (archival)