Fbxo40 (F-box protein 40) - Rat Genome Database

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Gene: Fbxo40 (F-box protein 40) Rattus norvegicus
Analyze
Symbol: Fbxo40
Name: F-box protein 40
RGD ID: 1309781
Description: Predicted to enable ubiquitin protein ligase activity and zinc ion binding activity. Predicted to be involved in muscle cell differentiation. Predicted to be active in cytoplasm. Orthologous to human FBXO40 (F-box protein 40); INTERACTS WITH bisphenol A; cyclophosphamide; paraquat.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: F-box only protein 40; LOC363790
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81177,299,826 - 77,318,086 (+)NCBIGRCr8
mRatBN7.21163,794,452 - 63,812,697 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1163,794,624 - 63,812,697 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01166,713,913 - 66,731,195 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1166,713,888 - 66,731,198 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01169,805,318 - 69,822,300 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41165,607,617 - 65,612,879 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11165,665,205 - 65,670,468 (+)NCBI
Celera1163,268,024 - 63,286,379 (+)NCBICelera
Cytogenetic Map11q21NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17928169   PMID:19028597  


Genomics

Comparative Map Data
Fbxo40
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81177,299,826 - 77,318,086 (+)NCBIGRCr8
mRatBN7.21163,794,452 - 63,812,697 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1163,794,624 - 63,812,697 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01166,713,913 - 66,731,195 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1166,713,888 - 66,731,198 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01169,805,318 - 69,822,300 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41165,607,617 - 65,612,879 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11165,665,205 - 65,670,468 (+)NCBI
Celera1163,268,024 - 63,286,379 (+)NCBICelera
Cytogenetic Map11q21NCBI
FBXO40
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383121,593,379 - 121,630,295 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3121,593,379 - 121,630,295 (+)EnsemblGRCh38hg38GRCh38
GRCh373121,312,226 - 121,349,142 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363122,794,860 - 122,831,829 (+)NCBINCBI36Build 36hg18NCBI36
Build 343122,794,953 - 122,829,612NCBI
Celera3119,721,852 - 119,758,855 (+)NCBICelera
Cytogenetic Map3q13.33NCBI
HuRef3118,686,314 - 118,723,298 (+)NCBIHuRef
CHM1_13121,275,741 - 121,312,709 (+)NCBICHM1_1
T2T-CHM13v2.03124,313,284 - 124,350,193 (+)NCBIT2T-CHM13v2.0
Fbxo40
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391636,783,823 - 36,811,321 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1636,783,822 - 36,810,829 (-)EnsemblGRCm39 Ensembl
GRCm381636,963,461 - 36,990,530 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1636,963,460 - 36,990,467 (-)EnsemblGRCm38mm10GRCm38
MGSCv371636,966,159 - 36,979,222 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361636,885,312 - 36,898,375 (-)NCBIMGSCv36mm8
Celera1637,376,963 - 37,388,325 (-)NCBICelera
Cytogenetic Map16B3NCBI
cM Map1626.32NCBI
Fbxo40
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542720,979,180 - 20,998,977 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542720,979,180 - 20,996,654 (+)NCBIChiLan1.0ChiLan1.0
FBXO40
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22119,550,057 - 119,588,185 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13119,554,834 - 119,592,962 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03118,695,215 - 118,730,183 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13125,604,930 - 125,639,658 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3125,604,930 - 125,639,658 (+)Ensemblpanpan1.1panPan2
FBXO40
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13324,841,998 - 24,899,973 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3324,880,530 - 24,897,129 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3324,869,274 - 24,926,898 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03325,084,229 - 25,142,217 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3325,122,484 - 25,142,217 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13324,882,504 - 24,940,457 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03324,924,936 - 24,982,927 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03325,481,797 - 25,540,040 (+)NCBIUU_Cfam_GSD_1.0
Fbxo40
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602129,460,291 - 129,477,016 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365368,055,765 - 8,064,522 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365368,045,171 - 8,064,492 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FBXO40
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13138,881,513 - 138,905,356 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113138,881,528 - 138,905,410 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213148,508,052 - 148,533,199 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FBXO40
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12259,259,107 - 59,295,391 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2259,256,354 - 59,295,017 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041107,058,641 - 107,065,604 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Fbxo40
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473126,562,650 - 26,579,272 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473126,561,050 - 26,579,450 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Fbxo40
113 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:143
Count of miRNA genes:108
Interacting mature miRNAs:112
Transcripts:ENSRNOT00000003340
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)115980279482566545Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)115980279482566553Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat

Markers in Region
RH142932  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21163,812,441 - 63,812,610 (+)MAPPERmRatBN7.2
Rnor_6.01166,732,132 - 66,732,300NCBIRnor6.0
Rnor_5.01169,823,425 - 69,823,593UniSTSRnor5.0
RGSC_v3.41165,613,945 - 65,614,113UniSTSRGSC3.4
Celera1163,286,012 - 63,286,180UniSTS
RH 3.4 Map11496.6UniSTS
Cytogenetic Map11q22UniSTS


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 31 8 11 8
Low 12 2 10 9 13 11
Below cutoff 2 27 13 9 13 19 26 22

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003340   ⟹   ENSRNOP00000003340
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1163,794,624 - 63,812,697 (+)Ensembl
Rnor_6.0 Ensembl1166,713,888 - 66,731,198 (+)Ensembl
RefSeq Acc Id: NM_001427448   ⟹   NP_001414377
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81177,300,123 - 77,318,086 (+)NCBI
RefSeq Acc Id: XM_006248404   ⟹   XP_006248466
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81177,299,826 - 77,318,081 (+)NCBI
mRatBN7.21163,794,453 - 63,812,692 (+)NCBI
Rnor_6.01166,713,913 - 66,731,195 (+)NCBI
Rnor_5.01169,805,318 - 69,822,300 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039088907   ⟹   XP_038944835
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81177,299,842 - 77,318,081 (+)NCBI
mRatBN7.21163,794,452 - 63,812,697 (+)NCBI
RefSeq Acc Id: XM_039088908   ⟹   XP_038944836
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81177,300,078 - 77,318,081 (+)NCBI
mRatBN7.21163,794,689 - 63,812,697 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001414377 (Get FASTA)   NCBI Sequence Viewer  
  XP_006248466 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944835 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944836 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000003340
  ENSRNOP00000003340.6
Reference Protein Sequences
RefSeq Acc Id: XP_006248466   ⟸   XM_006248404
- Peptide Label: isoform X1
- UniProtKB: F1LXQ1 (UniProtKB/TrEMBL),   A6IR98 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003340   ⟸   ENSRNOT00000003340
RefSeq Acc Id: XP_038944835   ⟸   XM_039088907
- Peptide Label: isoform X1
- UniProtKB: F1LXQ1 (UniProtKB/TrEMBL),   A6IR98 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038944836   ⟸   XM_039088908
- Peptide Label: isoform X1
- UniProtKB: F1LXQ1 (UniProtKB/TrEMBL),   A6IR98 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001414377   ⟸   NM_001427448
- UniProtKB: A6IR98 (UniProtKB/TrEMBL)
Protein Domains
F-box   TRAF-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LXQ1-F1-model_v2 AlphaFold F1LXQ1 1-710 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309781 AgrOrtholog
BioCyc Gene G2FUF-21247 BioCyc
Ensembl Genes ENSRNOG00000002459 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003340.8 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
  3.30.40.150 UniProtKB/TrEMBL
InterPro F-box_dom_cyclin-like UniProtKB/TrEMBL
  F-box_dom_like UniProtKB/TrEMBL
  Fbxo30/Fbxo40 UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
  Znf_TRAF UniProtKB/TrEMBL
  Znf_TRAF_N UniProtKB/TrEMBL
KEGG Report rno:363790 UniProtKB/TrEMBL
NCBI Gene 363790 ENTREZGENE
PANTHER F-BOX ONLY PROTEIN 40 UniProtKB/TrEMBL
  PTHR15933 UniProtKB/TrEMBL
Pfam F-box_4 UniProtKB/TrEMBL
  zf-TRAF_2 UniProtKB/TrEMBL
PhenoGen Fbxo40 PhenoGen
PROSITE FBOX UniProtKB/TrEMBL
  ZF_TRAF UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002459 RatGTEx
Superfamily-SCOP SSF81383 UniProtKB/TrEMBL
  TRAF domain-like UniProtKB/TrEMBL
UniProt A6IR98 ENTREZGENE, UniProtKB/TrEMBL
  F1LXQ1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Fbxo40  F-box protein 40   Fbxo40_predicted  F-box protein 40 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Fbxo40_predicted  F-box protein 40 (predicted)      Symbol and Name status set to approved 70820 APPROVED