Phf19 (PHD finger protein 19) - Rat Genome Database

Name: Phf19
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Phf19 (PHD finger protein 19) Rattus norvegicus

Analyze

Symbol:

Phf19

Name:

PHD finger protein 19

RGD ID:

1310390

Description:

Predicted to enable DNA binding activity; chromatin binding activity; and methylated histone binding activity. Predicted to be involved in several processes, including negative regulation of transcription by RNA polymerase II; positive regulation of histone H3-K27 methylation; and stem cell population maintenance. Predicted to be part of ESC/E(Z) complex. Predicted to be active in nucleus. Orthologous to human PHF19 (PHD finger protein 19); PARTICIPATES IN histone modification pathway; INTERACTS WITH all-trans-retinoic acid; bisphenol A; cadmium dichloride.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC296653

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):	PHF19 (PHD finger protein 19)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Phf19 (PHD finger protein 19)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Phf19 (PHD finger protein 19)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PHF19 (PHD finger protein 19)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PHF19 (PHD finger protein 19)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Phf19 (PHD finger protein 19)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PHF19 (PHD finger protein 19)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PHF19 (PHD finger protein 19)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Phf19 (PHD finger protein 19)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	PHF19 (PHD finger protein 19)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Phf19 (PHD finger protein 19)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	phf19 (PHD finger protein 19)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Pcl	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	18,175,281 - 18,197,289 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	3	18,175,282 - 18,196,405 (-)	Ensembl
Rnor_6.0	3	13,957,136 - 13,978,283 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	13,957,136 - 13,978,224 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	19,276,705 - 19,297,851 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	13,903,402 - 13,911,007 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	13,801,774 - 13,812,518 (-)	NCBI
Celera	3	12,896,198 - 12,917,286 (-)	NCBI		Celera
Cytogenetic Map	3	p11	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

(+)-catechin (ISO)

(-)-epigallocatechin 3-gallate (ISO)

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

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

3,4-methylenedioxymethamphetamine (ISO)

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

4,4'-sulfonyldiphenol (ISO)

acrolein (ISO)

acrylamide (ISO)

all-trans-retinoic acid (EXP,ISO)

alpha-pinene (ISO)

antirheumatic drug (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

bisphenol A (EXP,ISO)

Bisphenol B (ISO)

bisphenol F (ISO)

butanal (ISO)

cadmium dichloride (EXP)

calcitriol (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

chlorpyrifos (ISO)

chrysene (ISO)

cisplatin (ISO)

cobalt dichloride (EXP,ISO)

copper atom (ISO)

copper(0) (ISO)

coumestrol (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dicrotophos (ISO)

endosulfan (EXP)

Enterolactone (ISO)

fulvestrant (ISO)

gentamycin (EXP)

Indeno[1,2,3-cd]pyrene (ISO)

indometacin (ISO)

N-Nitrosopyrrolidine (ISO)

nickel atom (ISO)

ozone (ISO)

palbociclib (ISO)

paracetamol (EXP)

phenethyl isothiocyanate (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

propanal (ISO)

resveratrol (ISO)

silicon dioxide (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

testosterone (ISO)

tetraphene (ISO)

thioacetamide (EXP)

trichloroethene (ISO)

trichostatin A (ISO)

trimellitic anhydride (ISO)

troglitazone (ISO)

urethane (ISO)

valproic acid (ISO)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

chromatin organization (IBA)

negative regulation of transcription by RNA polymerase II (ISO)

positive regulation of histone H3-K27 methylation (ISO)

regulation of DNA-templated transcription (IBA)

stem cell differentiation (ISO)

stem cell population maintenance (ISO)

Cellular Component

cellular_component (ND)

ESC/E(Z) complex (ISO)

nucleus (IBA)

Molecular Function

chromatin binding (IBA)

DNA binding (IBA)

metal ion binding (IEA)

methylated histone binding (IBA,ISO)

molecular_function (ND)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

histone modification pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	SET for life: biochemical activities and biological functions of SET domain-containing proteins.	Herz HM, etal., Trends Biochem Sci. 2013 Dec;38(12):621-39. doi: 10.1016/j.tibs.2013.09.004. Epub 2013 Oct 20.
3.	Tudor: a versatile family of histone methylation 'readers'.	Lu R and Wang GG, Trends Biochem Sci. 2013 Nov;38(11):546-55. doi: 10.1016/j.tibs.2013.08.002. Epub 2013 Sep 10.
4.	Readout of epigenetic modifications.	Patel DJ and Wang Z, Annu Rev Biochem. 2013;82:81-118. doi: 10.1146/annurev-biochem-072711-165700.
5.	GOA pipeline	RGD automated data pipeline
6.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
7.	Comprehensive gene review and curation	RGD comprehensive gene curation
8.	Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put.	Simon JA and Kingston RE, Mol Cell. 2013 Mar 7;49(5):808-24. doi: 10.1016/j.molcel.2013.02.013.

Additional References at PubMed

PMID:22438827	PMID:23104054	PMID:23160351	PMID:23273982	PMID:33611744

Genomics

Comparative Map Data

Phf19
(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	18,175,281 - 18,197,289 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	3	18,175,282 - 18,196,405 (-)	Ensembl
Rnor_6.0	3	13,957,136 - 13,978,283 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	13,957,136 - 13,978,224 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	19,276,705 - 19,297,851 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	13,903,402 - 13,911,007 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	13,801,774 - 13,812,518 (-)	NCBI
Celera	3	12,896,198 - 12,917,286 (-)	NCBI		Celera
Cytogenetic Map	3	p11	NCBI

PHF19
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	9	120,855,651 - 120,904,128 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	9	120,855,651 - 120,894,896 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	9	123,617,929 - 123,657,174 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	122,657,752 - 122,679,427 (-)	NCBI	NCBI36		hg18	NCBI36
Celera	9	94,266,198 - 94,288,032 (-)	NCBI
Cytogenetic Map	9	q33.2	NCBI
HuRef	9	93,235,537 - 93,254,614 (-)	NCBI		HuRef
CHM1_1	9	123,765,090 - 123,786,747 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	9	133,051,794 - 133,091,037 (-)	NCBI

