Phf10 (PHD finger protein 10) - Rat Genome Database

Name: Phf10
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Phf10 (PHD finger protein 10) Rattus norvegicus

Analyze

Symbol:

Phf10

Name:

PHD finger protein 10

RGD ID:

1305266

Description:

Predicted to have metal ion binding activity. Involved in embryonic brain development. Predicted to localize to npBAF complex and nucleoplasm. Orthologous to human PHF10 (PHD finger protein 10); PARTICIPATES IN SWI/SNF family mediated chromatin remodeling pathway; INTERACTS WITH acetamide; bisphenol A; flutamide.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

BAF45a; BRG1-associated factor 45a; LOC292404

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):	PHF10 (PHD finger protein 10)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, Panther
Mus musculus (house mouse):	Phf10 (PHD finger protein 10)	HGNC	NCBI, HomoloGene, Inparanoid, Panther, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Phf10 (PHD finger protein 10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PHF10 (PHD finger protein 10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PHF10 (PHD finger protein 10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Phf10 (PHD finger protein 10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PHF10 (PHD finger protein 10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	PHF10 (PHD finger protein 10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Phf10 (PHD finger protein 10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	PHF10 (PHD finger protein 10)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Mus musculus (house mouse):	Phf10 (PHD finger protein 10)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	phf10 (PHD finger protein 10)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	phf-10	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PhylomeDB)
Drosophila melanogaster (fruit fly):	e(y)3	Alliance	DIOPT (OrthoFinder\|OrthoInspector)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	55,952,249 - 55,968,994 (-)	NCBI
Rnor_6.0 Ensembl	1	56,951,518 - 56,967,895 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	56,951,516 - 56,967,893 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	58,134,862 - 58,191,474 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	53,874,298 - 53,890,546 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	53,877,244 - 53,893,500 (-)	NCBI
Celera	1	52,164,139 - 52,178,581 (-)	NCBI		Celera
Cytogenetic Map	1	q12	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

(-)-demecolcine (ISO)

1,2-dimethylhydrazine (ISO)

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

2-hydroxypropanoic acid (ISO)

3,4-methylenedioxymethamphetamine (ISO)

acetamide (EXP)

aflatoxin B1 (ISO)

Aroclor 1254 (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

butanal (ISO)

carbon nanotube (ISO)

casticin (ISO)

cobalt dichloride (ISO)

copper atom (ISO)

copper(0) (ISO)

coumestrol (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dorsomorphin (ISO)

enzyme inhibitor (ISO)

flutamide (EXP)

folic acid (ISO)

formaldehyde (ISO)

lead diacetate (EXP,ISO)

manganese(II) chloride (EXP)

menadione (ISO)

methotrexate (ISO)

methyl methanesulfonate (ISO)

methylparaben (ISO)

N-methyl-4-phenylpyridinium (EXP)

paracetamol (ISO)

paraquat (ISO)

quercetin (ISO)

rac-lactic acid (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

Soman (EXP)

tetrachloromethane (ISO)

uranium atom (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

embryonic brain development (IEP)

negative regulation of transcription, DNA-templated (IBA)

nervous system development (IEA,ISO)

positive regulation of transcription by RNA polymerase II (IBA)

Cellular Component

cellular_component (ND)

chromatin (IBA)

npBAF complex (IEA,ISO,ISS)

nucleoplasm (IEA,ISO)

Molecular Function

histone binding (IBA)

metal ion binding (IEA)

molecular_function (ND)

protein binding (ISO)

transcription coregulator activity (IBA)

Molecular Pathway Annotations Click to see Annotation Detail View

SWI/SNF family mediated chromatin remodeling pathway (ISO)

References

References - curated


1.	Conti V, etal., Brain. 2013 Nov;136(Pt 11):3378-94. doi: 10.1093/brain/awt249. Epub 2013 Sep 20.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Hargreaves DC and Crabtree GR, Cell Res. 2011 Mar;21(3):396-420. doi: 10.1038/cr.2011.32. Epub 2011 Mar 1.
4.	MGD data from the GO Consortium
5.	RGD automated data pipeline
6.	RGD automated import pipeline for gene-chemical interactions
7.	RGD comprehensive gene curation
8.	Shain AH and Pollack JR, PLoS One. 2013;8(1):e55119. doi: 10.1371/journal.pone.0055119. Epub 2013 Jan 23.

