Pou4f2 (POU class 4 homeobox 2) - Rat Genome Database

Name: Pou4f2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Pou4f2 (POU class 4 homeobox 2) Rattus norvegicus

Analyze

Symbol:

Pou4f2

Name:

POU class 4 homeobox 2

RGD ID:

620075

Description:

Predicted to have several functions, including DNA-binding transcription factor activity, RNA polymerase II-specific; p53 binding activity; and promoter-specific chromatin binding activity. Involved in several processes, including cellular response to oxygen levels; positive regulation of cardiac muscle cell apoptotic process; and spermatogenesis. Predicted to localize to several cellular components, including euchromatin; nuclear speck; and transcription regulator complex. Orthologous to human POU4F2 (POU class 4 homeobox 2); PARTICIPATES IN p53 signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride; bisphenol A.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

brain-3B; brain-specific homeobox/POU domain protein 3B; Brn-3.2; Brn-3B; Brn3b; POU domain, class 4, transcription factor 2

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):	POU4F2 (POU class 4 homeobox 2)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Pou4f2 (POU domain, class 4, transcription factor 2)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Pou4f2 (POU class 4 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	POU4F2 (POU class 4 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	POU4F2 (POU class 4 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pou4f2 (POU class 4 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	POU4F2 (POU class 4 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	POU4F2 (POU class 4 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pou4f2 (POU class 4 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	POU4F3 (POU class 4 homeobox 3)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	POU4F2 (POU class 4 homeobox 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Mus musculus (house mouse):	Pou4f2 (POU domain, class 4, transcription factor 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Danio rerio (zebrafish):	pou4f2 (POU class 4 homeobox 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Caenorhabditis elegans (roundworm):	unc-86	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Drosophila melanogaster (fruit fly):	acj6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	19	29,486,686 - 29,490,327 (+)	NCBI
Rnor_6.0 Ensembl	19	33,160,180 - 33,163,821 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	19	33,160,180 - 33,163,821 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	19	44,051,763 - 44,055,404 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	19	31,388,907 - 31,392,548 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	19	31,395,364 - 31,395,583 (+)	NCBI
Celera	19	28,985,198 - 28,988,839 (+)	NCBI		Celera
Cytogenetic Map	19	q11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (ISO)

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

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

cadmium dichloride (EXP)

choline (ISO)

copper atom (EXP)

copper(0) (EXP)

daidzein (ISO)

diazinon (ISO)

entinostat (ISO)

folic acid (ISO)

fonofos (ISO)

genistein (ISO)

glycitein (ISO)

L-methionine (ISO)

lead diacetate (EXP,ISO)

lead(0) (ISO)

lead(2+) (ISO)

lipopolysaccharide (ISO)

methoxychlor (EXP)

methylmercury chloride (ISO)

N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine (ISO)

parathion (ISO)

pirinixic acid (ISO)

sodium arsenite (EXP,ISO)

terbufos (ISO)

valproic acid (ISO)

vorinostat (ISO)

zinc sulfate (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

axon extension (ISO)

axon guidance (ISO)

axonogenesis (ISO)

cellular response to cytokine stimulus (ISO,ISS)

cellular response to estradiol stimulus (ISO,ISS)

cellular response to insulin stimulus (ISO)

cellular response to oxygen levels (IMP)

dorsal root ganglion development (ISO,ISS)

heart development (ISO)

intracellular estrogen receptor signaling pathway (ISO)

intrinsic apoptotic signaling pathway by p53 class mediator (ISO,ISS)

MAPK cascade (ISO)

negative regulation of adipose tissue development (ISO)

negative regulation of amacrine cell differentiation (ISO,ISS)

negative regulation of cell differentiation (ISO,ISS)

negative regulation of DNA-binding transcription factor activity (ISO,ISS)

negative regulation of transcription by RNA polymerase II (ISO)

neuromuscular process controlling balance (ISO)

neuron differentiation (ISO)

positive regulation of axon extension (ISO,ISS)

positive regulation of cardiac muscle cell apoptotic process (IMP)

positive regulation of cell differentiation (ISO,ISS)

positive regulation of glucose import (ISO)

positive regulation of osteoclast differentiation (ISO,ISS)

positive regulation of programmed cell death (ISO,ISS)

positive regulation of transcription by RNA polymerase II (ISO,ISS)

positive regulation of transcription regulatory region DNA binding (ISO,ISS)

regulation of DNA-binding transcription factor activity (ISO,ISS)

regulation of gene expression (IMP)

regulation of retinal ganglion cell axon guidance (ISO,ISS)

regulation of transcription by RNA polymerase II (IBA)

retina development in camera-type eye (ISO)

retinal ganglion cell axon guidance (ISO)

sensory perception of sound (ISO)

spermatogenesis (IEP)

Cellular Component

cellular_component (ND)

chromatin (IBA)

cytoplasm (ISO,ISS)

euchromatin (IEA,ISO)

nuclear speck (ISO,ISS)

nucleus (ISO,ISS)

transcription regulator complex (ISO)

Molecular Function

chromatin binding (ISO)

DNA-binding transcription activator activity, RNA polymerase II-specific (ISO,ISS)

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA,ISO,ISS)

DNA-binding transcription repressor activity, RNA polymerase II-specific (ISO)

molecular_function (ND)

p53 binding (ISO)

promoter-specific chromatin binding (ISO,ISS)

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IBA,ISO)

sequence-specific DNA binding (ISO,ISS)

Molecular Pathway Annotations Click to see Annotation Detail View

p53 signaling pathway (ISO)

References

References - curated


1.	Beckerman R and Prives C, Cold Spring Harb Perspect Biol. 2010 Aug;2(8):a000935. doi: 10.1101/cshperspect.a000935. Epub 2010 Apr 28.
2.	Budhram-Mahadeo V, etal., Cell Death Dis. 2014 Oct 30;5:e1503. doi: 10.1038/cddis.2014.452.
3.	Budhram-Mahadeo V, etal., Int J Biochem Cell Biol. 2001 Oct;33(10):1027-39.
4.	Ensor E, etal., J Biol Chem 2001 Feb 16;276(7):5204-12.
5.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6.	GOA data from the GO Consortium
7.	MGD data from the GO Consortium
8.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
9.	RGD automated data pipeline
10.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11.	RGD automated import pipeline for gene-chemical interactions
12.	RGD comprehensive gene curation

Additional References at PubMed

PMID:7623109	PMID:7691107	PMID:7904822	PMID:7935408	PMID:8290353	PMID:8537352	PMID:8637595	PMID:8670054	PMID:9448000	PMID:9630743	PMID:9735355	PMID:10357904
PMID:11163266	PMID:11807038	PMID:12609742	PMID:17145718	PMID:17637757	PMID:17668438	PMID:17855369	PMID:18367606	PMID:18368538	PMID:18434421	PMID:19266028	PMID:19389377
PMID:20609388	PMID:20826655	PMID:21241485	PMID:21875655	PMID:23805044	PMID:24643061	PMID:25587060	PMID:25775587	PMID:25786379	PMID:26670484	PMID:28594399	PMID:31413277

Genomics

Comparative Map Data

Pou4f2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	19	29,486,686 - 29,490,327 (+)	NCBI
Rnor_6.0 Ensembl	19	33,160,180 - 33,163,821 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	19	33,160,180 - 33,163,821 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	19	44,051,763 - 44,055,404 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	19	31,388,907 - 31,392,548 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	19	31,395,364 - 31,395,583 (+)	NCBI
Celera	19	28,985,198 - 28,988,839 (+)	NCBI		Celera
Cytogenetic Map	19	q11	NCBI

POU4F2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	4	146,638,893 - 146,642,474 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	4	146,638,893 - 146,642,474 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	4	147,560,045 - 147,563,626 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	4	147,779,495 - 147,783,073 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	4	147,917,692 - 147,921,228	NCBI
Celera	4	144,880,585 - 144,884,163 (+)	NCBI
Cytogenetic Map	4	q31.22	NCBI
HuRef	4	143,287,267 - 143,290,856 (+)	NCBI		HuRef
CHM1_1	4	147,537,342 - 147,540,923 (+)	NCBI		CHM1_1

Pou4f2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	8	79,159,638 - 79,163,276 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	8	79,159,639 - 79,163,274 (-)	Ensembl
GRCm38	8	78,433,009 - 78,436,647 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	8	78,433,010 - 78,436,645 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	8	80,956,908 - 80,960,551 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	8	81,329,081 - 81,332,724 (-)	NCBI			mm8
Celera	8	82,709,269 - 82,712,912 (-)	NCBI		Celera
Cytogenetic Map	8	C1	NCBI