Phf19
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	34,783,764 - 34,804,365 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	2	34,783,769 - 34,804,038 (-)	Ensembl
GRCm38	2	34,893,752 - 34,914,353 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	34,893,757 - 34,914,026 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	34,749,275 - 34,769,496 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	34,715,764 - 34,735,985 (-)	NCBI			mm8
Celera	2	34,593,706 - 34,613,934 (-)	NCBI		Celera
Cytogenetic Map	2	B	NCBI

Phf19
(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	7,160,249 - 7,179,318 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955419	7,160,249 - 7,179,323 (+)	NCBI	ChiLan1.0	ChiLan1.0

PHF19
(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	120,330,111 - 120,349,274 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	120,330,111 - 120,369,459 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	9	91,982,511 - 92,030,060 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

PHF19
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	11	73,895,104 - 73,911,030 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	11	72,308,039 - 72,351,904 (-)	NCBI
ROS_Cfam_1.0	11	75,032,636 - 75,077,220 (-)	NCBI
ROS_Cfam_1.0 Ensembl	11	75,034,546 - 75,073,866 (-)	Ensembl
UMICH_Zoey_3.1	11	73,543,019 - 73,585,390 (-)	NCBI
UNSW_CanFamBas_1.0	11	73,572,259 - 73,616,852 (-)	NCBI
UU_Cfam_GSD_1.0	11	74,310,058 - 74,355,088 (-)	NCBI

Phf19
(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_024404947	189,540,151 - 189,558,130 (-)	NCBI
SpeTri2.0	NW_004936487	9,310,327 - 9,326,650 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PHF19
(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	260,899,452 - 260,920,110 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	260,899,462 - 260,919,776 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	293,000,910 - 293,012,340 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PHF19
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	12	18,698,705 - 18,722,702 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	12	18,702,523 - 18,720,446 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666035	24,290,767 - 24,314,063 (-)	NCBI	Vero_WHO_p1.0

Phf19
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624760	14,468,461 - 14,487,091 (+)	Ensembl	HetGla_female_1.0		hetGla2
HetGla 1.0	NW_004624760	14,468,418 - 14,486,942 (+)	NCBI	HetGla_female_1.0		hetGla2

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
70202	Alc19	Alcohol consumption QTL 19	2.5		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	3	1	27494778	Rat
631679	Cm10	Cardiac mass QTL 10	7.34	0.0001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	1	31158234	Rat
631831	Alc8	Alcohol consumption QTL 8	2.7		consumption behavior trait (VT:0002069)	calculated ethanol drink intake rate (CMO:0001615)	3	1	33230976	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	diastolic blood pressure (CMO:0000005)	3	1	33278763	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	1	33278763	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	pulse pressure (CMO:0000292)	3	1	33278763	Rat
631545	Bp85	Blood pressure QTL 85	3.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	1	33278763	Rat
4889966	Bss95	Bone structure and strength QTL 95	4.4		tibia area (VT:1000281)	tibia-fibula cross-sectional area (CMO:0001718)	3	1	36847613	Rat
2312664	Scl62	Serum cholesterol level QTL 62		0.05	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	1	38710544	Rat
631568	Bp92	Blood pressure QTL 92	2.2	0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	1	39874793	Rat
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	91609953	Rat
1298526	Arunc3	Aerobic running capacity QTL 3	2.2		exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	8227194	33703538	Rat
10401810	Kidm53	Kidney mass QTL 53			kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	8227194	47233430	Rat
70203	Gcr2	Gastric cancer resistance QTL 2	2.6		stomach morphology trait (VT:0000470)	stomach tumor susceptibility score (CMO:0002043)	3	8658162	27494778	Rat
1358357	Srcrtb1	Stress Responsive Cort Basal QTL 1	6.36	0.002	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	8658162	27494778	Rat
6893355	Bw101	Body weight QTL 101	0.4	0.38	body mass (VT:0001259)	body weight (CMO:0000012)	3	10778704	30357018	Rat
6893363	Bw105	Body weight QTL 105	2.6	0.0036	body mass (VT:0001259)	body weight (CMO:0000012)	3	10778704	30357018	Rat
1558654	Bw56	Body weight QTL 56	4.5	0.0000171	body mass (VT:0001259)	body weight (CMO:0000012)	3	10778704	30357018	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	3	10778704	50302886	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	3	10778704	50302886	Rat
1558647	Cm46	Cardiac mass QTL 46	5.4	0.0000055	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	10778823	30356773	Rat
1558650	Cm48	Cardiac mass QTL 48	4	0.0001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	3	10778823	30356773	Rat
1558657	Cm43	Cardiac mass QTL 43	6.6	0.0000000293	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	10778823	30356773	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10861912	89878372	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	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	15005422	76927699	Rat
631676	Cm8	Cardiac mass QTL 8	7.03	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	3	16954708	61954708	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	17374703	35528639	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	17374703	35528639	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	17374703	35528639	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	17374703	35528639	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	heart rate (CMO:0000002)	3	17374703	35528639	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	heart rate (CMO:0000002)	3	17374703	35528639	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	body weight (CMO:0000012)	3	17374703	35528639	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	body weight (CMO:0000012)	3	17374703	35528639	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	529
Count of miRNA genes:	262
Interacting mature miRNAs:	317
Transcripts:	ENSRNOT00000025528
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	2									12	11	1
Low	1	41	57	41	19	41	2	2	74	23	23	10	2
Below cutoff		2					6	9			7		6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106570	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006233971	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008761740	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017591661	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039104781	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039104782	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039104783	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005501843	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH474001	(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:

ENSRNOT00000025528 ⟹ ENSRNOP00000025528

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	18,175,282 - 18,196,405 (-)	Ensembl
Rnor_6.0 Ensembl	3	13,957,136 - 13,978,224 (-)	Ensembl

