Pou4f1 (POU class 4 homeobox 1) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Pou4f1 (POU class 4 homeobox 1) Rattus norvegicus
Analyze
Symbol: Pou4f1
Name: POU class 4 homeobox 1
RGD ID: 620074
Description: Exhibits RNA polymerase II repressing transcription factor binding activity. Involved in negative regulation of neuron apoptotic process and spermatogenesis. Predicted to localize to several cellular components, including RNA polymerase II transcription regulator complex; neuron projection; and nuclear chromatin. Orthologous to human POU4F1 (POU class 4 homeobox 1); PARTICIPATES IN p53 signaling pathway; INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; lead diacetate.
Type: protein-coding
RefSeq Status: MODEL
Also known as: brain-3A; brain-specific homeobox/POU domain protein 3A; brn-3A; Brn3a; LOW QUALITY PROTEIN: POU domain, class 4, transcription factor 1; POU domain, class 4, transcription factor 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
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
Rnor_6.01588,618,255 - 88,622,712 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1588,620,470 - 88,622,413 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01592,114,015 - 92,118,240 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41588,535,625 - 88,539,256 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11588,553,052 - 88,553,272 (-)NCBI
Celera1580,380,878 - 80,387,018 (-)NCBICelera
Cytogenetic Map15q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cell migration in hindbrain  (IEA,ISO)
cellular response to cytokine stimulus  (IEA,ISO,ISS)
cellular response to estradiol stimulus  (IEA,ISO,ISS)
central nervous system neuron differentiation  (IEA,ISO)
habenula development  (IEA,ISO)
heart development  (ISO)
innervation  (IEA,ISO)
intrinsic apoptotic signaling pathway by p53 class mediator  (IEA,ISO,ISS)
mesoderm development  (IEA,ISO)
negative regulation of apoptotic process  (ISO,TAS)
negative regulation of gene expression  (ISO)
negative regulation of neuron apoptotic process  (IEA,IMP,ISO)
negative regulation of programmed cell death  (ISO,ISS)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
negative regulation of transcription elongation by RNA polymerase I  (IEA,ISO)
nervous system development  (ISO)
neuron differentiation  (ISO)
neuron fate specification  (IEA,ISO)
neuron projection development  (IEA,ISO,ISS)
peripheral nervous system neuron development  (IEA,ISO)
peripheral nervous system neuron differentiation  (ISO)
positive regulation of apoptotic process  (IEA,ISO)
positive regulation of cell cycle arrest  (IEA,ISO,ISS)
positive regulation of gene expression  (ISO,ISS)
positive regulation of osteoclast differentiation  (IEA,ISO,ISS)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
positive regulation of transcription regulatory region DNA binding  (IEA,ISO,ISS)
proprioception involved in equilibrioception  (IEA,ISO)
regulation of DNA-binding transcription factor activity  (IEA,ISO,ISS)
regulation of neurogenesis  (IEA,ISO)
regulation of transcription by RNA polymerase II  (IBA)
regulation of transcription, DNA-templated  (ISO)
sensory system development  (IEA,ISO)
spermatogenesis  (IEP)
suckling behavior  (IEA,ISO)
transcription by RNA polymerase II  (TAS)
trigeminal nerve development  (IEA,ISO)
ventricular compact myocardium morphogenesis  (IEA,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:1383937   PMID:2739723   PMID:7623109   PMID:7935408   PMID:8290353   PMID:8621561   PMID:8876243   PMID:8955272   PMID:8972215   PMID:9448000   PMID:12810599   PMID:12934100  
PMID:15532030   PMID:15968082   PMID:16040009   PMID:16752387   PMID:17145718   PMID:17196582   PMID:17239249   PMID:17668438   PMID:18303621   PMID:18368538   PMID:18421303   PMID:18839516  
PMID:19877281   PMID:19906978   PMID:20096094   PMID:20228055   PMID:21315070   PMID:21734270   PMID:23805044   PMID:26200499   PMID:28594399  


Genomics

Comparative Map Data
Pou4f1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01588,618,255 - 88,622,712 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1588,620,470 - 88,622,413 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01592,114,015 - 92,118,240 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41588,535,625 - 88,539,256 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11588,553,052 - 88,553,272 (-)NCBI
Celera1580,380,878 - 80,387,018 (-)NCBICelera
Cytogenetic Map15q22NCBI
POU4F1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1378,598,362 - 78,603,552 (-)EnsemblGRCh38hg38GRCh38
GRCh381378,598,362 - 78,603,552 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371379,173,227 - 79,177,695 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361378,071,228 - 78,075,696 (-)NCBINCBI36hg18NCBI36
Build 341378,071,232 - 78,075,696NCBI
Celera1360,071,661 - 60,076,129 (-)NCBI
Cytogenetic Map13q31.1NCBI
HuRef1359,873,428 - 59,878,003 (-)NCBIHuRef
CHM1_11379,141,107 - 79,145,483 (-)NCBICHM1_1
Pou4f1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914104,699,111 - 104,705,554 (-)NCBIGRCm39mm39
GRCm3814104,461,675 - 104,468,118 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14104,461,676 - 104,467,999 (-)EnsemblGRCm38mm10GRCm38
MGSCv3714104,861,537 - 104,867,216 (-)NCBIGRCm37mm9NCBIm37
MGSCv3614103,347,999 - 103,353,678 (-)NCBImm8
Celera14103,076,392 - 103,080,281 (-)NCBICelera
Cytogenetic Map14E2.3NCBI
Pou4f1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540428,812,762 - 28,818,024 (+)NCBIChiLan1.0ChiLan1.0
POU4F1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11378,863,468 - 78,863,992 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01359,821,614 - 59,829,671 (-)NCBIMhudiblu_PPA_v0panPan3
POU4F1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12231,992,657 - 31,997,066 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pou4f1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365112,857,017 - 2,859,705 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POU4F1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1150,730,428 - 50,732,340 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11150,729,746 - 50,732,626 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21155,418,338 - 55,421,499 (-)NCBISscrofa10.2Sscrofa10.2susScr3
POU4F1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1357,667,248 - 57,673,071 (-)NCBI
Pou4f1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475121,812,567 - 21,817,837 (+)NCBI

Position Markers
PMC125354P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01588,620,494 - 88,620,767NCBIRnor6.0
Rnor_5.01592,116,254 - 92,116,527UniSTSRnor5.0
RGSC_v3.41588,537,237 - 88,537,510UniSTSRGSC3.4
Celera1580,384,969 - 80,385,242UniSTS
Cytogenetic Map15q22UniSTS
Pou4f1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01588,620,027 - 88,620,104NCBIRnor6.0
Rnor_5.01592,115,787 - 92,115,864UniSTSRnor5.0
RGSC_v3.41588,536,770 - 88,536,847UniSTSRGSC3.4
Celera1580,384,502 - 80,384,579UniSTS
Cytogenetic Map15q22UniSTS
UniSTS:465489  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01588,620,455 - 88,620,618NCBIRnor6.0
Rnor_5.01592,116,215 - 92,116,378UniSTSRnor5.0
RGSC_v3.41588,537,198 - 88,537,361UniSTSRGSC3.4
Celera1580,384,930 - 80,385,093UniSTS
Cytogenetic Map15q22UniSTS
UniSTS:470675  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01588,620,466 - 88,620,618NCBIRnor6.0
Rnor_5.01592,116,226 - 92,116,378UniSTSRnor5.0
RGSC_v3.41588,537,209 - 88,537,361UniSTSRGSC3.4
Celera1580,384,941 - 80,385,093UniSTS
Cytogenetic Map15q22UniSTS
UniSTS:276144  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01588,621,472 - 88,622,469NCBIRnor6.0
Rnor_5.01592,117,134 - 92,118,131UniSTSRnor5.0
RGSC_v3.41588,538,315 - 88,539,312UniSTSRGSC3.4
Cytogenetic Map15q22UniSTS
Pou4f1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01588,621,586 - 88,622,420NCBIRnor6.0
Rnor_5.01592,117,248 - 92,118,082UniSTSRnor5.0
RGSC_v3.41588,538,429 - 88,539,263UniSTSRGSC3.4
Celera1580,386,144 - 80,386,978UniSTS
Cytogenetic Map15q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)153321910189640841Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)153321910189640841Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)153321910189640841Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1543097470106550657Rat
1576315Schws6Schwannoma susceptibility QTL 60.0069nervous system integrity trait (VT:0010566)post-insult time of death (CMO:0002005)1561447766106447766Rat
61477Aia4Adjuvant induced arthritis QTL 43joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)156259641099372139Rat
631516Gluco31Glucose level QTL 317blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1562596410103164962Rat
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1565520564110520564Rat
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1575527634111246239Rat
2300326Plaw1Placental weight QTL 1150.005placenta mass (VT:0004257)placenta wet weight (CMO:0002088)1575761024109400896Rat
1331724Bp223Blood pressure QTL 2233.53715arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1581255292103165069Rat
1641889Colcr6Colorectal carcinoma resistance QTL 62.90.0126intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)1581255292109133904Rat
70182BpQTLcluster12Blood pressure QTL cluster 123.53arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)1581255430103164962Rat
1581555Eae19Experimental allergic encephalomyelitis QTL 194.7nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)158394771498027710Rat
70155Gcs1Gastric cancer susceptibility QTL13.8stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)1583947714111246239Rat
1549844Bss7Bone structure and strength QTL 76.4femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1584050550111246239Rat
2317055Aia10Adjuvant induced arthritis QTL 103.41joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1584050550111246239Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:54
Count of miRNA genes:50
Interacting mature miRNAs:54
Transcripts:ENSRNOT00000012828
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 15
Low 37 20
Below cutoff 3 4 40 31 13 31 7 8 20 27 16 3 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000092174   ⟹   ENSRNOP00000074614
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1588,620,470 - 88,622,413 (-)Ensembl
RefSeq Acc Id: XM_006222050   ⟹   XP_006222112
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1580,380,878 - 80,387,018 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770931   ⟹   XP_008769153
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01588,618,255 - 88,622,712 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_006222112 (Get FASTA)   NCBI Sequence Viewer  
  XP_008769153 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK70502 (Get FASTA)   NCBI Sequence Viewer  
  EDM02474 (Get FASTA)   NCBI Sequence Viewer  
  P20266 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006222112   ⟸   XM_006222050
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008769153   ⟸   XM_008770931
- Peptide Label: isoform X1
- UniProtKB: P20266 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074614   ⟸   ENSRNOT00000092174
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)
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
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
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)
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
F344/NRrrc (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
FHH/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)
FHH/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
FHL/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)
FHL/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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WKY/Gcrc (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
WKY/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
WKY/NCrl (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
WKY/NHsd (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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620074 AgrOrtholog
Ensembl Genes ENSRNOG00000060662 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000074614 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000092174 UniProtKB/TrEMBL
Gene3D-CATH 1.10.260.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Cro/C1-type_HTH UniProtKB/Swiss-Prot
  Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lambda_DNA-bd_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  POU UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  POU4-TF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  POU_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:114503 UniProtKB/Swiss-Prot
NCBI Gene 114503 ENTREZGENE
PANTHER PTHR11636:SF42 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pou UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pou4f1 PhenoGen
PRINTS POUDOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  POU_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  POU_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  POU_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  POU UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF47413 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.232568 ENTREZGENE
UniProt A0A0G2K8H8_RAT UniProtKB/TrEMBL
  P20266 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q91XM4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-24 Pou4f1  POU class 4 homeobox 1  Pou4f1  POU domain, class 4, transcription factor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Pou4f1  POU domain, class 4, transcription factor 1      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Pou4f1  POU domain, class 4, transcription factor 1      Symbol and Name status set to provisional 70820 PROVISIONAL