Pou4f2
(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_004955428	2,324,834 - 2,329,205 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955428	2,325,775 - 2,329,122 (+)	NCBI	ChiLan1.0	ChiLan1.0

POU4F2
(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	4	150,626,392 - 150,629,961 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	4	150,626,392 - 150,629,961 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	4	138,969,157 - 138,972,730 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

POU4F2
(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	15	45,031,094 - 45,032,784 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	15	45,030,818 - 45,034,446 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Pou4f2
(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_004936535	2,705,184 - 2,711,785 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

POU4F2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	8	82,044,644 - 82,046,307 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	8	82,044,443 - 82,046,377 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	8	87,200,440 - 87,201,609 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

POU4F2
(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	7	93,150,105 - 93,160,977 (+)	NCBI
ChlSab1.1 Ensembl	7	93,150,186 - 93,151,857 (+)	Ensembl

Pou4f2
(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_004624853	5,446,575 - 5,448,704 (+)	NCBI

Position Markers

Pou4f2

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	19	33,161,210 - 33,161,300	NCBI	Rnor6.0
Rnor_5.0	19	44,052,793 - 44,052,883	UniSTS	Rnor5.0
Celera	19	28,986,228 - 28,986,318	UniSTS
Cytogenetic Map	19	q11	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
9590298	Uminl5	Urine mineral level QTL 5	3.59	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	19	1	38221845	Rat
9590250	Scort11	Serum corticosterone level QTL 11	23.45	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	19	1	38221845	Rat
9590090	Insglur8	Insulin/glucose ratio QTL 8	10.81	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	19	1	38221845	Rat
8552935	Pigfal10	Plasma insulin-like growth factor 1 level QTL 10	5.7		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	19	1	38221845	Rat
2317848	Alcrsp21	Alcohol response QTL 21	1.899999976158142	0.05	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	19	1044648	46044648	Rat
61447	Tcas1	Tongue tumor susceptibility QTL 1	6.08		tongue integrity trait (VT:0010553)	squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)	19	1957707	46957707	Rat
7247442	Uae39	Urinary albumin excretion QTL 39			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	19	2432963	47217667	Rat
724566	Uae12	Urinary albumin excretion QTL 12	5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	19	2432963	62275575	Rat
9589102	Slep13	Serum leptin concentration QTL 13	4.63	0.001	blood leptin amount (VT:0005667)	plasma leptin level (CMO:0000781)	19	3701835	48701835	Rat
8694186	Bw152	Body weight QTL 152	3.34	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	19	3701835	48701835	Rat
724565	Tcas5	Tongue tumor susceptibility QTL 5	10.04		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	19	5007571	43907843	Rat
1331737	Uae29	Urinary albumin excretion QTL 29	5.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	19	6506761	60220581	Rat
724518	Uae19	Urinary albumin excretion QTL 19	5.5		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	19	8072545	47318201	Rat
61423	Cia14	Collagen induced arthritis QTL 14	3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	19	11303927	47879277	Rat
61407	Scl12	Serum cholesterol level QTL 12		0.001	blood HDL cholesterol amount (VT:0000184)	serum high density lipoprotein cholesterol level (CMO:0000361)	19	15294524	33991703	Rat
1558656	Prcs1	Prostate cancer susceptibility QTL 1	5		prostate integrity trait (VT:0010571)	percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)	19	15939528	38798459	Rat
1331788	Rf45	Renal function QTL 45	2.818		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	19	17028003	52538299	Rat
1578764	Stresp19	Stress response QTL 19	3.6	0.001	blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	19	18993982	62275575	Rat
7411549	Bw130	Body weight QTL 130	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	19	19177495	62275575	Rat
2298478	Eau8	Experimental allergic uveoretinitis QTL 8		0.0163	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	19	21407787	62275575	Rat
1549835	Tcas7	Tongue tumor susceptibility QTL 7		0.001	tongue integrity trait (VT:0010553)	squamous cell carcinoma of the head and neck tumor number (CMO:0001876)	19	24455726	43907843	Rat
61328	Eae8	Experimental allergic encephalomyelitis QTL 8	4		nervous system integrity trait (VT:0010566)	percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)	19	24457627	37140233	Rat
61350	Bp32	Blood pressure QTL 32		0.012	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	19	24818257	62275575	Rat
1354633	Bw28	Body weight QTL 28	6.04		body mass (VT:0001259)	body weight (CMO:0000012)	19	31194301	41686140	Rat
1354600	Salc2	Saline consumption QTL 2	9.91	0.001	drinking behavior trait (VT:0001422)	saline drink intake rate (CMO:0001627)	19	31194301	41686140	Rat
1354607	Gmadr1	Adrenal mass QTL 1	5.83		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	19	31194301	41686140	Rat
724546	Kidm3	Kidney mass QTL 3	3.1		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	19	32994392	62275575	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	234
Count of miRNA genes:	141
Interacting mature miRNAs:	192
Transcripts:	ENSRNOT00000016422
Prediction methods:	Miranda, Targetscan
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hepatobiliary system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system
High
Medium							17
Low							13
Below cutoff	1	2	2	2	2	1	28	1	6	1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_134355	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF390076	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473972	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000313	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000016422 ⟹ ENSRNOP00000016422

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	19	33,160,180 - 33,163,821 (+)	Ensembl

RefSeq Acc Id:

NM_134355 ⟹ NP_599182

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	19	29,486,686 - 29,490,327 (+)	NCBI
Rnor_6.0	19	33,160,180 - 33,163,821 (+)	NCBI
Rnor_5.0	19	44,051,763 - 44,055,404 (+)	NCBI
RGSC_v3.4	19	31,388,907 - 31,392,548 (+)	RGD
Celera	19	28,985,198 - 28,988,839 (+)	RGD

Sequence:

show sequence

GGGGCACTTTGGGGCGCTGAGGTCTGAAGCCAGCGCCACCCGGAGCAGGGCAACAGCTTGAGCA
GACCCAGCAGGCGACACAGAAGCGGAGCCAGACTGGGAGAGCCGAGCCTGGAAGCGGTGGCCGC
TGAGCACAACTTTGCCGTGTTGTTCCCTCTGCTGCTCCCGCCGGGTACTTCTCCGGAGGGTCGG
TAGCTGGGACCAGAGTGAGCCAGCGACGAGCGCGCCGCGCAAGGAAAGATGATGATGATGTCCC
TGAATAGCAAGCAGGCGTTCAGCATGCCTCATGCCGGCAGCCTGCATGTGGAGCCCAAGTACTC
GGCGCTGCACAGTGCCTCCCCGGGTTCCTCTGCGCCCGCGGCGCCCTCGGCCAGTTCCCCTAGC
AGCTCCAGCAACGCTGGCAGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGTGGTGGCGGAGGCC
GGAGCAGCAGTTCCAGCAGCAGTGGCAGCGGCGGCGGCGGCGGCGGGGGCTCGGAGGCGATGCG
GAGAGCTTGTCTTCCAACCCCACCGAGCAATATATTCGGCGGTCTGGATGAGAGTCTGCTGGCC
CGTGCCGAGGCTCTGGCCGCCGTGGACATCGTCTCCCAGAGTAAGAGCCACCACCACCATCCGC
CCCACCACAGCCCCTTCAAGCCGGACGCCACTTACCACACCATGAACACCATCCCGTGCACGTC
TGCCGCTTCCTCTTCATCCGTGCCCATCTCGCACCCGTCCGCTCTGGCTGGCACCCACCACCAT
CACCACCACCACCATCACCACCACCACCAGCCACATCAGGCTCTGGAGGGCGAGCTGCTGGAGC
ACCTGAGCCCCGGGCTGGCCCTGGGAGCCATGGCGGGCCCCGACGGCACGGTGGTGTCCACTCC
GGCTCACGCACCGCACATGGCCACCATGAACCCCATGCACCAAGCAGCCCTGAGCATGGCCCAC
GCGCACGGTCTGCCCTCGCACATGGGCTGCATGAGCGACGTGGATGCAGACCCGCGGGACCTGG
AGGCGTTCGCCGAGCGCTTCAAGCAGCGACGCATCAAGCTGGGAGTGACCCAGGCGGATGTGGG
TTCGGCGCTGGCCAACCTCAAGATACCGGGCGTAGGCTCGCTCAGCCAGAGCACCATCTGCAGG
TTTGAGTCCCTCACGCTGTCGCACAACAACATGATCGCGCTCAAGCCCATCCTGCAGGCGTGGC
TGGAGGAAGCAGAGAAATCCCACCGCGAGAAGCTCACCAAGCCCGAGCTCTTCAATGGCGCGGA
GAAGAAGCGCAAGCGCACGTCCATCGCGGCGCCCGAGAAGCGCTCACTGGAAGCCTACTTCGCC
ATCCAGCCAAGGCCCTCCTCGGAGAAGATCGCGGCCATCGCCGAGAAGCTGGATCTCAAGAAAA