RefSeq Acc Id:

NM_001106570 ⟹ NP_001100040

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	18,175,281 - 18,196,369 (-)	NCBI
Rnor_6.0	3	13,957,136 - 13,978,224 (-)	NCBI
Rnor_5.0	3	19,276,705 - 19,297,851 (-)	NCBI
RGSC_v3.4	3	13,903,402 - 13,911,007 (-)	RGD
Celera	3	12,896,198 - 12,917,286 (-)	RGD

Sequence:

show sequence

TGGTGGCCAGACTCCAAGTGGGACCGGCTGACGCGCTGCCTCGCGAAGCTGATGGAGACGCAAG
CTCTGGAACCAGGGACTCAGGAAGCCTTTGGTGCCACCAGCCCTAACAAGGGGGCCCCGTCTAA
GACCAAAAAGAACTTCAAAGACTTGATGTCTAAGGTGACAGAGGGACAGTTTGTGCTATGCCGG
TGGACTGACGGGCTATACTACCTTGGCAAGATCAAGCGGGTCAGCAGTCCTAAGCAAAGCTGCC
TCGTGACTTTCGAAGACAATTCCAAATACTGGGTCCTTTGGAAGGACATCCAGCATGCTGGTGT
TCCAGGAGAGGAGCCCAAGTGTGATGTCTGCATGGGGAAGACTTCAGGACCGATGAACGAGATC
CTCATCTGTGGGAAGTGTGGCCTGGGTTACCACCAACAGTGCCACATCCCCATAGCAGTCGATG
CCAACTGGCCCCTCCTCACTCACTGGTTCTGCCGACGCTGCATTTTCGCACTGGCTGTGAGGAA
AGGCGGTGCGCTGAAGAAAGGCGCCATCGCCAAGACGCTGCAGGCAGTGAAAATGGTGCTGTCC
TACCAGCCTGAGGAGCTCGATTGGGATTCGCCCCATCGCACCAACCAGCAGCAATGCTACTGCT
ACTGCGGCGGGCCTGGAGAGTGGTACTTACGGATGCTACAGTGCTACCGGTGTAGGCAGTGGTT
CCATGAAGCCTGTACACAGTGCCTAAGTGAGCCTATGGTGTTTGGAGACCGGTTCTACCTGTTC
TTCTGCTCCGTGTGTAACCAAGGCCCAGAGTATATCGAGAGGTTGCCCCTGAGATGGGTAGACA
TAGTTCACCTGGCCCTCTATAACCTGGGAGTACAGAGCAAGAAGAGGTACTTCGACTTTGAGGA
GATCCTGGCCTTTGTCAACCACCACTGGGAGCTCCTGCAGCTTGGCAAGCTCACGAGCACCCCT
GTGACAGAGCGAGGGCCGCATCTCCTCAACGCTCTCAACAGTTACAAAAGCCGGTTCCTGTGTG
GCAAGGAGATTAAGAAGAAGAAATGCATCTTCCGACTGCGCGTCCGTGTCCCGCCCGCCCCTCC
AGGAAAACTGCTTCCGGACAGGGCACAGATGCCAAGTGACAAAGGGACCTTTGAGCTGCTTCGT
AAGAGAGGAAAGAGCAAGCCTGGTTTGTTGCCTCAGGAATCCCAGCAGCAGAAAAGGCGAGTTT
ATAGAAGAAAAAGATCAAAGTTTTTGCTGGAAGATGCTATTCCCAGTAGTGACTTCACCTCAGC
CTGGAGCACGGACCACCACCTGGCCAGCATATTCGACTTTACACTGGATGAAATTCAGAGTTTA
AAAAGTGGCAGCTCAGGCCAGACCTTCTTCTCAGACGTGGATTCTACCGATGCTGCTAGCACCT
CAGGCTCTGCGTCCACCAGCCTCTCCCAGGACTCCAGATGGACAGTAGGCAGCCGTAAGAGGAA
GCTGGCGGCCAAAGCGTACAGGCCCCTGCGGGCAAAGCATCGGGCAGCCGAGCCGGATGGGAGA
TGCGCCTCAGACAGCAGTGCAGAGGGAGCTCCGGGCCCTGAGCAGCAGGATGAAGGCATCGACA
GCCACACGTTCGAAAGCATCAGTGGAGATGACTCCTCCCTGTCCCATCTCAAGTCCTCTATCAC
CAACTACTTCGGTGCAGCTGGGCGGTTGGCCTGCGGGGAAAAGTATCAGGTGTTGGCTCGGAGG
GTCACTCCAGAAGGCAAGGTTCAGTACCTGTTGGAATGGGAGGGCACTACCCCTTACTGATTAT
CCCTCAGAGGCTGCCCAGAGGCTGCAAACCAAAGGAGGGGCAGAAGAAGCCCCTGGGTCCCTGT
TTTCTCCAGGCTTACGGTGGTGGAGGGAAGCAGGACATCCTGGCCGCAGCCCCTGCCTGCTGTC
TGCCAGGCCAAGGTCTGTGTGCTGCTGTACCAGTTGCCCGAGTCTCTGAGGCCCTGCTGGCTCT
CTCTCGTCTATATCACACTCCATACCCTCAAACTTTCCATTGGTTCCTCCGATGGTACCCTGGC
TGTGACCCCTGATCTGAGGCCTGAAACTGATTTTCGTTGTCCCCAGTTCTCCATCTTCTGACCT
CTCCCCTGCTTGGGTGTTTCATGCGGACACACATCTTCCATGCACATATGCTCATCTGTCCCTC
ACTGGGACCACAGTGAGGAAAGGGAACCCTGTGGGTCTTCCACTTTCTCACCAGTACCCCTCAC
CCAGGAGAGTAGGGGATGCCTGAGAAAGTTCAGGATGCCTGCGACCCAGAGCCTGGGAAGTGAT
GGCCTGGGTCTCTACTGAAGGGACGAGAATCAGGGTCTTTTATTGAGGCTGGGAAGGGGGACTA
AGGGAGTCAAGGCCAAGGCTCCCAGAAGTTTGCCTGTCCCCAGCAACAGCTCTTCACTGTTGCC
GCAGACTAGAGCCTGGCCTTGCTACATAGACGTGTTCTTGAACGCGCAGATCTGGGAGGAAACG
ATGGGGAGGACCCATCCCAAACACTGTGTATACAGACAAACACCACCACACATCCCCACCAGGG
TGCCCTGGCCCTGTCCTTGGCCTCTTCCAGGGATAAATGCTGCAGTTAAATGTGAAAACCAAGC
TCCGGCCTCCTCTGGCCTGTGAACCAGCCTTGGCCCCACAGAGAAGCACAAAAGACACCCCAAG
ACACCCCTCTCCTGCATAGCTCCTGCCTTGCCCAGAAGCTGACAATCACTTTGGGGATGGGGCA
GCCGGGGGCGGGGAGAGAGGGCAGTTCCCAAGGGTCTGAATCATTGGTTCCCTTCAGAAAGGAA
GTCTTTGTCATCGATGGTAAAATAGAATTCTTAGAATGGACAAACTCAGCCGTGTCCGGAGGGA
AACCAAAACTAGGAGGTAGGCAGGGAGTCCTTATTTTTGCCTGCAGAAACAGAAACTGACTCGC
TCGGTTGGACAATTAGAAAGAAGTGCCTTTGGGGTGGGAGGCAGGGGCACCAGACTGGGACCAG
CTTCCCTGACTGCTGCTGTGGCTTCTGGCTGGGAGTGGGGAAATGGACCATCGCATGGCGACAT
CAGACTATATCAGAAGTGCTGATTTCCCCATGAGTGGGTCTGACCCCTCCACATCCACCTGTGA
GCATTAAGGAGGAGGGGGAGTCCCTGAGGTAGGCTAGACGGTCCCTGCCATACACCTCAGCAAC
CATAGTGCCTTGCAAAGGAACCTCACCTCTCACTAGACACAGCTACCCACGTCCATCTGCTTCC
CCGTCTTGGCTCAGGCAGGGCTCAGCAGATGGACACTGAGACCAGTTCTCAGTCCCACAGCTGC
TGCCACTGAGGTCCCCAAGTGGGTCCCGGTGGAAGGAGAGTTGTAAAGCCAACTCCCAGGCCAG
CAGGCATGTGGGAACTGGGGTCAAGTTTGTGGCTTCCTGTTGGCTTCTGTGAGCACGGCAACCT
CCAACATGTGTTTTCCAGGCTACTGGGGAAGCCAGAGAGTTTAGGATGGCTGTTTGTACATCTG
TCCCTCCTCCCCTGCTGTGCCCCAGAAGCTCTAGGCCTGAGGAGCAGGAAGGCAGGTGGGGTGC
TCATCCCGCTGGGGAAGCTAGCACAAGGCCTGACCAGGTCCTGGACTCCTCAAGGCAGCATTTC
ACCCCTACATGACAATAGCTGCATTACTGCCAACCGATGGTACGACCCTGTGCACCTTTGAAGA
GATTCTGGTTTTAAATTGCTGCTTTTAATAGTATTTGTTATATTAAAGTTATAATTGACGTGTC
TGGTTTACAACAT