Additional References at PubMed

PMID:12477932	PMID:17640523

Genomics

Comparative Map Data

Phf10
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	55,952,249 - 55,968,994 (-)	NCBI
Rnor_6.0 Ensembl	1	56,951,518 - 56,967,895 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	56,951,516 - 56,967,893 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	58,134,862 - 58,191,474 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	53,874,298 - 53,890,546 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	53,877,244 - 53,893,500 (-)	NCBI
Celera	1	52,164,139 - 52,178,581 (-)	NCBI		Celera
Cytogenetic Map	1	q12	NCBI

PHF10
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	6	169,703,902 - 169,725,566 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	6	169,703,902 - 169,724,500 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	6	170,103,998 - 170,124,596 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	169,845,926 - 169,865,909 (-)	NCBI	NCBI36		hg18	NCBI36
Celera	6	170,814,186 - 170,834,281 (-)	NCBI
Cytogenetic Map	6	q27	NCBI
HuRef	6	167,523,776 - 167,540,978 (-)	NCBI		HuRef
CHM1_1	6	170,366,215 - 170,386,295 (-)	NCBI		CHM1_1

Phf10
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	15,165,256 - 15,181,522 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	17	15,165,271 - 15,181,535 (-)	Ensembl
GRCm38	17	14,944,994 - 14,961,260 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	14,945,009 - 14,961,273 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	15,081,999 - 15,098,237 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	17	14,681,585 - 14,697,808 (-)	NCBI			mm8
MGSCv36	17	14,105,368 - 14,152,496 (-)	NCBI			mm8
Celera	17	15,745,693 - 15,760,216 (-)	NCBI		Celera
Cytogenetic Map	17	A2	NCBI

Phf10
(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_004955411	3,911,791 - 3,930,912 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955411	3,911,966 - 3,926,995 (+)	NCBI	ChiLan1.0	ChiLan1.0

PHF10
(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	6	172,608,779 - 172,831,580 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	172,608,894 - 172,831,584 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	6	167,776,108 - 167,796,711 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

PHF10
(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	12	71,787,082 - 71,998,243 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	12	71,955,354 - 71,998,283 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Phf10
(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_004936489	18,158,164 - 18,177,122 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PHF10
(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	555,355 - 576,713 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	555,649 - 576,781 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	933,787 - 954,103 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PHF10
(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	13	97,512,754 - 97,532,903 (-)	NCBI
ChlSab1.1 Ensembl	13	97,512,867 - 97,532,896 (-)	Ensembl

Phf10
(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_004624850	5,633,967 - 5,652,283 (-)	NCBI

Position Markers

RH130186

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	56,952,235 - 56,952,392	NCBI	Rnor6.0
Rnor_5.0	1	58,135,581 - 58,135,738	UniSTS	Rnor5.0
RGSC_v3.4	1	53,875,017 - 53,875,174	UniSTS	RGSC3.4
Celera	1	52,164,858 - 52,165,015	UniSTS
RH 3.4 Map	1	658.8	UniSTS
Cytogenetic Map	1	q12	UniSTS

RH132671

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	56,951,061 - 56,951,265	NCBI	Rnor6.0
Rnor_5.0	1	58,134,407 - 58,134,611	UniSTS	Rnor5.0
RGSC_v3.4	1	53,873,843 - 53,874,047	UniSTS	RGSC3.4
Celera	1	52,163,684 - 52,163,888	UniSTS
Cytogenetic Map	1	q12	UniSTS

BF396946

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	56,960,832 - 56,960,996	NCBI	Rnor6.0
Rnor_5.0	1	58,144,178 - 58,144,342	UniSTS	Rnor5.0
RGSC_v3.4	1	53,883,614 - 53,883,778	UniSTS	RGSC3.4
Celera	1	52,173,455 - 52,173,619	UniSTS
RH 3.4 Map	1	671.8	UniSTS
Cytogenetic Map	1	q12	UniSTS

RH140578

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	56,993,926 - 56,994,133	NCBI	Rnor6.0
Rnor_5.0	1	58,177,003 - 58,177,210	UniSTS	Rnor5.0
RGSC_v3.4	1	53,917,050 - 53,917,257	UniSTS	RGSC3.4
RH 3.4 Map	1	658.6	UniSTS
Cytogenetic Map	1	q12	UniSTS

RH142080

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	56,954,405 - 56,954,589	NCBI	Rnor6.0
Rnor_5.0	1	58,137,751 - 58,137,935	UniSTS	Rnor5.0
RGSC_v3.4	1	53,877,187 - 53,877,371	UniSTS	RGSC3.4
Celera	1	52,167,028 - 52,167,212	UniSTS
RH 3.4 Map	1	675.9	UniSTS
Cytogenetic Map	1	q12	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
738020	Pia8	Pristane induced arthritis QTL 8	4.7		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	1	64407321	Rat
1554320	Bmd1	Bone mineral density QTL 1	12.2	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	254393	86904217	Rat
631688	Hcas2	Hepatocarcinoma susceptibility QTL 2	3	0.0001	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	5655769	122614963	Rat
4889451	Eae29	Experimental allergic encephalomyelitis QTL 29	5.51		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	1	5655772	85706974	Rat
1300167	Hrtrt2	Heart rate QTL 2	4.35		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	11314489	75844121	Rat
2313062	Bmd73	Bone mineral density QTL 73	3.9	0.0001	tibia mineral mass (VT:1000283)	cortical volumetric bone mineral density (CMO:0001730)	1	11314489	83657083	Rat
2313065	Bss67	Bone structure and strength QTL 67	3.1	0.0001	tibia area (VT:1000281)	tibia total energy absorbed before break (CMO:0001736)	1	11314489	83657083	Rat
2313069	Bss68	Bone structure and strength QTL 68	2.9	0.0001	tibia size trait (VT:0100001)	tibia total energy absorbed before break (CMO:0001736)	1	11314489	83657083	Rat
2313075	Bss66	Bone structure and strength QTL 66	3.4	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	11314489	83657083	Rat
2313077	Bss69	Bone structure and strength QTL 69	3.5	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	11314489	83657083	Rat
2313092	Bmd72	Bone mineral density QTL 72	2.5	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	11314489	83657083	Rat
2313097	Bss70	Bone structure and strength QTL 70	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	11314489	83657083	Rat
631508	Sald1	Serum aldosterone level QTL 1	3.7		blood aldosterone amount (VT:0005346)	serum aldosterone level (CMO:0000487)	1	12493439	57493439	Rat
2302038	Pia31	Pristane induced arthritis QTL 31	5.5	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)	1	13629251	58629251	Rat
634353	Rends2	Renal damage susceptibility QTL 2		0.05	kidney blood vessel morphology trait (VT:0000530)	organ lesion measurement (CMO:0000677)	1	20341560	58000154	Rat
724520	Bp145	Blood pressure QTL 145	2.1	0.0024	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	21079305	66079305	Rat
1357400	Bw62	Body weight QTL62	4.05		inguinal fat pad mass (VT:0010424)	inguinal fat pad weight to body weight ratio (CMO:0001253)	1	23406428	68406428	Rat
631495	Bp96	Blood pressure QTL 96	4.52		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	23406428	108057505	Rat
1358192	Ept13	Estrogen-induced pituitary tumorigenesis QTL 13	3.4		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	24297799	78748000	Rat
1358359	Sradr1	Stress Responsive Adrenal Weight QTL 1	4.74		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	25951907	130917265	Rat
1331785	Rf27	Renal function QTL 27	4.643		urine sodium amount (VT:0006274)	urine sodium level (CMO:0000129)	1	31489454	79689689	Rat
1354643	Foco2	Food consumption QTL 2	7.17	0.0001	eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	1	34449112	79449112	Rat
1354599	Bw29	Body weight QTL 29	3.46	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	34449112	79449112	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34993530	173445086	Rat
1300172	Bp172	Blood pressure QTL 172	3.56		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	35377508	94364229	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	35377692	217372257	Rat
9589820	Insglur3	Insulin/glucose ratio QTL 3	10.75	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	1	35854167	80854167	Rat
8552900	Pigfal1	Plasma insulin-like growth factor 1 level QTL 1	7.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	35854167	80854167	Rat
8552948	Pigfal11	Plasma insulin-like growth factor 1 level QTL 11	4.7		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	35854167	80854167	Rat
1331732	Srn4	Serum renin concentration QTL 4	4.467		renin activity (VT:0005581)	plasma renin activity level (CMO:0000116)	1	36033165	79689689	Rat
1331792	Rf29	Renal function QTL 29	4.589		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	1	36033165	79689689	Rat
2302059	Pia36	Pristane induced arthritis QTL 36	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	41907249	86907249	Rat
2313051	Bss57	Bone structure and strength QTL 57	3.7	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	43579208	126240667	Rat
2313059	Bss55	Bone structure and strength QTL 55	3.2	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	1	43579208	126240667	Rat
2313072	Bss53	Bone structure and strength QTL 53	4.3	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	43579208	126240667	Rat
2313078	Bss54	Bone structure and strength QTL 54	3.5	0.0001	tibia area (VT:1000281)	tibia midshaft cross-sectional area (CMO:0001717)	1	43579208	126240667	Rat
2313094	Bss58	Bone structure and strength QTL 58	3.7	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	43579208	126240667	Rat
2313098	Bmd70	Bone mineral density QTL 70	3.6	0.0001	tibia mineral mass (VT:1000283)	cortical volumetric bone mineral density (CMO:0001730)	1	43579208	126240667	Rat
2313099	Bss56	Bone structure and strength QTL 56	2.4	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	1	43579208	126240667	Rat
1331778	Rf28	Renal function QTL 28	4.66		urine potassium amount (VT:0010539)	urine potassium excretion rate (CMO:0000761)	1	46113461	79689689	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	49147799	156446783	Rat
4889962	Bss94	Bone structure and strength QTL 94	3.8		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	49547328	83657083	Rat
1578649	Bmd8	Bone mineral density QTL 8	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	49578577	94578577	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	49578577	169852184	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49578693	217054291	Rat
1578756	Iddm22	Insulin dependent diabetes mellitus QTL 22	2.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	50522714	57861469	Rat
6903308	Scl36	Serum cholesterol QTL 36	2	0.0125	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	50522714	94225616	Rat
4889919	Bss86	Bone structure and strength QTL 86	4.1		tibia area (VT:1000281)	tibia midshaft total cross-sectional area (CMO:0001715)	1	53851348	83657083	Rat
4889929	Bss87	Bone structure and strength QTL 87	6.7		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	53851348	83657083	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	19
Count of miRNA genes:	18
Interacting mature miRNAs:	19
Transcripts:	ENSRNOT00000020865
Prediction methods:	Miranda, Rnahybrid
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	37	57	41	19	41	8	11	74	35	41	11	8
Low		6
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001024747	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017588876	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC098049	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474033	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000023	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000085273 ⟹ ENSRNOP00000072702

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	56,951,518 - 56,967,895 (-)	Ensembl

RefSeq Acc Id:

NM_001024747 ⟹ NP_001019918

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	55,952,253 - 55,968,590 (-)	NCBI
Rnor_6.0	1	56,951,516 - 56,967,893 (-)	NCBI
Rnor_5.0	1	58,134,862 - 58,191,474 (-)	NCBI
RGSC_v3.4	1	53,874,298 - 53,890,546 (-)	RGD
Celera	1	52,164,139 - 52,178,581 (-)	RGD

Sequence:

show sequence

CGACGGCGCGACGAACGACGGAGGCGCGGGGTCGCTGGGCGCTGATGGCAGCGGGCCGGGCCCG
GGCGGGCGCTGATCCCCCGCGGCGGTTGCGGACAGTTTTCGGACCCGAGGCCTCCCCCGGAGCG
CCAGTCCCCGAAGGATGATAATGAAGATAACTCAAATGATGGGGGTCATCCATCTAAAAGAAGA
CGAATGGGTTCAGGGGATAGTTCAAGAAGTTGCGAGACTTCAAGTCAAGATCTTAGCTTCAGTT
ACTACCCAGCAGAAAACTTAATAGAATACAAATGGCCACCTGATGAAACAGGAGAATACTACAT
GCTTCAGGAGCAAGTCAGTGAATATCTGGGTGTGACCTCCTTCAAGCGGAAATATCCAGATTTA
GAGCGACGAGATTTATCTCACAAGGAGAAACTGTACCTGAGAGAATTAAACGTCATCACGGAAA
CACAGTGCACACTAGGTTTAACAGCATTGCGCAGTGATGAAGTGATTGACTTAATGATAAAAGA
ATATCCAGCTAAACACGCTGAATATTCTGTTATTCTACAAGAAAAGGAACGTCAGAGAATTACA
GATCATTATAAAGAGTATTCTCAAATGCAGCAACAGAGTACTCAGAAAGTCGAAGCCAGCAAAG
TGCCTGAGTACATTAAGAAAGCCGCCAAGAAGGCAGCAGAGTTTAACAGCAACTTAAACCGGGA
GCGCATGGAAGAAAGAAGAGCGTACTTTGACTTGCAGACGCATGTCATCCAAGTGCCTCAAGGG
AAGTACAAAGTGTTGCCAACAGACCGAACGAAGGTCAGTTCCTATCCAGTGGCTCTCATCCCCG
GGCAGTTCCAGGAGTACTATAAGAGGTACTCACCAGATGAGCTTCGGTACTTGCCATTAAACAC
AGCCCTGTATGAGCCGCCCCTGGACCCAGAGCTCCCGGCACTAGATAGTGATGGAGACTCAGAT
GACGGTGAAGACGGTGGAGGGGATGAGAAGCGGAAGAATAAAGGCACTTCGGACAGCTCCTCAG
GCAATGTGTCTGAAGGAGACAGCCCCCCTGACAGCCAGGAGGACACCTTCCAGGGAAGACAGAA
ATCAAAAGACAAAATGGCCACGCCAAGAAAAGACGGCTCCAAACGTTCTGTACTGTCCAAATCA
GTTCCTGGGTACAAGCCAAAGGTCATTCCAAATGCTCTATGTGGAATTTGTCTGAAGGGTAAGG
AGTCCAACAAGAAAGGAAAGGCTGAATCACTTATACACTGCTCCCAGTGTGATAACAGTGGCCA
CCCTTCTTGCTTGGATATGACCATGGAGCTTGTTTCTATGATTAAGACCTACCCATGGCAGTGT
ATGGAATGTAAGACATGCATTATATGTGGACAGCCCCACCATGAAGAAGAAATGATGTTCTGTG
ATGTGTGTGACAGAGGTTATCATACTTTTTGTGTGGGCCTTGGTGCTATTCCATCAGGTCGCTG
GATTTGTGACTGTTGTCAGCGAGCTCCCCCAACACCCAGGAAAGTGGGCAGAAGGGGGAAAAAC
AGCAAAGAGGGGTAAATAGGCTTTGACCCTCGTGTTTGGGATATTTGGTGCCAATTTATTTACA
ACACTTTCATTTTTATGCCAATAAAGAACTTTTTTTGAAATTAA

hide sequence

RefSeq Acc Id:

XM_017588876 ⟹ XP_017444365

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	55,952,249 - 55,968,994 (-)	NCBI
Rnor_6.0	1	56,951,516 - 56,967,785 (-)	NCBI

Sequence:

show sequence

CCGAGGCCTCCCCCGGAGCGCCAGTCCCCGAAGGATGATAATGAAGATAACTCAAATGATGGGG
GTCATCCATCTAAAAGAAGACGAATGGGTTCAGGGGATAGTTCAAGAAGTTGCGAGACTTCAAG
TCAAGATCTTAGCTTCAGTTACTACCCAGCAGAAAACTTAATAGAATACAAATGGCCACCTGAT
GAAACAGGAGAATACTACATGCTTCAGGAGCAAGTCAGTGAATATCTGGGTGTGACCTCCTTCA
AGCGGAAATATCCAGAGCGACGAGATTTATCTCACAAGGAGAAACTGTACCTGAGAGAATTAAA
CGTCATCACGGAAACACAGTGCACACTAGGTTTAACAGCATTGCGCAGTGATGAAGTGATTGAC
TTAATGATAAAAGAATATCCAGCTAAACACGCTGAATATTCTGTTATTCTACAAGAAAAGGAAC
GTCAGAGAATTACAGATCATTATAAAGAGTATTCTCAAATGCAGCAACAGAGTACTCAGAAAGT
CGAAGCCAGCAAAGTGCCTGAGTACATTAAGAAAGCCGCCAAGAAGGCAGCAGAGTTTAACAGC
AACTTAAACCGGGAGCGCATGGAAGAAAGAAGAGCGTACTTTGACTTGCAGACGCATGTCATCC
AAGTGCCTCAAGGGAAGTACAAAGTGTTGCCAACAGACCGAACGAAGGTCAGTTCCTATCCAGT
GGCTCTCATCCCCGGGCAGTTCCAGGAGTACTATAAGAGGTACTCACCAGATGAGCTTCGGTAC
TTGCCATTAAACACAGCCCTGTATGAGCCGCCCCTGGACCCAGAGCTCCCGGCACTAGATAGTG
ATGGAGACTCAGATGACGGTGAAGACGGTGGAGGGGATGAGAAGCGGAAGAATAAAGGCACTTC
GGACAGCTCCTCAGGCAATGTGTCTGAAGGAGACAGCCCCCCTGACAGCCAGGAGGACACCTTC
CAGGGAAGACAGAAATCAAAAGACAAAATGGCCACGCCAAGAAAAGACGGCTCCAAACGTTCTG
TACTGTCCAAATCAGTTCCTGGGTACAAGCCAAAGGTCATTCCAAATGCTCTATGTGGAATTTG
TCTGAAGGGTAAGGAGTCCAACAAGAAAGGAAAGGCTGAATCACTTATACACTGCTCCCAGTGT
GATAACAGTGGCCACCCTTCTTGCTTGGATATGACCATGGAGCTTGTTTCTATGATTAAGACCT
ACCCATGGCAGTGTATGGAATGTAAGACATGCATTATATGTGGACAGCCCCACCATGAAGAAGA
AATGATGTTCTGTGATGTGTGTGACAGAGGTTATCATACTTTTTGTGTGGGCCTTGGTGCTATT
CCATCAGGTCGCTGGATTTGTGACTGTTGTCAGCGAGCTCCCCCAACACCCAGGAAAGTGGGCA
GAAGGGGGAAAAACAGCAAAGAGGGGTAAATAGGCTTTGACCCTCGTGTTTGGGATATTTGGTG
CCAATTTATTTACAACACTTTCATTTTTATGCCAATAAAGAACTTTTTTTGAAATTAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001019918	(Get FASTA)	NCBI Sequence Viewer
	XP_017444365	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH98049	(Get FASTA)	NCBI Sequence Viewer
	EDL99837	(Get FASTA)	NCBI Sequence Viewer
	Q4V7A6	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001019918 ⟸ NM_001024747

