Foxp4 (forkhead box P4) - Rat Genome Database
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Gene: Foxp4 (forkhead box P4) Rattus norvegicus
Analyze
Symbol: Foxp4
Name: forkhead box P4
RGD ID: 1311386
Description: Predicted to have DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and identical protein binding activity. Predicted to be involved in several processes, including embryonic foregut morphogenesis; lung secretory cell differentiation; and negative regulation of lung goblet cell differentiation. Predicted to localize to nucleus. Orthologous to human FOXP4 (forkhead box P4); INTERACTS WITH (+)-schisandrin B; amphetamine; bis(2-ethylhexyl) phthalate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: CCR4-NOT transcription complex subunit 3-like; forkhead box protein P4; LOC102555622; LOC363185; serine/arginine repetitive matrix protein 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
mRatBN7.2913,058,506 - 13,115,406 (+)NCBI
Rnor_6.0 Ensembl915,068,399 - 15,125,318 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0915,068,378 - 15,124,962 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0913,993,012 - 14,049,324 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.498,509,028 - 8,579,597 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.198,508,860 - 8,579,597 (+)NCBI
Celera910,812,577 - 10,868,280 (+)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:14701752   PMID:15361625   PMID:18561326   PMID:22675208  


Genomics

Comparative Map Data
Foxp4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2913,058,506 - 13,115,406 (+)NCBI
Rnor_6.0 Ensembl915,068,399 - 15,125,318 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0915,068,378 - 15,124,962 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0913,993,012 - 14,049,324 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.498,509,028 - 8,579,597 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.198,508,860 - 8,579,597 (+)NCBI
Celera910,812,577 - 10,868,280 (+)NCBICelera
Cytogenetic Map9q12NCBI
FOXP4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl641,546,381 - 41,602,384 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl641,546,426 - 41,602,384 (+)EnsemblGRCh38hg38GRCh38
GRCh38641,546,381 - 41,602,384 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37641,514,119 - 41,570,122 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36641,622,142 - 41,678,100 (+)NCBINCBI36hg18NCBI36
Build 34641,622,141 - 41,678,099NCBI
Celera643,067,608 - 43,123,566 (+)NCBI
Cytogenetic Map6p21.1NCBI
HuRef641,232,474 - 41,288,223 (+)NCBIHuRef
CHM1_1641,517,252 - 41,573,197 (+)NCBICHM1_1
Foxp4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391748,178,058 - 48,235,557 (-)NCBIGRCm39mm39
GRCm39 Ensembl1748,178,058 - 48,235,570 (-)Ensembl
GRCm381747,867,133 - 47,924,632 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1747,867,133 - 47,924,645 (-)EnsemblGRCm38mm10GRCm38
MGSCv371748,004,082 - 48,061,581 (-)NCBIGRCm37mm9NCBIm37
MGSCv361747,330,324 - 47,387,634 (-)NCBImm8
Celera1751,308,820 - 51,367,567 (-)NCBICelera
Cytogenetic Map17CNCBI
Foxp4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554378,014,939 - 8,057,033 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554378,029,346 - 8,056,243 (+)NCBIChiLan1.0ChiLan1.0
FOXP4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1642,455,809 - 42,496,205 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl642,459,420 - 42,496,205 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0641,133,751 - 41,189,709 (+)NCBIMhudiblu_PPA_v0panPan3
FOXP4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11210,239,402 - 10,292,892 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1210,258,166 - 10,291,125 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1210,269,034 - 10,322,552 (+)NCBI
ROS_Cfam_1.01210,719,170 - 10,772,709 (+)NCBI
UMICH_Zoey_3.11210,250,401 - 10,304,021 (+)NCBI
UNSW_CanFamBas_1.01210,352,401 - 10,387,661 (+)NCBI
UU_Cfam_GSD_1.01210,427,587 - 10,481,623 (+)NCBI
Foxp4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_ltri_2NW_02440494645,614,056 - 45,646,094 (+)NCBI
SpeTri2.0NW_00493647618,314,108 - 18,346,149 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FOXP4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl736,754,754 - 36,793,527 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1736,760,643 - 36,793,620 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2742,037,738 - 42,088,634 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FOXP4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11730,554,702 - 30,608,845 (-)NCBI
ChlSab1.1 Ensembl1730,554,055 - 30,589,849 (-)Ensembl
Foxp4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475417,402,788 - 17,445,469 (-)NCBI

Position Markers
BE121233  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0915,110,867 - 15,111,033NCBIRnor6.0
Rnor_5.0914,035,229 - 14,035,395UniSTSRnor5.0
RGSC_v3.498,565,502 - 8,565,668UniSTSRGSC3.4
Celera910,853,881 - 10,854,047UniSTS
RH 3.4 Map928.5UniSTS
Cytogenetic Map9q12UniSTS
RH130703  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0915,124,614 - 15,124,808NCBIRnor6.0
Rnor_5.0914,048,976 - 14,049,170UniSTSRnor5.0
RGSC_v3.498,579,249 - 8,579,443UniSTSRGSC3.4
Celera910,867,932 - 10,868,126UniSTS
RH 3.4 Map937.2UniSTS
Cytogenetic Map9q12UniSTS
REN59994  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0915,084,341 - 15,084,594NCBIRnor6.0
Rnor_6.0916,283,735 - 16,283,988NCBIRnor6.0
Rnor_5.0915,200,360 - 15,200,613UniSTSRnor5.0
Rnor_5.0914,008,954 - 14,009,207UniSTSRnor5.0
RGSC_v3.498,525,906 - 8,526,159UniSTSRGSC3.4
Celera910,828,506 - 10,828,759UniSTS
Cytogenetic Map9q12UniSTS
stSG634860  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0915,113,110 - 15,114,093NCBIRnor6.0
Rnor_5.0914,037,472 - 14,038,455UniSTSRnor5.0
RGSC_v3.498,567,745 - 8,568,728UniSTSRGSC3.4
Celera910,856,128 - 10,857,263UniSTS
Cytogenetic Map9q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9129467098Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9288097747880977Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9498609549986095Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9572425425692342Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RChigh CD8 T cell count to CD45RClow CD8 T cell count ratio (CMO:0001990)91086939115509311Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9235572247355722Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9235572247355722Rat
1578675Bss17Bone structure and strength QTL 173.8femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)9190783415555026Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9145029794Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9498609549986095Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9288097747375681Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)91242546357425463Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9140383872Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9140383872Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)91242546357425463Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9140383872Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9116520166Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)91221677157216771Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:563
Count of miRNA genes:212
Interacting mature miRNAs:259
Transcripts:ENSRNOT00000064229
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 3 14 17 11 9 11 66 23 34 3
Low 29 40 30 10 30 5 8 8 12 7 8 5
Below cutoff 3 3 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000064229   ⟹   ENSRNOP00000060921
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl915,068,399 - 15,124,962 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087107   ⟹   ENSRNOP00000070287
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl915,068,405 - 15,125,318 (+)Ensembl
RefSeq Acc Id: NM_001108788   ⟹   NP_001102258
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0915,068,399 - 15,124,962 (+)NCBI
Rnor_5.0913,993,012 - 14,049,324 (+)NCBI
RGSC_v3.498,509,028 - 8,579,597 (+)RGD
Celera910,812,577 - 10,868,280 (+)RGD
Sequence:
RefSeq Acc Id: NM_001389210   ⟹   NP_001376139
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2913,058,700 - 13,115,406 (+)NCBI
RefSeq Acc Id: XM_008766868   ⟹   XP_008765090
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2913,058,506 - 13,113,879 (+)NCBI
Rnor_6.0915,068,378 - 15,124,962 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008766869   ⟹   XP_008765091
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0915,068,380 - 15,124,962 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008766870   ⟹   XP_008765092
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2913,058,506 - 13,113,879 (+)NCBI
Rnor_6.0915,068,380 - 15,124,962 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008766871   ⟹   XP_008765093
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2913,058,506 - 13,113,953 (+)NCBI
Rnor_6.0915,068,378 - 15,124,962 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596504   ⟹   XP_017451993
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0915,103,485 - 15,124,962 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596505   ⟹   XP_017451994
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0915,104,492 - 15,124,962 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039083810   ⟹   XP_038939738
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2913,058,506 - 13,113,953 (+)NCBI
RefSeq Acc Id: XM_039083811   ⟹   XP_038939739
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2913,058,506 - 13,113,953 (+)NCBI
RefSeq Acc Id: XM_039083812   ⟹   XP_038939740
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2913,094,522 - 13,113,953 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001102258   ⟸   NM_001108788
- Sequence:
RefSeq Acc Id: XP_008765090   ⟸   XM_008766868
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008765091   ⟸   XM_008766869
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008765093   ⟸   XM_008766871
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008765092   ⟸   XM_008766870
- Peptide Label: isoform X5
- UniProtKB: A0A0G2JXI7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451993   ⟸   XM_017596504
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017451994   ⟸   XM_017596505
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000070287   ⟸   ENSRNOT00000087107
RefSeq Acc Id: ENSRNOP00000060921   ⟸   ENSRNOT00000064229
RefSeq Acc Id: XP_038939738   ⟸   XM_039083810
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939739   ⟸   XM_039083811
- Peptide Label: isoform X2
RefSeq Acc Id: NP_001376139   ⟸   NM_001389210
RefSeq Acc Id: XP_038939740   ⟸   XM_039083812
- Peptide Label: isoform X6
Protein Domains
Fork-head

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)
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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:1311386 AgrOrtholog
Ensembl Genes ENSRNOG00000022804 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000060921 UniProtKB/TrEMBL
  ENSRNOP00000070287 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064229 UniProtKB/TrEMBL
  ENSRNOT00000087107 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro FOXP-CC UniProtKB/TrEMBL
  TF_fork_head UniProtKB/TrEMBL
  TF_fork_head_CS_2 UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:363185 UniProtKB/TrEMBL
NCBI Gene 363185 ENTREZGENE
Pfam Fork_head UniProtKB/TrEMBL
  FOXP-CC UniProtKB/TrEMBL
PhenoGen Foxp4 PhenoGen
PRINTS FORKHEAD UniProtKB/TrEMBL
PROSITE FORK_HEAD_2 UniProtKB/TrEMBL
  FORK_HEAD_3 UniProtKB/TrEMBL
SMART SM00339 UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
UniProt A0A0G2JXI7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZPZ7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Foxp4  forkhead box P4  LOC102555622  CCR4-NOT transcription complex subunit 3-like  Data Merged 737654 PROVISIONAL
2013-12-18 LOC102555622  CCR4-NOT transcription complex subunit 3-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Foxp4  forkhead box P4   Foxp4_predicted  forkhead box P4 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Foxp4_predicted  forkhead box P4 (predicted)      Symbol and Name status set to approved 70820 APPROVED