hide sequence

RefSeq Acc Id:

XM_006233971 ⟹ XP_006234033

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	18,175,282 - 18,197,090 (-)	NCBI
Rnor_6.0	3	13,957,137 - 13,978,283 (-)	NCBI
Rnor_5.0	3	19,276,705 - 19,297,851 (-)	NCBI

Sequence:

show sequence

AGGGGCGGACACTCGGCCGGGCAGTCCTGGGCCGAGCGCACCACCGCCACCGATGTGCTTGGTG
GCCAGACTCCAAGTGGGACCGGCTGACGCGCTGCCTCGCGCAGAAGCTGATGGAGACGCAAGCT
CTGGAACCAGGGACTCAGGAAGCCTTTGGTGCCACCAGCCCTAACAAGGGGGCCCCGTCTAAGA
CCAAAAAGAACTTCAAAGACTTGATGTCTAAGGTGACAGAGGGACAGTTTGTGCTATGCCGGTG
GACTGACGGGCTATACTACCTTGGCAAGATCAAGCGGGTCAGCAGTCCTAAGCAAAGCTGCCTC
GTGACTTTCGAAGACAATTCCAAATACTGGGTCCTTTGGAAGGACATCCAGCATGCTGGTGTTC
CAGGAGAGGAGCCCAAGTGTGATGTCTGCATGGGGAAGACTTCAGGACCGATGAACGAGATCCT
CATCTGTGGGAAGTGTGGCCTGGGTTACCACCAACAGTGCCACATCCCCATAGCAGTCGATGCC
AACTGGCCCCTCCTCACTCACTGGTTCTGCCGACGCTGCATTTTCGCACTGGCTGTGAGGAAAG
GCGGTGCGCTGAAGAAAGGCGCCATCGCCAAGACGCTGCAGGCAGTGAAAATGGTGCTGTCCTA
CCAGCCTGAGGAGCTCGATTGGGATTCGCCCCATCGCACCAACCAGCAGCAATGCTACTGCTAC
TGCGGCGGGCCTGGAGAGTGGTACTTACGGATGCTACAGTGCTACCGGTGTAGGCAGTGGTTCC
ATGAAGCCTGTACACAGTGCCTAAGTGAGCCTATGGTGTTTGGAGACCGGTTCTACCTGTTCTT
CTGCTCCGTGTGTAACCAAGGCCCAGAGTATATCGAGAGGTTGCCCCTGAGATGGGTAGACATA
GTTCACCTGGCCCTCTATAACCTGGGAGTACAGAGCAAGAAGAGGTACTTCGACTTTGAGGAGA
TCCTGGCCTTTGTCAACCACCACTGGGAGCTCCTGCAGCTTGGCAAGCTCACGAGCACCCCTGT
GACAGAGCGAGGGCCGCATCTCCTCAACGCTCTCAACAGTTACAAAAGCCGGTTCCTGTGTGGC
AAGGAGATTAAGAAGAAGAAATGCATCTTCCGACTGCGCGTCCGTGTCCCGCCCGCCCCTCCAG
GAAAACTGCTTCCGGACAGGGCACAGATGCCAAGTGACAAAGGGACCTTTGAGCTGCTTCGTAA
GAGAGGAAAGAGCAAGCCTGGTTTGTTGCCTCAGGAATCCCAGCAGCAGAAAAGGCGAGTTTAT
AGAAGAAAAAGATCAAAGTTTTTGCTGGAAGATGCTATTCCCAGTAGTGACTTCACCTCAGCCT
GGAGCACGGACCACCACCTGGCCAGCATATTCGACTTTACACTGGATGAAATTCAGAGTTTAAA
AAGTGGCAGCTCAGGCCAGACCTTCTTCTCAGACGTGGATTCTACCGATGCTGCTAGCACCTCA
GGCTCTGCGTCCACCAGCCTCTCCCAGGACTCCAGATGGACAGTAGGCAGCCGTAAGAGGAAGC
TGGCGGCCAAAGCGTACAGGCCCCTGCGGGCAAAGCATCGGGCAGCCGAGCCGGATGGGAGATG
CGCCTCAGACAGCAGTGCAGAGGGAGCTCCGGGCCCTGAGCAGCAGGATGAAGGCATCGACAGC
CACACGTTCGAAAGCATCAGTGGAGATGACTCCTCCCTGTCCCATCTCAAGTCCTCTATCACCA
ACTACTTCGGTGCAGCTGGGCGGTTGGCCTGCGGGGAAAAGTATCAGGTGTTGGCTCGGAGGGT
CACTCCAGAAGGCAAGGTTCAGTACCTGTTGGAATGGGAGGGCACTACCCCTTACTGATTATCC
CTCAGAGGCTGCCCAGAGGCTGCAAACCAAAGGAGGGGCAGAAGAAGCCCCTGGGTCCCTGTTT
TCTCCAGGCTTACGGTGGTGGAGGGAAGCAGGACATCCTGGCCGCAGCCCCTGCCTGCTGTCTG
CCAGGCCAAGGTCTGTGTGCTGCTGTACCAGTTGCCCGAGTCTCTGAGGCCCTGCTGGCTCTCT
CTCGTCTATATCACACTCCATACCCTCAAACTTTCCATTGGTTCCTCCGATGGTACCCTGGCTG
TGACCCCTGATCTGAGGCCTGAAACTGATTTTCGTTGTCCCCAGTTCTCCATCTTCTGACCTCT
CCCCTGCTTGGGTGTTTCATGCGGACACACATCTTCCATGCACATATGCTCATCTGTCCCTCAC
TGGGACCACAGTGAGGAAAGGGAACCCTGTGGGTCTTCCACTTTCTCACCAGTACCCCTCACCC
AGGAGAGTAGGGGATGCCTGAGAAAGTTCAGGATGCCTGCGACCCAGAGCCTGGGAAGTGATGG
CCTGGGTCTCTACTGAAGGGACGAGAATCAGGGTCTTTTATTGAGGCTGGGAAGGGGGACTAAG
GGAGTCAAGGCCAAGGCTCCCAGAAGTTTGCCTGTCCCCAGCAACAGCTCTTCACTGTTGCCGC
AGACTAGAGCCTGGCCTTGCTACATAGACGTGTTCTTGAACGCGCAGATCTGGGAGGAAACGAT
GGGGAGGACCCATCCCAAACACTGTGTATACAGACAAACACCACCACACATCCCCACCAGGGTG
CCCTGGCCCTGTCCTTGGCCTCTTCCAGGGATAAATGCTGCAGTTAAATGTGAAAACCAAGCTC
CGGCCTCCTCTGGCCTGTGAACCAGCCTTGGCCCCACAGAGAAGCACAAAAGACACCCCAAGAC
ACCCCTCTCCTGCATAGCTCCTGCCTTGCCCAGAAGCTGACAATCACTTTGGGGATGGGGCAGC
CGGGGGCGGGGAGAGAGGGCAGTTCCCAAGGGTCTGAATCATTGGTTCCCTTCAGAAAGGAAGT
CTTTGTCATCGATGGTAAAATAGAATTCTTAGAATGGACAAACTCAGCCGTGTCCGGAGGGAAA
CCAAAACTAGGAGGTAGGCAGGGAGTCCTTATTTTTGCCTGCAGAAACAGAAACTGACTCGCTC
GGTTGGACAATTAGAAAGAAGTGCCTTTGGGGTGGGAGGCAGGGGCACCAGACTGGGACCAGCT
TCCCTGACTGCTGCTGTGGCTTCTGGCTGGGAGTGGGGAAATGGACCATCGCATGGCGACATCA
GACTATATCAGAAGTGCTGATTTCCCCATGAGTGGGTCTGACCCCTCCACATCCACCTGTGAGC
ATTAAGGAGGAGGGGGAGTCCCTGAGGTAGGCTAGACGGTCCCTGCCATACACCTCAGCAACCA
TAGTGCCTTGCAAAGGAACCTCACCTCTCACTAGACACAGCTACCCACGTCCATCTGCTTCCCC
GTCTTGGCTCAGGCAGGGCTCAGCAGATGGACACTGAGACCAGTTCTCAGTCCCACAGCTGCTG
CCACTGAGGTCCCCAAGTGGGTCCCGGTGGAAGGAGAGTTGTAAAGCCAACTCCCAGGCCAGCA
GGCATGTGGGAACTGGGGTCAAGTTTGTGGCTTCCTGTTGGCTTCTGTGAGCACGGCAACCTCC
AACATGTGTTTTCCAGGCTACTGGGGAAGCCAGAGAGTTTAGGATGGCTGTTTGTACATCTGTC
CCTCCTCCCCTGCTGTGCCCCAGAAGCTCTAGGCCTGAGGAGCAGGAAGGCAGGTGGGGTGCTC
ATCCCGCTGGGGAAGCTAGCACAAGGCCTGACCAGGTCCTGGACTCCTCAAGGCAGCATTTCAC
CCCTACATGACAATAGCTGCATTACTGCCAACCGATGGTACGACCCTGTGCACCTTTGAAGAGA
TTCTGGTTTTAAATTGCTGCTTTTAATAGTATTTGTTATATTAAAGTTATAATTGACGTGTCTG
GTTTACAACA

hide sequence

RefSeq Acc Id:

XM_008761740 ⟹ XP_008759962

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	18,175,282 - 18,187,353 (-)	NCBI
Rnor_6.0	3	13,957,137 - 13,968,942 (-)	NCBI

Sequence:

show sequence

AGAGGGGCGGACCCAGAGTGACAGCAGCGGGGCGGGGCCTCAGTGTCAGGCCTTGGAGGCGTGT
CTTGGATGGGCAAATCCAGAGTGCTCACTGGGGGCTAGGTCTAGGGTAGACGGGCCTAAAGTGA
CAGTCGCGAGGGCGGGGCCTAGGTGTCAGGCCACGGAAGCGGGATCTGGAGGGGCGGATCCTCG
ATGTCATTTTAGGGAGGGCAGATTGTTTAATGTTTAATTTTAATGTCGCTTTGCAGGAGGGAAA
CCCAGAGTAGTCTTTGGGGAAACCAAGCTTTGAGGGGCGGGCCCAGGGGGTAGGATGGCTGTCA
TAAGGCAGGTCTGGACCAATGGGAGCCAGGAGAGTTACCTAGGGATCTTAAAGGAAGGGTGCTG
AAAGTAAGCTCAGAGTGAGAACCTGTGCAGGTGCAATGGAGAGTAGAAGGCAGAGTGCTTTTCT
TGGAGTCACGTGAGAAAGGAGGAAGTGGTACTTACGGATGCTACAGTGCTACCGGTGTAGGCAG
TGGTTCCATGAAGCCTGTACACAGTGCCTAAGTGAGCCTATGGTGTTTGGAGACCGGTTCTACC
TGTTCTTCTGCTCCGTGTGTAACCAAGGCCCAGAGTATATCGAGAGGTTGCCCCTGAGATGGGT
AGACATAGTTCACCTGGCCCTCTATAACCTGGGAGTACAGAGCAAGAAGAGGTACTTCGACTTT
GAGGAGATCCTGGCCTTTGTCAACCACCACTGGGAGCTCCTGCAGCTTGGCAAGCTCACGAGCA
CCCCTGTGACAGAGCGAGGGCCGCATCTCCTCAACGCTCTCAACAGTTACAAAAGCCGGTTCCT
GTGTGGCAAGGAGATTAAGAAGAAGAAATGCATCTTCCGACTGCGCGTCCGTGTCCCGCCCGCC
CCTCCAGGAAAACTGCTTCCGGACAGGGCACAGATGCCAAGTGACAAAGGGACCTTTGAGCTGC
TTCGTAAGAGAGGAAAGAGCAAGCCTGGTTTGTTGCCTCAGGAATCCCAGCAGCAGAAAAGGCG
AGTTTATAGAAGAAAAAGATCAAAGTTTTTGCTGGAAGATGCTATTCCCAGTAGTGACTTCACC
TCAGCCTGGAGCACGGACCACCACCTGGCCAGCATATTCGACTTTACACTGGATGAAATTCAGA
GTTTAAAAAGTGGCAGCTCAGGCCAGACCTTCTTCTCAGACGTGGATTCTACCGATGCTGCTAG
CACCTCAGGCTCTGCGTCCACCAGCCTCTCCCAGGACTCCAGATGGACAGTAGGCAGCCGTAAG
AGGAAGCTGGCGGCCAAAGCGTACAGGCCCCTGCGGGCAAAGCATCGGGCAGCCGAGCCGGATG
GGAGATGCGCCTCAGACAGCAGTGCAGAGGGAGCTCCGGGCCCTGAGCAGCAGGATGAAGGCAT
CGACAGCCACACGTTCGAAAGCATCAGTGGAGATGACTCCTCCCTGTCCCATCTCAAGTCCTCT
ATCACCAACTACTTCGGTGCAGCTGGGCGGTTGGCCTGCGGGGAAAAGTATCAGGTGTTGGCTC
GGAGGGTCACTCCAGAAGGCAAGGTTCAGTACCTGTTGGAATGGGAGGGCACTACCCCTTACTG
ATTATCCCTCAGAGGCTGCCCAGAGGCTGCAAACCAAAGGAGGGGCAGAAGAAGCCCCTGGGTC
CCTGTTTTCTCCAGGCTTACGGTGGTGGAGGGAAGCAGGACATCCTGGCCGCAGCCCCTGCCTG
CTGTCTGCCAGGCCAAGGTCTGTGTGCTGCTGTACCAGTTGCCCGAGTCTCTGAGGCCCTGCTG
GCTCTCTCTCGTCTATATCACACTCCATACCCTCAAACTTTCCATTGGTTCCTCCGATGGTACC
CTGGCTGTGACCCCTGATCTGAGGCCTGAAACTGATTTTCGTTGTCCCCAGTTCTCCATCTTCT
GACCTCTCCCCTGCTTGGGTGTTTCATGCGGACACACATCTTCCATGCACATATGCTCATCTGT
CCCTCACTGGGACCACAGTGAGGAAAGGGAACCCTGTGGGTCTTCCACTTTCTCACCAGTACCC
CTCACCCAGGAGAGTAGGGGATGCCTGAGAAAGTTCAGGATGCCTGCGACCCAGAGCCTGGGAA
GTGATGGCCTGGGTCTCTACTGAAGGGACGAGAATCAGGGTCTTTTATTGAGGCTGGGAAGGGG
GACTAAGGGAGTCAAGGCCAAGGCTCCCAGAAGTTTGCCTGTCCCCAGCAACAGCTCTTCACTG
TTGCCGCAGACTAGAGCCTGGCCTTGCTACATAGACGTGTTCTTGAACGCGCAGATCTGGGAGG
AAACGATGGGGAGGACCCATCCCAAACACTGTGTATACAGACAAACACCACCACACATCCCCAC
CAGGGTGCCCTGGCCCTGTCCTTGGCCTCTTCCAGGGATAAATGCTGCAGTTAAATGTGAAAAC
CAAGCTCCGGCCTCCTCTGGCCTGTGAACCAGCCTTGGCCCCACAGAGAAGCACAAAAGACACC
CCAAGACACCCCTCTCCTGCATAGCTCCTGCCTTGCCCAGAAGCTGACAATCACTTTGGGGATG
GGGCAGCCGGGGGCGGGGAGAGAGGGCAGTTCCCAAGGGTCTGAATCATTGGTTCCCTTCAGAA
AGGAAGTCTTTGTCATCGATGGTAAAATAGAATTCTTAGAATGGACAAACTCAGCCGTGTCCGG
AGGGAAACCAAAACTAGGAGGTAGGCAGGGAGTCCTTATTTTTGCCTGCAGAAACAGAAACTGA
CTCGCTCGGTTGGACAATTAGAAAGAAGTGCCTTTGGGGTGGGAGGCAGGGGCACCAGACTGGG
ACCAGCTTCCCTGACTGCTGCTGTGGCTTCTGGCTGGGAGTGGGGAAATGGACCATCGCATGGC
GACATCAGACTATATCAGAAGTGCTGATTTCCCCATGAGTGGGTCTGACCCCTCCACATCCACC
TGTGAGCATTAAGGAGGAGGGGGAGTCCCTGAGGTAGGCTAGACGGTCCCTGCCATACACCTCA
GCAACCATAGTGCCTTGCAAAGGAACCTCACCTCTCACTAGACACAGCTACCCACGTCCATCTG
CTTCCCCGTCTTGGCTCAGGCAGGGCTCAGCAGATGGACACTGAGACCAGTTCTCAGTCCCACA
GCTGCTGCCACTGAGGTCCCCAAGTGGGTCCCGGTGGAAGGAGAGTTGTAAAGCCAACTCCCAG
GCCAGCAGGCATGTGGGAACTGGGGTCAAGTTTGTGGCTTCCTGTTGGCTTCTGTGAGCACGGC
AACCTCCAACATGTGTTTTCCAGGCTACTGGGGAAGCCAGAGAGTTTAGGATGGCTGTTTGTAC
ATCTGTCCCTCCTCCCCTGCTGTGCCCCAGAAGCTCTAGGCCTGAGGAGCAGGAAGGCAGGTGG
GGTGCTCATCCCGCTGGGGAAGCTAGCACAAGGCCTGACCAGGTCCTGGACTCCTCAAGGCAGC
ATTTCACCCCTACATGACAATAGCTGCATTACTGCCAACCGATGGTACGACCCTGTGCACCTTT
GAAGAGATTCTGGTTTTAAATTGCTGCTTTTAATAGTATTTGTTATATTAAAGTTATAATTGAC
GTGTCTGGTTTACAACA

hide sequence

RefSeq Acc Id:

XM_039104781 ⟹ XP_038960709

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	18,175,282 - 18,197,221 (-)	NCBI

RefSeq Acc Id:

XM_039104782 ⟹ XP_038960710

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	18,175,282 - 18,197,289 (-)	NCBI

RefSeq Acc Id:

XM_039104783 ⟹ XP_038960711

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	18,175,282 - 18,188,813 (-)	NCBI

RefSeq Acc Id:

XR_005501843

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	18,175,282 - 18,197,091 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001100040	(Get FASTA)	NCBI Sequence Viewer
	XP_006234033	(Get FASTA)	NCBI Sequence Viewer
	XP_008759962	(Get FASTA)	NCBI Sequence Viewer
	XP_038960709	(Get FASTA)	NCBI Sequence Viewer
	XP_038960710	(Get FASTA)	NCBI Sequence Viewer
	XP_038960711	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL93157	(Get FASTA)	NCBI Sequence Viewer
	EDL93158	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001100040 ⟸ NM_001106570

- UniProtKB:

F1M1Y4 (UniProtKB/TrEMBL)

- Sequence:

show sequence

METQALEPGTQEAFGATSPNKGAPSKTKKNFKDLMSKVTEGQFVLCRWTDGLYYLGKIKRVSSP
KQSCLVTFEDNSKYWVLWKDIQHAGVPGEEPKCDVCMGKTSGPMNEILICGKCGLGYHQQCHIP
IAVDANWPLLTHWFCRRCIFALAVRKGGALKKGAIAKTLQAVKMVLSYQPEELDWDSPHRTNQQ
QCYCYCGGPGEWYLRMLQCYRCRQWFHEACTQCLSEPMVFGDRFYLFFCSVCNQGPEYIERLPL
RWVDIVHLALYNLGVQSKKRYFDFEEILAFVNHHWELLQLGKLTSTPVTERGPHLLNALNSYKS
RFLCGKEIKKKKCIFRLRVRVPPAPPGKLLPDRAQMPSDKGTFELLRKRGKSKPGLLPQESQQQ
KRRVYRRKRSKFLLEDAIPSSDFTSAWSTDHHLASIFDFTLDEIQSLKSGSSGQTFFSDVDSTD
AASTSGSASTSLSQDSRWTVGSRKRKLAAKAYRPLRAKHRAAEPDGRCASDSSAEGAPGPEQQD
EGIDSHTFESISGDDSSLSHLKSSITNYFGAAGRLACGEKYQVLARRVTPEGKVQYLLEWEGTT
PY

hide sequence

RefSeq Acc Id:	XP_006234033 ⟸ XM_006233971
- Peptide Label:	isoform X1
- UniProtKB:	F1M1Y4 (UniProtKB/TrEMBL)
- Sequence:	show sequence METQALEPGTQEAFGATSPNKGAPSKTKKNFKDLMSKVTEGQFVLCRWTDGLYYLGKIKRVSSP KQSCLVTFEDNSKYWVLWKDIQHAGVPGEEPKCDVCMGKTSGPMNEILICGKCGLGYHQQCHIP IAVDANWPLLTHWFCRRCIFALAVRKGGALKKGAIAKTLQAVKMVLSYQPEELDWDSPHRTNQQ QCYCYCGGPGEWYLRMLQCYRCRQWFHEACTQCLSEPMVFGDRFYLFFCSVCNQGPEYIERLPL RWVDIVHLALYNLGVQSKKRYFDFEEILAFVNHHWELLQLGKLTSTPVTERGPHLLNALNSYKS RFLCGKEIKKKKCIFRLRVRVPPAPPGKLLPDRAQMPSDKGTFELLRKRGKSKPGLLPQESQQQ KRRVYRRKRSKFLLEDAIPSSDFTSAWSTDHHLASIFDFTLDEIQSLKSGSSGQTFFSDVDSTD AASTSGSASTSLSQDSRWTVGSRKRKLAAKAYRPLRAKHRAAEPDGRCASDSSAEGAPGPEQQD EGIDSHTFESISGDDSSLSHLKSSITNYFGAAGRLACGEKYQVLARRVTPEGKVQYLLEWEGTT PY hide sequence

RefSeq Acc Id:

XP_008759962 ⟸ XM_008761740

- Peptide Label:

isoform X3

- Sequence:

show sequence

MLQCYRCRQWFHEACTQCLSEPMVFGDRFYLFFCSVCNQGPEYIERLPLRWVDIVHLALYNLGV
QSKKRYFDFEEILAFVNHHWELLQLGKLTSTPVTERGPHLLNALNSYKSRFLCGKEIKKKKCIF
RLRVRVPPAPPGKLLPDRAQMPSDKGTFELLRKRGKSKPGLLPQESQQQKRRVYRRKRSKFLLE
DAIPSSDFTSAWSTDHHLASIFDFTLDEIQSLKSGSSGQTFFSDVDSTDAASTSGSASTSLSQD
SRWTVGSRKRKLAAKAYRPLRAKHRAAEPDGRCASDSSAEGAPGPEQQDEGIDSHTFESISGDD
SSLSHLKSSITNYFGAAGRLACGEKYQVLARRVTPEGKVQYLLEWEGTTPY

hide sequence

RefSeq Acc Id:

ENSRNOP00000025528 ⟸ ENSRNOT00000025528

RefSeq Acc Id:	XP_038960710 ⟸ XM_039104782
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038960709 ⟸ XM_039104781
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038960711 ⟸ XM_039104783
- Peptide Label:	isoform X2

Protein Domains

PHD-type

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-F1M1Y4-F1-model_v2	AlphaFold	F1M1Y4	1-578	view protein structure

Transcriptome

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

Promoters

RGD ID:

13692010

Promoter ID:

EPDNEW_R2535

Type:

multiple initiation site

Name:

Phf19_1

Description:

PHD finger protein 19

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	13,978,273 - 13,978,333	EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)

ACI/EurMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN-Lx/CubMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BUF/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

DA/OlaHsd (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE16/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GK/FarMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB10/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEW/Crl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF10A/StmMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LH/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LL/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LN/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/NRrrcMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MR/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MWF/Hsd (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHR/OlalpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SR/JrHsd (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SS/JrHsdMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WAG/RijCrl (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WN/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

Damaging Variants

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
3	13959296	13959297	A	C	snv	LE/Stm (2019), LE/Stm (RGD), LEXF1C/Stm (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), FXLE16/Stm (2020)

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
3	19278865	19278866	A	C	snv	LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), LE/Stm (KyushuU)
3	19280208	19280209	T	G	snv	SR/JrHsd (MCW), FHH/EurMcwi (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1310390	AgrOrtholog
BioCyc Gene	G2FUF-50073	BioCyc
Ensembl Genes	ENSRNOG00000018874	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000025528	ENTREZGENE
	ENSRNOP00000025528.5	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000025528	ENTREZGENE
	ENSRNOT00000025528.7	UniProtKB/TrEMBL
Gene3D-CATH	3.30.40.10	UniProtKB/TrEMBL
InterPro	KDM4_Tudor_2	UniProtKB/TrEMBL
	Mtf2_C_dom	UniProtKB/TrEMBL
	PHF19_PHD2	UniProtKB/TrEMBL
	Tudor	UniProtKB/TrEMBL
	Zinc_finger_PHD-type_CS	UniProtKB/TrEMBL
	Znf_FYVE_PHD	UniProtKB/TrEMBL
	Znf_PHD	UniProtKB/TrEMBL
	Znf_PHD-finger	UniProtKB/TrEMBL
	Znf_RING/FYVE/PHD	UniProtKB/TrEMBL
KEGG Report	rno:296653	UniProtKB/TrEMBL
NCBI Gene	296653	ENTREZGENE
Pfam	Mtf2_C	UniProtKB/TrEMBL
	PHD	UniProtKB/TrEMBL
	Tudor_2	UniProtKB/TrEMBL
PhenoGen	Phf19	PhenoGen
PROSITE	ZF_PHD_1	UniProtKB/TrEMBL
	ZF_PHD_2	UniProtKB/TrEMBL
SMART	PHD	UniProtKB/TrEMBL
	TUDOR	UniProtKB/TrEMBL
Superfamily-SCOP	FYVE_PHD_ZnF	UniProtKB/TrEMBL
UniProt	F1M1Y4	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Phf19	PHD finger protein 19	Phf19_predicted	PHD finger protein 19 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Phf19_predicted	PHD finger protein 19 (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)

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RGD Manual Annotations