Foxk1 (forkhead box K1) - Rat Genome Database

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Gene: Foxk1 (forkhead box K1) Rattus norvegicus
Analyze
Symbol: Foxk1
Name: forkhead box K1
RGD ID: 1309643
Description: Predicted to have 14-3-3 protein binding activity; DNA-binding transcription repressor activity, RNA polymerase II-specific; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including canonical glycolysis; cellular glucose homeostasis; and regulation of transcription, DNA-templated. Predicted to localize to cytoplasm and nucleus. Orthologous to human FOXK1 (forkhead box K1); INTERACTS WITH acetamide; bisphenol A; cobalt dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: forkhead box protein K1; LOC304298; LOC679672; RGD1309643; similar to forkhead box K1 isoform alpha; similar to RIKEN cDNA C330006K01
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
mRatBN7.21212,110,119 - 12,175,089 (-)NCBI
Rnor_6.0 Ensembl1214,180,029 - 14,244,316 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01214,183,436 - 14,244,634 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01216,212,041 - 16,270,069 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41212,513,060 - 12,568,394 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11212,522,087 - 12,598,295 (-)NCBI
Celera1213,898,413 - 13,956,060 (-)NCBICelera
Cytogenetic Map12q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:8007964   PMID:9271401   PMID:10620510   PMID:17670796   PMID:25402684   PMID:29861159   PMID:30700909  


Genomics

Comparative Map Data
Foxk1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21212,110,119 - 12,175,089 (-)NCBI
Rnor_6.0 Ensembl1214,180,029 - 14,244,316 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01214,183,436 - 14,244,634 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01216,212,041 - 16,270,069 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41212,513,060 - 12,568,394 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11212,522,087 - 12,598,295 (-)NCBI
Celera1213,898,413 - 13,956,060 (-)NCBICelera
Cytogenetic Map12q11NCBI
FOXK1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl74,682,295 - 4,771,442 (+)EnsemblGRCh38hg38GRCh38
GRCh3874,682,295 - 4,771,442 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3774,721,926 - 4,811,073 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3674,688,456 - 4,777,600 (+)NCBINCBI36hg18NCBI36
Celera74,681,702 - 4,770,725 (+)NCBI
Cytogenetic Map7p22.1NCBI
HuRef74,638,801 - 4,727,921 (+)NCBIHuRef
CHM1_174,721,765 - 4,810,819 (+)NCBICHM1_1
CRA_TCAGchr7v274,768,285 - 4,857,429 (+)NCBI
Foxk1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395142,387,252 - 142,447,770 (+)NCBIGRCm39mm39
GRCm39 Ensembl5142,387,252 - 142,447,766 (+)Ensembl
GRCm385142,401,497 - 142,462,015 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5142,401,497 - 142,462,011 (+)EnsemblGRCm38mm10GRCm38
MGSCv375142,877,451 - 142,937,969 (+)NCBIGRCm37mm9NCBIm37
MGSCv365142,653,971 - 142,714,489 (+)NCBImm8
Celera5139,456,420 - 139,517,061 (+)NCBICelera
Cytogenetic Map5G2NCBI
cM Map581.53NCBI
Foxk1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546011,018,177 - 11,067,443 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495546011,011,498 - 11,067,443 (-)NCBIChiLan1.0ChiLan1.0
FOXK1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.174,935,681 - 5,061,351 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl74,975,444 - 5,056,174 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v074,934,773 - 5,017,127 (+)NCBIMhudiblu_PPA_v0panPan3
FOXK1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1612,863,093 - 12,931,877 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl612,869,940 - 12,930,954 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha614,333,953 - 14,401,879 (-)NCBI
ROS_Cfam_1.0612,999,430 - 13,067,373 (-)NCBI
UMICH_Zoey_3.1612,810,158 - 12,878,093 (-)NCBI
UNSW_CanFamBas_1.0612,743,136 - 12,811,036 (-)NCBI
UU_Cfam_GSD_1.0613,019,324 - 13,087,278 (-)NCBI
Foxk1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344141,138,037 - 141,199,596 (-)NCBI
SpeTri2.0NW_0049367651,126,168 - 1,255,354 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FOXK1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl33,556,007 - 3,621,142 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.133,556,139 - 3,621,150 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.234,203,703 - 4,269,535 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FOXK1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12816,875,747 - 16,962,813 (-)NCBI
ChlSab1.1 Ensembl2816,880,884 - 16,962,734 (-)Ensembl
Foxk1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474028,533,708 - 28,585,880 (-)NCBI

Position Markers
D12Got25  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21212,168,838 - 12,168,962 (+)MAPPER
Rnor_6.01214,238,437 - 14,238,560NCBIRnor6.0
Rnor_5.01216,263,872 - 16,263,995UniSTSRnor5.0
RGSC_v3.41212,562,143 - 12,562,267RGDRGSC3.4
RGSC_v3.41212,562,144 - 12,562,267UniSTSRGSC3.4
RGSC_v3.11212,592,072 - 12,592,195RGD
Celera1213,949,713 - 13,949,828UniSTS
RH 3.4 Map12162.2UniSTS
RH 3.4 Map12162.2RGD
RH 2.0 Map12126.1RGD
Cytogenetic Map12p11UniSTS
L26507  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21212,116,079 - 12,116,197 (+)MAPPER
Rnor_6.01214,183,566 - 14,183,683NCBIRnor6.0
Rnor_5.01216,212,171 - 16,212,288UniSTSRnor5.0
RGSC_v3.41212,513,190 - 12,513,307UniSTSRGSC3.4
Cytogenetic Map12p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12122650917Rat
10450854Stl34Serum triglyceride level QTL 343.50.05blood LDL triglyceride amount (VT:0010699)blood lipoprotein triglyceride level (CMO:0002685)12122853017Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12123035872Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123758197Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12130749723Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12136919844Rat
7387292Kidm42Kidney mass QTL 423.030.0004kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)12138334225Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)1215081045150810Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1215081045150810Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)1249257845492578Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12247568747475687Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12251344247513442Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12251344247513442Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12421005149210051Rat
1600391Edcs2Endometrial carcinoma susceptibility QTL23.50.01uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)12824960820590080Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12895459327911196Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6922362652716770Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922363052716770Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12978983452716770Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121017588931975590Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)121025689031723732Rat
1331739Hrtrt14Heart rate QTL 143.56232heart pumping trait (VT:2000009)heart rate (CMO:0000002)121176499514489679Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)121176499537522089Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121312721127285590Rat
1331755Bp219Blood pressure QTL 2193.041arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121312721131723688Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121312721150320041Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:147
Count of miRNA genes:113
Interacting mature miRNAs:123
Transcripts:ENSRNOT00000001466
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 1 24 3 2 7 2 66 18 36 5
Low 2 19 54 39 12 39 8 11 8 17 5 6 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001466   ⟹   ENSRNOP00000001466
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1214,180,029 - 14,244,316 (-)Ensembl
RefSeq Acc Id: NM_001037219   ⟹   NP_001032296
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21212,115,950 - 12,175,089 (-)NCBI
Rnor_6.01214,183,436 - 14,244,634 (-)NCBI
Rnor_5.01216,212,041 - 16,270,069 (-)NCBI
RGSC_v3.41212,513,060 - 12,568,394 (-)RGD
Celera1213,898,413 - 13,956,060 (-)RGD
Sequence:
RefSeq Acc Id: XM_039089368   ⟹   XP_038945296
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21212,110,119 - 12,136,399 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001032296 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945296 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001032296   ⟸   NM_001037219
- Sequence:
RefSeq Acc Id: ENSRNOP00000001466   ⟸   ENSRNOT00000001466
RefSeq Acc Id: XP_038945296   ⟸   XM_039089368
- Peptide Label: isoform X1
Protein Domains
FHA   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)
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)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 16212520 16212521 C T snv MNS/Gib (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 14183915 14183916 C T snv MNS/Gib (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 12513539 12513540 C T snv MNS/Gib (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309643 AgrOrtholog
Ensembl Genes ENSRNOG00000001104 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001466 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001466 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro FHA_dom UniProtKB/TrEMBL
  SMAD_FHA_domain UniProtKB/TrEMBL
  TF_fork_head UniProtKB/TrEMBL
  TF_fork_head_CS UniProtKB/TrEMBL
  TF_fork_head_CS_2 UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
NCBI Gene 304298 ENTREZGENE
Pfam FHA UniProtKB/TrEMBL
  Fork_head UniProtKB/TrEMBL
PhenoGen Foxk1 PhenoGen
PRINTS FORKHEAD UniProtKB/TrEMBL
PROSITE FHA_DOMAIN UniProtKB/TrEMBL
  FORK_HEAD_1 UniProtKB/TrEMBL
  FORK_HEAD_2 UniProtKB/TrEMBL
  FORK_HEAD_3 UniProtKB/TrEMBL
SMART FHA UniProtKB/TrEMBL
  SM00339 UniProtKB/TrEMBL
Superfamily-SCOP SMAD_FHA UniProtKB/TrEMBL
  SSF46785 UniProtKB/TrEMBL
UniProt D3ZU55_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Foxk1  forkhead box K1  LOC686261  similar to forkhead box K1 isoform alpha  Data Merged 1643240 APPROVED
2008-09-09 Foxk1  forkhead box K1  RGD1309643  similar to RIKEN cDNA C330006K01   Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2008-09-09 RGD1309643  similar to RIKEN cDNA C330006K01   Foxk1  forkhead box K1  Data Merged 737654 APPROVED
2008-09-08 Foxk1  forkhead box K1  LOC679672  similar to forkhead box K1 isoform alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1309643  similar to RIKEN cDNA C330006K01   RGD1309643_predicted  similar to RIKEN cDNA C330006K01 (predicted)  'predicted' is removed 2292626 APPROVED
2006-11-19 LOC679672  similar to forkhead box K1 isoform alpha      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC686261  similar to forkhead box K1 isoform alpha      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-20 RGD1309643_predicted  similar to RIKEN cDNA C330006K01 (predicted)  LOC304298_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC304298_predicted  similar to RIKEN cDNA C330006K01 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL