Pou5f1 (POU class 5 homeobox 1) - Rat Genome Database

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Gene: Pou5f1 (POU class 5 homeobox 1) Rattus norvegicus
Analyze
Symbol: Pou5f1
Name: POU class 5 homeobox 1
RGD ID: 1359491
Description: Exhibits DNA-binding transcription activator activity, RNA polymerase II-specific; protein domain specific binding activity; and sequence-specific DNA binding activity. Involved in regulation of transcription, DNA-templated and response to cytokine. Localizes to nucleus. Human ortholog(s) of this gene implicated in embryonal carcinoma and seminoma. Orthologous to several human genes including POU5F1 (POU class 5 homeobox 1); PARTICIPATES IN hypoxia inducible factor pathway; INTERACTS WITH 3-isobutyl-1-methyl-7H-xanthine; all-trans-retinoic acid; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: POU domain, class 5, transcription factor 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,223,128 - 3,227,891 (-)NCBI
Rnor_6.0 Ensembl203,747,221 - 3,751,994 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0203,747,231 - 3,751,994 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0205,833,973 - 5,838,736 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera20650,325 - 655,095 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(20S)-ginsenoside Rg3  (ISO)
(S)-nicotine  (ISO)
1,7-phenanthroline  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-methoxy-17beta-estradiol  (ISO)
3,5,6-trichloro-2-pyridinol  (ISO)
3,5,6-trichloropyridine-2-one  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (EXP,ISO)
3-methyladenine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-nonylphenol  (ISO)
4-tert-Octylphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-bromoindirubin-3'-oxime  (ISO)
acetic acid  (ISO)
afatinib  (ISO)
all-trans-retinoic acid  (EXP,ISO)
apigenin  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bromochloroacetic acid  (ISO)
bucladesine  (ISO)
butanal  (ISO)
cadmium dichloride  (EXP)
cannabidiol  (EXP)
carbaryl  (ISO)
carbon nanotube  (ISO)
casticin  (ISO)
CHIR 99021  (ISO)
chlordecone  (ISO)
chlorpromazine  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
ciprofloxacin  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
cypermethrin  (ISO)
DDT  (ISO)
decabromodiphenyl ether  (ISO)
deoxycholic acid  (ISO)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dieldrin  (ISO)
diethyl maleate  (ISO)
dimethyl sulfoxide  (ISO)
dioxygen  (ISO)
entinostat  (ISO)
ethanol  (EXP,ISO)
eugenol  (ISO)
fluoxetine  (ISO)
fulvestrant  (ISO)
genistein  (ISO)
glycerol 2-phosphate  (ISO)
GW 3965  (ISO)
GW 4064  (ISO)
heptachlor  (ISO)
hexachlorophene  (ISO)
hydrogen peroxide  (ISO)
ibuprofen  (ISO)
indinavir  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
kaempferol  (ISO)
ketoconazole  (ISO)
L-ascorbic acid  (ISO)
lamivudine  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
lithium chloride  (ISO)
lupeol  (ISO)
LY294002  (ISO)
melatonin  (ISO)
metformin  (ISO)
methamphetamine  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
mono(2-ethylhexyl) phthalate  (EXP)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (ISO)
nickel dichloride  (ISO)
niclosamide  (ISO)
nicotine  (ISO)
nocodazole  (ISO)
Nonylphenol  (ISO)
p-tert-Amylphenol  (ISO)
paclitaxel  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenanthrene  (ISO)
phenol red  (ISO)
piperonyl butoxide  (ISO)
poly(I:C)  (ISO)
progesterone  (ISO)
quercetin  (ISO)
quinpirole  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
saquinavir  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
SR9243  (ISO)
SU6656  (ISO)
tamoxifen  (ISO)
Tanshinone I  (EXP,ISO)
taurocholic acid  (ISO)
tetrachloromethane  (ISO)
thymoquinone  (ISO)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
triptonide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
tubocurarine  (ISO)
valproic acid  (ISO)
zidovudine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
blastocyst development  (ISO)
blastocyst growth  (ISO)
BMP signaling pathway involved in heart induction  (ISO)
cardiac cell fate determination  (ISO)
cell fate commitment  (ISO)
cell fate commitment involved in formation of primary germ layer  (ISO)
cellular response to leukemia inhibitory factor  (ISO)
ectodermal cell fate commitment  (ISO)
endodermal cell fate commitment  (ISO)
endodermal cell fate specification  (ISO)
germ-line stem cell population maintenance  (ISO)
mesodermal cell fate commitment  (ISO)
negative regulation of calcium ion-dependent exocytosis  (ISO)
negative regulation of cell differentiation  (ISO)
negative regulation of gene expression  (ISO,ISS)
negative regulation of gene silencing by miRNA  (ISO)
negative regulation of pri-miRNA transcription by RNA polymerase II  (ISO)
negative regulation of protein kinase B signaling  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
positive regulation of canonical Wnt signaling pathway  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of protein kinase B signaling  (ISO)
positive regulation of SMAD protein signal transduction  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of transcription initiation from RNA polymerase II promoter  (ISO)
positive regulation of transcription, DNA-templated  (ISO)
regulation of asymmetric cell division  (ISO)
regulation of DNA methylation-dependent heterochromatin assembly  (ISO)
regulation of gene expression  (ISO)
regulation of heart induction by regulation of canonical Wnt signaling pathway  (ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO)
regulation of transcription, DNA-templated  (IDA,ISO)
response to cytokine  (IEP)
response to organic substance  (ISO)
response to retinoic acid  (ISO)
response to wounding  (ISO)
somatic stem cell population maintenance  (ISO)
stem cell differentiation  (ISO)
stem cell population maintenance  (ISO)
transcription by RNA polymerase II  (ISO)
trophectodermal cell differentiation  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:1690859   PMID:1967980   PMID:1972777   PMID:2357966   PMID:7590241   PMID:7945330   PMID:7958450   PMID:7969117   PMID:8960364   PMID:9507072   PMID:9649510   PMID:9814708  
PMID:10742100   PMID:12477932   PMID:12615074   PMID:12641567   PMID:12665572   PMID:14502573   PMID:15047715   PMID:15183310   PMID:15486564   PMID:15525667   PMID:15863505   PMID:15977177  
PMID:15988017   PMID:16153702   PMID:16325584   PMID:16518401   PMID:16611995   PMID:16767105   PMID:17097055   PMID:17138661   PMID:17507372   PMID:17541407   PMID:17882221   PMID:17938240  
PMID:17982423   PMID:18000303   PMID:18096721   PMID:18191611   PMID:18281244   PMID:18388306   PMID:18400104   PMID:18423437   PMID:18425773   PMID:18448678   PMID:18467660   PMID:18662995  
PMID:18710938   PMID:18755297   PMID:18985733   PMID:19274063   PMID:19409607   PMID:19480014   PMID:19717550   PMID:19736317   PMID:19784378   PMID:19796622   PMID:19816951   PMID:19915186  
PMID:20123909   PMID:20336070   PMID:20439489   PMID:20458727   PMID:20713518   PMID:20720167   PMID:20720539   PMID:21076177   PMID:21258368   PMID:21295276   PMID:21828274   PMID:22344693  
PMID:22527699   PMID:22528735   PMID:22658674   PMID:22770845   PMID:22948967   PMID:22992956   PMID:23376973   PMID:23495099   PMID:23508100   PMID:23824537   PMID:24036311   PMID:24268575  
PMID:24315442   PMID:24427323   PMID:24481450   PMID:25335925   PMID:25397698   PMID:25901318   PMID:26691508   PMID:27096226   PMID:28325116   PMID:28948165   PMID:29153991   PMID:29212575  


Genomics

Comparative Map Data
Pou5f1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,223,128 - 3,227,891 (-)NCBI
Rnor_6.0 Ensembl203,747,221 - 3,751,994 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0203,747,231 - 3,751,994 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0205,833,973 - 5,838,736 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera20650,325 - 655,095 (-)NCBICelera
Cytogenetic Map20p12NCBI
POU5F1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl631,164,337 - 31,180,731 (-)EnsemblGRCh38hg38GRCh38
GRCh38631,164,337 - 31,170,682 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37631,132,114 - 31,138,459 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36631,240,093 - 31,246,430 (-)NCBINCBI36hg18NCBI36
Build 34631,240,107 - 31,242,024NCBI
Celera632,732,336 - 32,738,691 (-)NCBI
Cytogenetic Map6p21.33NCBI
HuRef630,934,532 - 30,940,887 (-)NCBIHuRef
CHM1_1631,134,214 - 31,140,570 (-)NCBICHM1_1
Pou5f1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,816,929 - 35,821,674 (+)NCBIGRCm39mm39
GRCm39 Ensembl1735,816,915 - 35,821,669 (+)Ensembl
GRCm381735,506,032 - 35,510,777 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,506,018 - 35,510,772 (+)EnsemblGRCm38mm10GRCm38
MGSCv371735,642,984 - 35,647,722 (+)NCBIGRCm37mm9NCBIm37
MGSCv361735,114,104 - 35,118,822 (+)NCBImm8
Celera1739,020,984 - 39,025,724 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.69NCBI
Pou5f1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955583995,707 - 1,003,202 (-)NCBIChiLan1.0ChiLan1.0
POU5F1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1631,775,343 - 31,781,426 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl631,775,343 - 31,781,426 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0630,910,421 - 30,916,465 (-)NCBIMhudiblu_PPA_v0panPan3
Pou5f1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494634,462,312 - 34,467,659 (-)NCBI
SpeTri2.0NW_004936837827,568 - 838,933 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POU5F1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1723,564,654 - 23,570,691 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2727,262,690 - 27,268,388 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap7p1.1NCBI
POU5F1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11741,306,523 - 41,313,065 (+)NCBI
Vero_WHO_p1.0NW_02366604430,855,264 - 30,861,857 (-)NCBI
Pou5f1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475424,758,055 - 24,764,723 (+)NCBI

Position Markers
UniSTS:464794  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21351,425,686 - 51,425,842 (+)MAPPER
Rnor_6.01356,892,764 - 56,892,919NCBIRnor6.0
Rnor_5.01361,910,941 - 61,911,096UniSTSRnor5.0
RGSC_v3.41353,165,495 - 53,165,650UniSTSRGSC3.4
Celera1351,685,560 - 51,685,715UniSTS
Cytogenetic Map13q13UniSTS
Oct4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21351,425,619 - 51,425,820 (+)MAPPER
Rnor_6.01356,892,697 - 56,892,897NCBIRnor6.0
Rnor_5.01361,910,874 - 61,911,074UniSTSRnor5.0
RGSC_v3.41353,165,428 - 53,165,628UniSTSRGSC3.4
Celera1351,685,493 - 51,685,693UniSTS
Cytogenetic Map13q13UniSTS
Pou5f1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,223,376 - 3,223,553 (+)MAPPER
Rnor_6.0203,747,480 - 3,747,656NCBIRnor6.0
Rnor_5.0205,834,222 - 5,834,398UniSTSRnor5.0
Celera20650,574 - 650,750UniSTS
Cytogenetic Map20p12UniSTS
Pou5f1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,224,521 - 3,224,868 (+)MAPPER
Rnor_6.0203,748,625 - 3,748,971NCBIRnor6.0
Rnor_5.0205,835,367 - 5,835,713UniSTSRnor5.0
Celera20651,719 - 652,065UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2015192000Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2020187706567419Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2031518156896013Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2031518156896013Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:224
Count of miRNA genes:148
Interacting mature miRNAs:167
Transcripts:ENSRNOT00000072288
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 5
Low 3 16 10 8 10 2 1 24 3
Below cutoff 8 13 9 10 9 1 4 27 15 7 8 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000072288   ⟹   ENSRNOP00000065216
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,747,221 - 3,751,994 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084526
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,747,855 - 3,749,031 (-)Ensembl
RefSeq Acc Id: NM_001009178   ⟹   NP_001009178
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,223,128 - 3,227,891 (-)NCBI
Rnor_6.0203,747,231 - 3,751,994 (-)NCBI
Rnor_5.0205,833,973 - 5,838,736 (-)NCBI
Celera20650,325 - 655,095 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001009178 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI58567 (Get FASTA)   NCBI Sequence Viewer  
  CAE84020 (Get FASTA)   NCBI Sequence Viewer  
  EDL86771 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001009178   ⟸   NM_001009178
- UniProtKB: Q6MG27 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000065216   ⟸   ENSRNOT00000072288
Protein Domains
Homeobox   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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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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

Database Acc Id Source(s)
AGR Gene RGD:1359491 AgrOrtholog
Ensembl Genes ENSRNOG00000046487 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065216 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000072288 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.260.40 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9092936 IMAGE-MGC_LOAD
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  Lambda_DNA-bd UniProtKB/TrEMBL
  POU UniProtKB/TrEMBL
  POU_dom_5 UniProtKB/TrEMBL
  POU_specific UniProtKB/TrEMBL
KEGG Report rno:294562 UniProtKB/TrEMBL
MGC_CLONE MGC:187285 IMAGE-MGC_LOAD
NCBI Gene 294562 ENTREZGENE
PANTHER PTHR11636:SF86 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
  Pou UniProtKB/TrEMBL
PhenoGen Pou5f1 PhenoGen
PRINTS POUDOMAIN UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
  POU_1 UniProtKB/TrEMBL
  POU_2 UniProtKB/TrEMBL
  POU_3 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
  POU UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
  Lambda_like_DNA UniProtKB/TrEMBL
UniProt Q6MG27 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-24 Pou5f1  POU class 5 homeobox 1  Pou5f1  POU domain, class 5, transcription factor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Pou5f1  POU domain, class 5, transcription factor 1      Symbol and Name updated 1559027 APPROVED
2005-07-29 Pou5f1  POU domain, class 5, transcription factor 1      Symbol and Name status set to provisional 70820 PROVISIONAL