Pou3f4 (POU class 3 homeobox 4) - Rat Genome Database

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Gene: Pou3f4 (POU class 3 homeobox 4) Rattus norvegicus
Analyze
Symbol: Pou3f4
Name: POU class 3 homeobox 4
RGD ID: 61947
Description: Exhibits DNA-binding transcription factor activity; double-stranded DNA binding activity; and minor groove of adenine-thymine-rich DNA binding activity. Involved in transcription by RNA polymerase II. Localizes to nucleus. Human ortholog(s) of this gene implicated in X-linked deafness 2. Orthologous to human POU3F4 (POU class 3 homeobox 4); INTERACTS WITH 6-propyl-2-thiouracil; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: brain-4; brain-specific homeobox/POU domain protein 4; brn-4; oct-9; octamer-binding protein 9; octamer-binding transcription factor 9; OTF-9; POU domain, class 3, transcription factor 4; RHS2; RHS2 class III POU protein
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
mRatBN7.2X75,858,646 - 75,859,923 (+)NCBI
Rnor_6.0 EnsemblX82,143,789 - 82,145,066 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X82,143,789 - 82,145,066 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X82,301,578 - 82,302,855 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X99,214,446 - 99,215,723 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X99,287,906 - 99,289,156 (+)NCBI
CeleraX77,112,524 - 77,113,801 (+)NCBICelera
Cytogenetic MapXq31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9105675   PMID:9889200   PMID:10587581   PMID:10868931   PMID:14681019   PMID:15574296   PMID:15655183   PMID:17141158   PMID:18231833   PMID:18831054   PMID:20105446   PMID:21663595  
PMID:26060893   PMID:31518606  


Genomics

Comparative Map Data
Pou3f4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X75,858,646 - 75,859,923 (+)NCBI
Rnor_6.0 EnsemblX82,143,789 - 82,145,066 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X82,143,789 - 82,145,066 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X82,301,578 - 82,302,855 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X99,214,446 - 99,215,723 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X99,287,906 - 99,289,156 (+)NCBI
CeleraX77,112,524 - 77,113,801 (+)NCBICelera
Cytogenetic MapXq31NCBI
POU3F4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX83,508,290 - 83,512,127 (+)EnsemblGRCh38hg38GRCh38
GRCh38X83,508,290 - 83,512,127 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X82,763,298 - 82,767,135 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X82,649,941 - 82,651,431 (+)NCBINCBI36hg18NCBI36
Build 34X82,569,445 - 82,570,920NCBI
CeleraX83,000,650 - 83,002,156 (+)NCBI
Cytogenetic MapXq21.1NCBI
HuRefX76,337,125 - 76,338,589 (+)NCBIHuRef
CHM1_1X82,657,165 - 82,658,671 (+)NCBICHM1_1
Pou3f4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X109,857,985 - 109,862,714 (+)NCBIGRCm39mm39
GRCm39 EnsemblX109,857,886 - 109,860,813 (+)Ensembl
GRCm38X110,814,379 - 110,819,108 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX110,814,280 - 110,817,207 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X108,009,804 - 108,010,889 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X107,017,184 - 107,018,269 (+)NCBImm8
CeleraX97,632,784 - 97,633,869 (+)NCBICelera
Cytogenetic MapXE1NCBI
cM MapX48.2NCBI
Pou3f4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555292,726,133 - 2,727,218 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555292,726,121 - 2,727,311 (+)NCBIChiLan1.0ChiLan1.0
POU3F4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X82,666,699 - 82,668,337 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX82,666,757 - 82,667,842 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X72,563,887 - 72,568,233 (+)NCBIMhudiblu_PPA_v0panPan3
POU3F4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X64,427,161 - 64,428,825 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX64,427,325 - 64,428,410 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX55,185,767 - 55,187,326 (+)NCBI
ROS_Cfam_1.0X65,745,624 - 65,747,183 (+)NCBI
UMICH_Zoey_3.1X63,406,449 - 63,408,008 (+)NCBI
UNSW_CanFamBas_1.0X65,024,007 - 65,025,564 (+)NCBI
UU_Cfam_GSD_1.0X64,613,109 - 64,614,668 (+)NCBI
Pou3f4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X58,133,789 - 58,135,350 (+)NCBI
SpeTri2.0NW_0049365474,454,239 - 4,455,460 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POU3F4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX66,765,066 - 66,766,160 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X66,765,044 - 66,766,642 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X76,477,799 - 76,479,225 (+)NCBISscrofa10.2Sscrofa10.2susScr3
POU3F4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X72,379,656 - 72,381,186 (+)NCBI
ChlSab1.1 EnsemblX72,379,979 - 72,381,064 (+)Ensembl
Pou3f4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248525,036,585 - 5,040,160 (-)NCBI

Position Markers
AU049792  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X82,145,063 - 82,145,225NCBIRnor6.0
Rnor_5.0X82,302,852 - 82,303,014UniSTSRnor5.0
RGSC_v3.4X99,215,720 - 99,215,882UniSTSRGSC3.4
CeleraX77,113,798 - 77,113,960UniSTS
Cytogenetic MapXq31UniSTS
Pou3f4  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X82,143,855 - 82,144,283NCBIRnor6.0
Rnor_5.0X82,301,644 - 82,302,072UniSTSRnor5.0
RGSC_v3.4X99,214,512 - 99,214,940UniSTSRGSC3.4
CeleraX77,112,590 - 77,113,018UniSTS
Cytogenetic MapXq31UniSTS
Pou3f4  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X82,143,908 - 82,144,882NCBIRnor6.0
Rnor_5.0X82,301,697 - 82,302,671UniSTSRnor5.0
RGSC_v3.4X99,214,565 - 99,215,539UniSTSRGSC3.4
CeleraX77,112,643 - 77,113,617UniSTS
Cytogenetic MapXq31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:33
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000003724
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 hepatobiliary system nervous system renal system reproductive system
High
Medium 45
Low 2 2 2 29 10 6
Below cutoff 1 16 5 4 4 21 19

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003724   ⟹   ENSRNOP00000003724
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX82,143,789 - 82,145,066 (+)Ensembl
RefSeq Acc Id: NM_017252   ⟹   NP_058948
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X75,858,646 - 75,859,923 (+)NCBI
Rnor_6.0X82,143,789 - 82,145,066 (+)NCBI
Rnor_5.0X82,301,578 - 82,302,855 (+)NCBI
RGSC_v3.4X99,214,446 - 99,215,723 (+)RGD
CeleraX77,112,524 - 77,113,801 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_058948 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA42042 (Get FASTA)   NCBI Sequence Viewer  
  CAA77855 (Get FASTA)   NCBI Sequence Viewer  
  EDM07095 (Get FASTA)   NCBI Sequence Viewer  
  P62516 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_058948   ⟸   NM_017252
- UniProtKB: P62516 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003724   ⟸   ENSRNOT00000003724
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)
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)
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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:61947 AgrOrtholog
Ensembl Genes ENSRNOG00000002784 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000003724 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003724 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.260.40 UniProtKB/Swiss-Prot
InterPro 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
  TF_POU_3 UniProtKB/Swiss-Prot
KEGG Report rno:29589 UniProtKB/Swiss-Prot
NCBI Gene 29589 ENTREZGENE
Pfam Homeodomain UniProtKB/Swiss-Prot
  Pou UniProtKB/Swiss-Prot
PhenoGen Pou3f4 PhenoGen
PIRSF Transcription_factor_POU UniProtKB/Swiss-Prot
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 P62516 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary P25216 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-24 Pou3f4  POU class 3 homeobox 4  Pou3f4  POU domain, class 3, transcription factor 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Pou3f4  POU domain, class 3, transcription factor 4      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference