Cenpf (centromere protein F) - Rat Genome Database

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Gene: Cenpf (centromere protein F) Rattus norvegicus
Analyze
Symbol: Cenpf
Name: centromere protein F
RGD ID: 628667
Description: Predicted to enable several functions, including dynein complex binding activity; protein C-terminus binding activity; and protein homodimerization activity. Predicted to be involved in several processes, including metaphase plate congression; regulation of G2/M transition of mitotic cell cycle; and ventricular system development. Predicted to act upstream of or within regulation of striated muscle tissue development. Predicted to be located in several cellular components, including cytoskeleton; midbody; and nucleus. Predicted to be part of ciliary transition fiber and outer kinetochore. Predicted to be active in chromosome, centromeric region; nucleus; and spindle pole. Human ortholog(s) of this gene implicated in Stromme syndrome. Orthologous to human CENPF (centromere protein F); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: centromere autoantigen F; LEK/centromere protein; Lek1
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
mRatBN7.213101,184,127 - 101,229,714 (-)NCBI
Rnor_6.0 Ensembl13108,132,499 - 108,178,609 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.013108,132,499 - 108,178,609 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013112,758,855 - 112,804,965 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413105,920,242 - 105,965,655 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.113106,125,141 - 106,126,183 (-)NCBI
Celera13100,670,298 - 100,715,841 (-)NCBICelera
Cytogenetic Map13q26NCBI
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
(-)-demecolcine  (ISO)
(R)-mevalonic acid  (ISO)
1,1-dichloroethene  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrolein  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (EXP,ISO)
aflatoxin M1  (ISO)
aldehydo-D-glucosamine  (EXP)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-D-glucosamine  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
choline  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cryptolepine  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diazinon  (EXP)
dieldrin  (EXP)
dioxygen  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
etoposide  (ISO)
fenvalerate  (EXP)
folic acid  (ISO)
folpet  (ISO)
furan  (EXP)
genistein  (ISO)
geraniol  (ISO)
glycidol  (EXP)
hydrogen peroxide  (ISO)
indole-3-methanol  (EXP)
indometacin  (ISO)
irinotecan  (ISO)
isobutanol  (ISO)
L-methionine  (ISO)
leflunomide  (ISO)
lithium chloride  (ISO)
lovastatin  (ISO)
lucanthone  (ISO)
malathion  (ISO)
menadione  (ISO)
methotrexate  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
methylseleninic acid  (ISO)
miconazole  (ISO)
mitomycin C  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-Nitrosopyrrolidine  (ISO)
nickel dichloride  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
paclitaxel  (ISO)
palbociclib  (ISO)
paracetamol  (ISO)
PCB138  (EXP,ISO)
phenethyl isothiocyanate  (EXP,ISO)
phenformin  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
PhIP  (ISO)
pinosylvin  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
propanal  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
SP2509  (ISO)
sunitinib  (ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (ISO)
thalidomide  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trans-pinosylvin  (ISO)
tremolite asbestos  (ISO)
triazines  (ISO)
triclosan  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:7542657   PMID:7642639   PMID:7651420   PMID:7904902   PMID:9763420   PMID:11084331   PMID:12154071   PMID:12974617   PMID:15494374   PMID:15677469   PMID:15870278   PMID:16252009  
PMID:17363900   PMID:17600710   PMID:25564561  


Genomics

Comparative Map Data
Cenpf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.213101,184,127 - 101,229,714 (-)NCBI
Rnor_6.0 Ensembl13108,132,499 - 108,178,609 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.013108,132,499 - 108,178,609 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013112,758,855 - 112,804,965 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413105,920,242 - 105,965,655 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.113106,125,141 - 106,126,183 (-)NCBI
Celera13100,670,298 - 100,715,841 (-)NCBICelera
Cytogenetic Map13q26NCBI
CENPF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1214,603,195 - 214,664,571 (+)EnsemblGRCh38hg38GRCh38
GRCh381214,603,195 - 214,664,571 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371214,776,538 - 214,837,914 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361212,843,155 - 212,904,537 (+)NCBINCBI36hg18NCBI36
Build 341211,164,926 - 211,226,307NCBI
Celera1187,999,934 - 188,061,298 (+)NCBI
Cytogenetic Map1q41NCBI
HuRef1185,450,388 - 185,511,761 (+)NCBIHuRef
CHM1_11216,048,789 - 216,110,152 (+)NCBICHM1_1
Cenpf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391189,372,803 - 189,420,302 (-)NCBIGRCm39mm39
GRCm39 Ensembl1189,372,803 - 189,420,283 (-)Ensembl
GRCm381189,640,606 - 189,688,107 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1189,640,606 - 189,688,086 (-)EnsemblGRCm38mm10GRCm38
MGSCv371191,464,485 - 191,511,965 (-)NCBIGRCm37mm9NCBIm37
MGSCv361191,341,394 - 191,388,874 (-)NCBImm8
Celera1196,559,635 - 196,607,121 (-)NCBICelera
Cytogenetic Map1H6NCBI
cM Map195.03NCBI
Cenpf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554063,223,993 - 3,273,714 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554063,225,788 - 3,273,037 (-)NCBIChiLan1.0ChiLan1.0
CENPF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11195,025,577 - 195,086,518 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1195,024,877 - 195,086,518 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01190,170,414 - 190,231,478 (+)NCBIMhudiblu_PPA_v0panPan3
CENPF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1712,558,455 - 12,618,637 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl712,555,143 - 12,617,996 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha712,129,485 - 12,194,142 (+)NCBI
ROS_Cfam_1.0712,265,629 - 12,330,197 (+)NCBI
UMICH_Zoey_3.1712,188,652 - 12,253,247 (+)NCBI
UNSW_CanFamBas_1.0712,293,025 - 12,357,544 (+)NCBI
UU_Cfam_GSD_1.0712,421,098 - 12,482,469 (+)NCBI
Cenpf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934461,632,209 - 61,686,939 (-)NCBI
SpeTri2.0NW_0049366283,642,281 - 3,695,262 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CENPF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9128,948,497 - 129,012,218 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19128,948,386 - 129,012,241 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29141,675,880 - 141,740,104 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CENPF
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12514,914,805 - 14,972,811 (-)NCBI
ChlSab1.1 Ensembl2514,914,809 - 14,972,796 (-)Ensembl
Vero_WHO_p1.0NW_02366605515,379,185 - 15,438,265 (-)NCBI
Cenpf
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477119,657,489 - 19,702,506 (+)NCBI

Position Markers
RH143346  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.213101,190,612 - 101,190,778 (+)MAPPER
Rnor_6.013108,138,984 - 108,139,149NCBIRnor6.0
Rnor_5.013112,765,340 - 112,765,505UniSTSRnor5.0
RGSC_v3.413105,926,598 - 105,926,763UniSTSRGSC3.4
Celera13100,676,784 - 100,676,949UniSTS
RH 3.4 Map13692.9UniSTS
Cytogenetic Map13q27UniSTS
RH138998  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.213101,221,531 - 101,221,656 (+)MAPPER
Rnor_6.013108,170,472 - 108,170,596NCBIRnor6.0
Rnor_5.013112,796,828 - 112,796,952UniSTSRnor5.0
RGSC_v3.413105,957,518 - 105,957,642UniSTSRGSC3.4
RGSC_v3.42211,884,456 - 211,884,580UniSTSRGSC3.4
Celera13100,707,704 - 100,707,828UniSTS
RH 3.4 Map13691.8UniSTS
Cytogenetic Map13q27UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1380403559108770687Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1386833393114033958Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:147
Count of miRNA genes:111
Interacting mature miRNAs:131
Transcripts:ENSRNOT00000004525
Prediction methods:Miranda, 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 26 31 22 15 22 1 1 41 21 33 1 1
Low 2 14 20 13 4 13 3 3 19 12 8 10 3
Below cutoff 3 6 6 6 4 6 14 2 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004525   ⟹   ENSRNOP00000004525
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl13108,132,499 - 108,178,609 (-)Ensembl
RefSeq Acc Id: NM_001100827   ⟹   NP_001094297
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.213101,184,127 - 101,229,669 (-)NCBI
Rnor_6.013108,132,499 - 108,178,609 (-)NCBI
Rnor_5.013112,758,855 - 112,804,965 (-)NCBI
RGSC_v3.413105,920,242 - 105,965,655 (-)RGD
Celera13100,670,298 - 100,715,841 (-)RGD
Sequence:
RefSeq Acc Id: XM_039090398   ⟹   XP_038946326
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.213101,184,127 - 101,229,714 (-)NCBI
RefSeq Acc Id: XM_039090399   ⟹   XP_038946327
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.213101,184,127 - 101,229,478 (-)NCBI
RefSeq Acc Id: XM_039090400   ⟹   XP_038946328
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.213101,184,127 - 101,229,714 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001094297 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946326 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946327 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946328 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK53814 (Get FASTA)   NCBI Sequence Viewer  
  EDL94964 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001094297   ⟸   NM_001100827
- Sequence:
RefSeq Acc Id: ENSRNOP00000004525   ⟸   ENSRNOT00000004525
RefSeq Acc Id: XP_038946328   ⟸   XM_039090400
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038946326   ⟸   XM_039090398
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946327   ⟸   XM_039090399
- Peptide Label: isoform X1
Protein Domains
CENP-F_C_Rb_bdg   CENP-F_leu_zip   CENP-F_N

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699104
Promoter ID:EPDNEW_R9629
Type:multiple initiation site
Name:Cenpf_1
Description:centromere protein F
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013108,178,604 - 108,178,664EPDNEW

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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628667 AgrOrtholog
Ensembl Genes ENSRNOG00000003388 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004525 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004525 ENTREZGENE, UniProtKB/TrEMBL
InterPro Cenp-F UniProtKB/TrEMBL
  Centromere_CenpF_leu-rich_rpt UniProtKB/TrEMBL
  Centromere_CenpF_N UniProtKB/TrEMBL
  Centromere_CenpF_Rb-prot-bd UniProtKB/TrEMBL
NCBI Gene 257649 ENTREZGENE
PANTHER PTHR18874 UniProtKB/TrEMBL
Pfam Cenp-F_leu_zip UniProtKB/TrEMBL
  Cenp-F_N UniProtKB/TrEMBL
  Rb-bdg_C_Cenp-F UniProtKB/TrEMBL
PhenoGen Cenpf PhenoGen
UniProt E9PT83_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-25 Cenpf  centromere protein F  Cenpf  centromere autoantigen F  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Cenpf  centromere autoantigen F  Lek1  LEK/centromere protein  Symbol and Name updated 1299863 APPROVED
2003-02-27 Lek1  LEK/centromere protein      Symbol and Name status set to provisional 70820 PROVISIONAL