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FBXO40 Gene

protein-coding   GIFtS: 47
GCID: GC03P121312

F-Box Protein 40

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
F-Box Protein 401 2
FBX402 3 5
Muscle Disease-Related Protein2 3
KIAA11953 5
F-Box Only Protein 402

External Ids:    HGNC: 298161   Entrez Gene: 517252   Ensembl: ENSG000001638337   OMIM: 6091075   UniProtKB: Q9UH903   

Export aliases for FBXO40 gene to outside databases

Previous GC identifers: GC03P122634 GC03P122794 GC03P118686


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for FBXO40 Gene:
Members of the F-box protein family, such as FBXO40, are characterized by an approximately 40-amino acid F-box
motif. SCF complexes, formed by SKP1 (MIM 601434), cullin (see CUL1; MIM 603134), and F-box proteins, act as
protein-ubiquitin ligases. F-box proteins interact with SKP1 through the F box, and they interact with
ubiquitination targets through other protein interaction domains (Jin et al., 2004 (PubMed 15520277)).(supplied
by OMIM, Mar 2008)

GeneCards Summary for FBXO40 Gene:
FBXO40 (F-box protein 40) is a protein-coding gene. GO annotations related to this gene include ubiquitin-protein ligase activity. An important paralog of this gene is FBXO30.

UniProtKB/Swiss-Prot: FBX40_HUMAN, Q9UH90
Function: Probable substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase
complex that may function in myogenesis (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000003.11  NC_018914.2  NT_005612.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the FBXO40 gene promoter:
         HOXA9B   HOXA9   AML1a   CUTL1   HNF-3beta   FOXL1   FOXJ2 (long isoform)   Sox9   FOXJ2   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFBXO40 promoter sequence
   Search Chromatin IP Primers for FBXO40

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FBXO40


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3q13.33   Ensembl cytogenetic band:  3q13.33   HGNC cytogenetic band: 3q21.1

FBXO40 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FBXO40 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P121312:  view genomic region     (about GC identifiers)

Start:
121,311,966 bp from pter      End:
121,349,139 bp from pter
Size:
37,174 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: FBX40_HUMAN, Q9UH90 (See protein sequence)
Recommended Name: F-box only protein 40  
Size: 709 amino acids; 79782 Da
Subunit: Directly interacts with SKP1 and CUL1 (By similarity)
Miscellaneous: The expression decreases in the dystrophic muscle of Limb-girdle muscular dystrophy (LGMD) patient
Sequence caution: Sequence=BAA86509.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: B2RAX7 Q32M70 Q9ULM5

Explore the universe of human proteins at neXtProt for FBXO40: NX_Q9UH90

Explore proteomics data for FBXO40 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See FBXO40 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_057382.2  
    ENSEMBL proteins: 
     ENSP00000337510  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    FBXO: F-boxes / "other"

    4 InterPro protein domains:
     IPR008974 TRAF-like
     IPR001810 F-box_dom
     IPR001293 Znf_TRAF
     IPR013323 SIAH-type

    Graphical View of Domain Structure for InterPro Entry Q9UH90

    ProtoNet protein and cluster: Q9UH90

    UniProtKB/Swiss-Prot: FBX40_HUMAN, Q9UH90
    Similarity: Contains 1 F-box domain
    Similarity: Contains 1 TRAF-type zinc finger


    Find genes that share domains with FBXO40           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: FBX40_HUMAN, Q9UH90
    Function: Probable substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase
    complex that may function in myogenesis (By similarity)

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0004842ubiquitin-protein ligase activity IEA--
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--
         
    Find genes that share ontologies with FBXO40           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for FBXO40:
     Increased cell death HMECs cel  Synthetic lethal with Ras 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for FBXO40
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    SwitchGear 3'UTR luciferase reporter plasmidFBXO40 3' UTR sequence
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    FBX40_HUMAN, Q9UH90: Cytoplasm (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytoskeleton4
    nucleus4
    cytosol3

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ----
    GO:0005737cytoplasm ISS--
    GO:0005813centrosome ----

    Find genes that share ontologies with FBXO40           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for FBXO40
    Interactions:

        Search GeneGlobe Interaction Network for FBXO40

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for FBXO40 (ENSP000003375104) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0042692muscle cell differentiation ISS17928169

    Find genes that share ontologies with FBXO40           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for FBXO40 (FBX40)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for FBXO40 gene: 
    NM_016298.3  

    Unigene Cluster for FBXO40:

    F-box protein 40
    Hs.272564  [show with all ESTs]
    Unigene Representative Sequence: AB033021
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000338040(uc003eeg.2)
    miRNA
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    hsa-miR-300 hsa-miR-218-1* hsa-miR-4267 hsa-miR-376a* hsa-miR-489 hsa-miR-28-5p hsa-miR-497* hsa-miR-192*
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      QuantiFast Probe-based Assays in human, mouse, rat FBXO40

    Additional mRNA sequence: 

    AB033021.1 AF163259.1 AF204674.1 AK314400.1 BC109275.1 BC109276.1 

    1 DOTS entry:

    DT.75161355 

    19 AceView cDNA sequences:

    CF552189 BU188482 AF204674 BX500612 BF477618 AA112110 BU619808 AB033021 
    AF163259 BX500290 NM_016298 BX282446 AA111925 BF576463 BX500755 BX502468 
    F34242 AL693987 BE968725 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    FBXO40 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AACAGCGAGT
    FBXO40 Expression
    About this image

    FBXO40 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    FBXO40 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.272564

    UniProtKB/Swiss-Prot: FBX40_HUMAN, Q9UH90
    Tissue specificity: Expressed only in heart and skeletal muscle

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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for FBXO40 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Fbxo401 , 5 F-box protein 401, 5 84.77(n)1
    85.15(a)1
      16 (26.32 cM)5
    2072151  NM_001037321.11  NP_001032398.11 
     369634605 
    chicken
    (Gallus gallus)
    Aves FBXO401 F-box protein 40 68.66(n)
    67.64(a)
      426341  XM_424000.4  XP_424000.3 
    lizard
    (Anolis carolinensis)
    Reptilia FBXO406
    F-box protein 40
    57(a)
    1 ↔ 1
    GL343473.1(4889-21373)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia fbxo401 F-box protein 40 62.74(n)
    58.66(a)
      100492195  XM_004912286.1  XP_004912343.1 
    zebrafish
    (Danio rerio)
    Actinopterygii si:dkeyp-69c1.101 si:dkeyp-69c1.10 56.86(n)
    49.33(a)
      566344  XM_005161251.1  XP_005161308.1 


    ENSEMBL Gene Tree for FBXO40 (if available)
    TreeFam Gene Tree for FBXO40 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for FBXO40 gene
    FBXO302  
    1 SIMAP similar gene for FBXO40 using alignment to 2 protein entries:     FBX40_HUMAN (see all proteins):
    FBXO30

    Find genes that share paralogs with FBXO40           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for FBXO40 (see all 863)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs356377711,2
    C--121285562(+) AAAAA-/AAGTGAA 1 -- int11Minor allele frequency- AA:0.00NA 2
    rs1924950481,2
    --121310256(+) AAATTA/CTCAAT 1 -- us2k10--------
    rs1483066581,2
    C--121310275(+) AACAAA/GCTAAA 1 -- us2k10--------
    rs1833292361,2
    --121310279(+) AACTAA/TATTTA 1 -- us2k10--------
    rs1414538751,2
    --121310379(+) ATACAC/TGATAT 1 -- us2k10--------
    rs1887890121,2
    --121310399(+) AAAGGA/GCAAAA 1 -- us2k10--------
    rs1925714871,2
    --121310440(+) AAGCAG/TTTGAT 1 -- us2k10--------
    rs1825959041,2
    C--121310527(+) GGCCAA/TCTACA 1 -- us2k10--------
    rs1864774701,2
    --121310544(+) CACAGG/TTAACA 1 -- us2k10--------
    rs1913287751,2
    C--121310584(+) TCCCCC/GCTAAG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for FBXO40 (121311966 - 121349139 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for FBXO40:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv877381CNV Gain21882294
    nsv10310CNV Gain18304495
    nsv877382CNV Gain21882294
    dgv1489e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 609107    OMIM disorders: --


    Find genes that share disorders with FBXO40           About GenesLikeMe

    Genetic Association Database (GAD): FBXO40

    Export disorders for FBXO40 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for FBXO40 gene, integrated from 10 sources (see all 14):
    (articles sorted by number of sources associating them with FBXO40)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10574462)1, 2, 3 Nagase T.... Ohara O. (DNA Res. 1999)
    2. FBXO40, a gene encoding a novel muscle-specific F-box protein, is upregulated in denervation-related muscle atrophy. (PubMed id 17928169)1, 2, 9 Ye J.... Zhu D. (Gene 2007)
    3. A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. (PubMed id 19734545)1, 4 Need A.C....Goldstein D.B. (Hum. Mol. Genet. 2009)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    5. A genome-wide association study in Caucasian women points out a putative role of the STXBP5L gene in facial photoaging. (PubMed id 23223146)1 Le Clerc S....Zagury J.F. (J. Invest. Dermatol. 2013)
    6. Quantitative analysis of HSP90-client interactions reveals principles of substrate recognition. (PubMed id 22939624)1 Taipale M....Lindquist S. (Cell 2012)
    7. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    8. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    9. The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)2 Muzny D.M....Gibbs R.A. (Nature 2006)
    10. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
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      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 51725 HGNC: 29816 AceView: FBXO40 Ensembl:ENSG00000163833 euGenes: HUgn51725
    ECgene: FBXO40 H-InvDB: FBXO40

    (According to HUGE)
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    HUGE: KIAA1195

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for FBXO40 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for FBXO40 gene:
    Search GeneIP for patents involving FBXO40

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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