- Sequence:

show sequence

MGSGDSSRSCETSSQDLSFSYYPAENLIEYKWPPDETGEYYMLQEQVSEYLGVTSFKRKYPDLE
RRDLSHKEKLYLRELNVITETQCTLGLTALRSDEVIDLMIKEYPAKHAEYSVILQEKERQRITD
HYKEYSQMQQQSTQKVEASKVPEYIKKAAKKAAEFNSNLNRERMEERRAYFDLQTHVIQVPQGK
YKVLPTDRTKVSSYPVALIPGQFQEYYKRYSPDELRYLPLNTALYEPPLDPELPALDSDGDSDD
GEDGGGDEKRKNKGTSDSSSGNVSEGDSPPDSQEDTFQGRQKSKDKMATPRKDGSKRSVLSKSV
PGYKPKVIPNALCGICLKGKESNKKGKAESLIHCSQCDNSGHPSCLDMTMELVSMIKTYPWQCM
ECKTCIICGQPHHEEEMMFCDVCDRGYHTFCVGLGAIPSGRWICDCCQRAPPTPRKVGRRGKNS
KEG

hide sequence

RefSeq Acc Id:

XP_017444365 ⟸ XM_017588876

- Peptide Label:

isoform X1

- Sequence:

show sequence

MGSGDSSRSCETSSQDLSFSYYPAENLIEYKWPPDETGEYYMLQEQVSEYLGVTSFKRKYPERR
DLSHKEKLYLRELNVITETQCTLGLTALRSDEVIDLMIKEYPAKHAEYSVILQEKERQRITDHY
KEYSQMQQQSTQKVEASKVPEYIKKAAKKAAEFNSNLNRERMEERRAYFDLQTHVIQVPQGKYK
VLPTDRTKVSSYPVALIPGQFQEYYKRYSPDELRYLPLNTALYEPPLDPELPALDSDGDSDDGE
DGGGDEKRKNKGTSDSSSGNVSEGDSPPDSQEDTFQGRQKSKDKMATPRKDGSKRSVLSKSVPG
YKPKVIPNALCGICLKGKESNKKGKAESLIHCSQCDNSGHPSCLDMTMELVSMIKTYPWQCMEC
KTCIICGQPHHEEEMMFCDVCDRGYHTFCVGLGAIPSGRWICDCCQRAPPTPRKVGRRGKNSKE
G

hide sequence

RefSeq Acc Id:

ENSRNOP00000072702 ⟸ ENSRNOT00000085273

Protein Domains

PHD-type

Transcriptome

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

Promoters

RGD ID:

13689639

Promoter ID:

EPDNEW_R164

Type:

single initiation site

Name:

Phf10_1

Description:

PHD finger protein 10

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	56,967,904 - 56,967,964	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN/SsN (MCW)

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

F344/NCrl (RGD)

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

F344/NRrrc (MCW)

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

FHH/EurMcwi (MCW)

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

FHH/EurMcwi (RGD)

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

FHL/EurMcwi (MCW)

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

FHL/EurMcwi (RGD)

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TAB

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

GH/OmrMcwi (MCW)

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

GK/Ox (RGD)

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

LE/Stm (RGD)

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LH/MavRrrc (RGD)

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

LL/MavRrrc (RGD)

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

LN/MavRrrc (RGD)

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

M520/N (MCW)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (MCW)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
1	58168656	58168657	G	A	snv	LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1305266	AgrOrtholog
Ensembl Genes	ENSRNOG00000061312	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000072702	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000085273	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	3.30.40.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7457308	IMAGE-MGC_LOAD
InterPro	PHF10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Znf_FYVE_PHD	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Znf_PHD	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Znf_PHD-finger	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Znf_RING/FYVE/PHD	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE	MGC:116207	IMAGE-MGC_LOAD
NCBI Gene	292404	ENTREZGENE
PANTHER	PTHR10615:SF174	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	PHD	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Phf10	PhenoGen
PROSITE	ZF_PHD_1	UniProtKB/Swiss-Prot
	ZF_PHD_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	PHD	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF57903	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0G2K3M7_RAT	UniProtKB/TrEMBL
	PHF10_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-12-06	Phf10	PHD finger protein 10	Phf10_predicted	PHD finger protein 10 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Phf10_predicted	PHD finger protein 10 (predicted)			Symbol and Name status set to approved	70820	APPROVED

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

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

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

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

RGD Manual Annotations