ACGTAGTGCGCGTCTGGTTCTGCAACCAGAGGCAGAAACAGAAGAGAATGAAATACTCAGCCGG
CATTTAGGGACCCTTCTCCAGGGATGGCCCTTTCCCTTCGCCCTCTCTTTTCTAACCCCCCTCT
TGTCTCTCCTGCCTCTTTTCTTTCTACTTTGGCTATCAGAAACAATTCCGGTAAATGTGAACCC
AGACCAAGTCAGGAGCAAAGAAACAAGCAGCTGAGCCCAAATCAGAAAGATTGTGAATTGATTT
CGCAAAGTGAAGAAAAAACAAAATCACAAACACACCACAAAAGGAATTTGTCACGTTGTAACAG
AGCTGTCCCTTTTAAGCGCACCTCGACTGCTCAGCTTCATCAGAGGAAGTGTGGAGCTGGTTGT
CAACAGGAAGACAGAGGGACAAGCTTCTGAAAACCCCGCAAGAATGAGCAAGTAAGATTTGTTT
TTATTCTTACAGACGTCACCTTGTTCACGTTTAAAAGTACACTTTGCAGCTATTTTTCAGAAAT
AGAAATTGATTCAGGACTGAAACTCGAAGCTAGAGTTGATGCTTAATGTGACACGATAGAGACG
CCTCTAAAGTATTTTGAATTAAAAAAAGATGGCAGATTTTCTGCATTTACACTGTATATTATAT
ATATATTTTTATTGTGGTTCTTATCGCTTTCTTCCTTCTCTAAAGTGTTAATACTTACGAAGGA
GTTGCGCCTGCTGTGTTCACTGATCTTGACAACTATTATTAGATTATTGCCGTACAACCTTCTG
TAAATTATTAATTTATCTCTCTGGCAACTTAATTTTGTGCACATCCTAACTAACTAAACTTCTT
TAGTCTGAAAAATAAAACCGGCGGATACATATAGGTAGTGATGCTCAAATGTTCTTTTTTCTTT
TTCCGTCTGATGAGTTCCCTGGAGTTTCACAGCTTTCCCGCTTAGACTGTGTTCTCTTCGGCCT
AGTTGTATATTCTCACTTTGAATGAAGATTGTTTCCTCCCTTTGTTTTTAACTGGTAGCGTTCT
AATTTGTGAGCTGACACTTGATAATGGATGTCTTAATCGTGTAGATCTGATTCACTGTCCGAAG
TCTTGTTTACTTCCTTCCATATTTAATGGGGATTCCCACATTGTCCCCCGCAGCACACGTGCTC
TCTCACTCACTTTACAAGCCTACACACAGACACACAGTACACGTCTCTAACAGAAGAGAAGGGG
CAGTTGGAGGTACGACTGATAACCAGTGTATCCTTTTCCAGCCTAGGTGCGTTCTCCACTTGGT
GCTTACTCTGCTGGACTCAAAGATTTCACCCAGGTATTTCAATCTCCCAGCTTTTAGTTGCTTT
GTGGCTACATTTGACCTTTATAGGATCCTTCAGTTTTTCCTTTTAGGATGTTTGTTTGTAGGGG
AAAATTTTGGAACTATAAGAAAGACAGTGCACTGCCTGTAAATTCACAGTGTTTGGTAGAATCC
TTTTGGAGCACACACACAAGAATAGGTACACAGCGACTGGTACCTTCTCTATTGTAAATATTTC
ATTCAAAATGATGCACATATAAATATATTCTTACAGAATTTGCTGTAATTGTTGATCCATTTGA
GGCTCTCCAAAGTTCTGAGTTCTGTATATGACCTCGTTCCTTGTTTTTGTTAATGAATTATTTA
CTATAGTAATGTATTAAGTTATTTTGGGTGTTGTTTCATTGTCTTTCATCGAAGAGATGATTTT
AATGTTTTATTGGCAAAGTATGCTACTTTTTTCATTAAAATATGCTATTAATATTAAATGACTT
TTAAAACGTG

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Protein Sequences


Protein RefSeqs	NP_599182	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAK70503	(Get FASTA)	NCBI Sequence Viewer
	EDL92324	(Get FASTA)	NCBI Sequence Viewer
	G3V7L5	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_599182 ⟸ NM_134355

- UniProtKB:

G3V7L5 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MMMMSLNSKQAFSMPHAGSLHVEPKYSALHSASPGSSAPAAPSASSPSSSSNAGSGGGGGGGGG
GGGGGRSSSSSSSGSGGGGGGGSEAMRRACLPTPPSNIFGGLDESLLARAEALAAVDIVSQSKS
HHHHPPHHSPFKPDATYHTMNTIPCTSAASSSSVPISHPSALAGTHHHHHHHHHHHHQPHQALE
GELLEHLSPGLALGAMAGPDGTVVSTPAHAPHMATMNPMHQAALSMAHAHGLPSHMGCMSDVDA
DPRDLEAFAERFKQRRIKLGVTQADVGSALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKP
ILQAWLEEAEKSHREKLTKPELFNGAEKKRKRTSIAAPEKRSLEAYFAIQPRPSSEKIAAIAEK
LDLKKNVVRVWFCNQRQKQKRMKYSAGI

hide sequence

RefSeq Acc Id:

ENSRNOP00000016422 ⟸ ENSRNOT00000016422

Protein Domains

POU-specific

Transcriptome

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN/SsN (MCW)

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

F344/NCrl (RGD)

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

F344/NRrrc (MCW)

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

FHH/EurMcwi (MCW)

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

FHH/EurMcwi (RGD)

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

FHL/EurMcwi (MCW)

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

FHL/EurMcwi (RGD)

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

GH/OmrMcwi (MCW)

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

GK/Ox (RGD)

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

LE/Stm (RGD)

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LH/MavRrrc (RGD)

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

LL/MavRrrc (RGD)

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

LN/MavRrrc (RGD)

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

M520/N (MCW)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (MCW)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620075	AgrOrtholog
Ensembl Genes	ENSRNOG00000012167	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000016422	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000016422	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	1.10.260.40	UniProtKB/Swiss-Prot
InterPro	Cro/C1-type_HTH	UniProtKB/Swiss-Prot
	Homeobox-like_sf	UniProtKB/Swiss-Prot
	Homeobox_CS	UniProtKB/Swiss-Prot
	Homeobox_dom	UniProtKB/Swiss-Prot
	Lambda_DNA-bd_dom_sf	UniProtKB/Swiss-Prot
	POU	UniProtKB/Swiss-Prot
	POU_dom	UniProtKB/Swiss-Prot
KEGG Report	rno:171355	UniProtKB/Swiss-Prot
NCBI Gene	171355	ENTREZGENE
Pfam	Homeodomain	UniProtKB/Swiss-Prot
	Pou	UniProtKB/Swiss-Prot
PhenoGen	Pou4f2	PhenoGen
PRINTS	POUDOMAIN	UniProtKB/Swiss-Prot
PROSITE	HOMEOBOX_1	UniProtKB/Swiss-Prot
	HOMEOBOX_2	UniProtKB/Swiss-Prot
	POU_1	UniProtKB/Swiss-Prot
	POU_2	UniProtKB/Swiss-Prot
	POU_3	UniProtKB/Swiss-Prot
SMART	HOX	UniProtKB/Swiss-Prot
	POU	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot
	SSF47413	UniProtKB/Swiss-Prot
UniProt	G3V7L5	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2004-09-10	Pou4f2	POU domain, class 4, transcription factor 2			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Pou4f2	POU domain, class 4, transcription factor 2			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_process	enhances the survival of nerve growth factor-dependent sensory but not sympathetic neurons	724643

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