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FBXO31 (F-box protein 31)

Written2008-06Anthony J Bais
Immunogene Therapy Surgical Research Division, Boston University School of Medicine, Roger Williams Medical Center, 825 Chalkstone Avenue, Providence, RI 02908, USA

(Note : for Links provided by Atlas : click)

Identity

Alias_namesF-box only protein 31
Alias_symbol (synonym)FBX14
FBXO14
Fbx31
MGC15419
Other aliasFBX31
DKFZP434B027
DKFZp434J1815
FLJ22477
MGC9527
pp2386
HGNC (Hugo) FBXO31
LocusID (NCBI) 79791
Atlas_Id 44280
Location 16q24.2  [Link to chromosome band 16q24]
Location_base_pair Starts at 87326987 and ends at 87383793 bp from pter ( according to hg19-Feb_2009)  [Mapping FBXO31.png]
Local_order telomere; centromeric to JPH3 and telomeric to FOXL1
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
DEF8 (16q24.3) / FBXO31 (16q24.2)DSTN (20p12.1) / FBXO31 (16q24.2)

DNA/RNA

Description FBXO31 encodes one mRNA transcript, published analyses have not reordered alternative five prime transcript or start sequences.
  • FBXO31 is 3,635-bp in length, composed of 9 exons (1 to 9) spanning approximately 55-kb of genomic DNA, and has an ORF of 1,620-bp encoding a protein of 539 amino acids with a predicted mass of 61-kDa.
  • Alternative five prime transcripts may exist. Homologous mouse cDNA sequences extending further five prime have been used for RT-PCR to identify putative translation start sites and established that alternatively spliced five prime exons result in short and long isoforms. The short isoform is 3,635-bp in length (i.e. approximately with poly A), and is the predicted primary transcript. The long isoform is 3,725-bp in length, contains an additional five prime exon of 87-bp and has an ORF of 1,707-bp encoding a protein of 568 amino acids. An additional smaller isoform of 3,099-bp with an ORF of 1,104-bp and 367 amino acids was predicted in GenBank.
  • FBXO31 contains a moderate density C + G rich region (66% G + G with 9% CpG) spanning approximately 2.48-kb located within and five prime to the 350-bp exon 1.
  • The FBXO31 transcript has and an uncharacteristically short 23-bp five prime untranslated region.
    • Pseudogene None identified.

    Protein

    Description FBXO31 contains no significant homology to other known proteins apart from a characteristic 40 amino acid F-box domain at the COOH-terminal end.
  • FBXO31 forms part of the FBXO class of F-box proteins. Comparison of FBXO31 with the F-box domain of functionally demonstrated F-box proteins (i.e. Fbx1, Fbx2, Fbw1a, Fbw1b and Fbl1 ) indicates that FBXO31 matches the F-box consensus more closely than recognized F-box proteins from each of the three classes. Most F-box proteins notated as FBXO do not have recognizable substrate binding domains. In one instance Fbx7 has been shown to contain a proline-rich region that functions with SCF complexes in regulating Cdk1 - cyclin B - phosphorylated hepatoma up-regulated protein ( HURP ) proteolysis. This proline-rich region has been found in other FBXO proteins. The COOH-terminal end of FBXO31 contains a 175-aa glycine and arginine rich region with possible similar function.
  • FBXO31 contains six minimal D-box (RxxL) motifs. Proteins with RxxL motifs are often degraded via the APC/C( Cdh1 ) ubiquitin ligase.
    • Expression FBXO31 is widely expressed as a 3.6-kb transcript at similar levels in breast, testis, ovary, liver, uterus, prostate, colon, stomach, bladder, spinal cord, pancreas, trachea, kidney and thyroid. High expression is found in brain and low expression in bone marrow. FBXO31 is represented by the unigene cluster Hs.567582. cDNA clones from Hs.567582 express in the adrenal gland, blood, colon, germ cells, heart, kidney, liver, lung, muscle, placenta, synovial membrane, tonsil, cervix, lymph tissue, skin, mammary gland, testis, ovary, uterus, prostate, stomach, bladder, spinal cord, pancreas, thyroid and brain.
    Localisation Co-immunoprecipitation experiments indicate that the carboxy terminal domain of FBXO31 associates with the Skp1, Roc-1 and Cullin-1 proteins. Immuno-localization studies demonstrate that ectopic expression of FBXO31 causes a change of Skp1 localization from the nucleus to the cytoplasm. The Skp1 protein returns to a nuclear localization when co-expressed with a FBXO31 protein with a deleted F-box domain.
    Function FBXO31 is associated with the Skp1, Roc-1 and Cullin-1 proteins through its substrate F-box recognition domain and forms part of an SCF ubiquitination complex.
    The ubiquitin-dependant proteasome degradation pathway regulates protein abundance and the function of oncogenes, tumor suppressors, transcription factors and other signaling molecules. Ubiquitination begins with the addition of ubiquitin moieties to target proteins and follows a multi-step process, the end point being proteolysis of polyubiquitinated substrates by a 26S multi-protein complex. Ubiquitination of substrates targeted for degradation requires 3 classes of enzymes; the ubiquitin-activating enzymes (E1), the ubiquitin conjugating enzymes (E2) and the ubiquitin ligases (E3). E3 proteins participate in cell cycle progression. SCF complexes (a class of E3 ligases) regulate the G1-S phase transition. A wide variety of SCF targets include G1 phase cyclins, cyclin-dependant kinase inhibitors, DNA replication factors and transcription factors that promote cell cycle progression.
    F-box containing proteins act as substrate recognition components of the SCF ubiquitin-ligase complexes in the ubiquitin-dependant proteasome degradation pathway. These complexes contain four components; Skp1, Cullin, Rbx-Rocl-Hrtl and an F-box protein. The F-box motif tethers the F-box protein to other components of the SCF complex by binding the core SCF component Skp1. This motif is generally found in the amino half of the proteins and is often coupled with other protein domains in the variable carboxy terminus of the protein. The most common carboxy terminal domains include leucine-rich repeats (LRRs) and WD-40 domains. Regions rich in glycine and arginine have also been implicated as protein binding domains, although such domains contain a more definitive repeat region than present in FBXO31.
    F-box SCF ubiquitin ligase complexes are involved in proteolysis pathways critical to diverse cellular functions including muscle atrophy, DNA metabolism, ER-associated degradation, desmin-related myopathy, signal transduction, control of G1-S progression and orderly execution of cell cycle. Skp1, Cul1 and Rbx1 are invariant proteins of the SCF complex while the F-box proteins that bind to Skp1 are the components that impart functional specificity. For instance Skp2 specifically binds phosphorylated p27 resulting in its degradation and control of S phase entry in the cell cycle.
    Homology F-box domain containing no other significant homology.

    Mutations

    Note None recorded.

    Implicated in

    Note
      
    Entity Neurodegenerative disorders and cancer
    Note Aberrant ubiquitin-dependant proteasome degradation in neurodegenerative disorders and cancer.
    Precedence for disruption in neurodegenerative disorders. The Parkin gene functions as a E3 ubiquitin ligase often mutated in inherited forms of Parkinson's disease. In Alzheimer's disease defective ubiquitination of cerebral proteins has been identified. The Von Hippel-Lindau ( VHL ) tumor suppressor protein is part of a complex that functions as a ubiquitin-protein ligase E3. VHL associates the ligase complex to target proteins such as HIF1aand VDU1 (VHL interacting deubiquitinating enzyme 1). HIF-a has been shown to regulate genes involved in tumor angiogenesis; VDU1 has deubiquitinating activity.
    Aberrant ubiquitin-dependant proteasome degradation of SCF-FBXO31 complexes has been proposed as a mechanism for tumor progression. FBXO31 would function as a tumor suppressor by mediating generation of SCF-FBXO31 complexes that compete and balance levels of other SCF complexes normally targeted to degradation proteins required to maintain cell proliferation. An example is SCF complexes resulting in SCF-Skp2 E3 ligases that mediate ubiquitination and subsequent degradation of the CDK-inhibitor p27. Ectopic expression of FBXO31 would lower SCF-Skp2 complexes resulting in increased p27 and inhibition of transition from G1-S phase. This model corroborates with studies showing that high levels of Skp2 were associated with reduced levels of p27 in several cancers.
    Abnormal Protein None recorded
      
      
    Entity Breast cancer, Prostate cancer, and several other cancers
    Note Loss of heterozygosity (LOH) of 16q22-qter in breast cancer, prostate cancer, and several other cancers.
    This region is frequently deleted in several human cancers causing loss of heterozygosity. The 16q24.3 region including FBXO31 spans approximately 3-Mb from the marker D16S498 to the telomere and contains at least two smallest regions of overlap (SROs). These SROs are most frequently deleted in early and late stage breast cancer and in prostate cancer. Loss of normal function of FBXO31 may be a key event in the early stage of breast cancer. LOH on the whole 16q22-qter region is frequently detected in breast and prostate cancer. Micro-cell mediated transfer experiments with 16q22-qter fragments (the 360-kb YAC clone 792E1 at D16S476 and D16S498 and the 85-kb BAC clone 346J21 at D16S3048 and D16S3063) have been shown to induce senescence in human and rat breast tumor cell lines. FBXO31 encompasses the 792E1 clone and a partial region of 346J21, has been shown to induce senescence in the breast cancer cell line MCF-7 and is regarded as the cellular senescence gene. FBXO31 is a potential tumor suppressor shown to be down-regulated in breast cancer cell lines relative to normal breast expression and cause G1 phase cell cycle arrest of the MDA-MB-468 cell line.
    Quantitative gene expression analysis of 78 genes in the 16q24.3 region demonstrated that FBXO31 was one of two genes including CYBA with a moderately aberrant expression profile. Expression of FBXO31 was reduced 100 to 200-fold in MDA-MB-134 and SK-BR-3 and moderately reduced in the other cell lines. 68 other genes displayed normal expression, one displayed significantly aberrant expression ( CBFA2T3 ), six displayed mildly aberrant expression (DPEP1, CDH15, Hs.17074, Hs.189419, SLC7A5 and AA994450), and one gene displayed excessively reduced expression (CA5A). From microarray analysis FBXO31 was one of the 70-gene classifiers down-regulated in association with tumors of a favorable prognosis. The prognostic association between down-regulated FBXO31 and breast tumors corroborates with other studies demonstrating that LOH of chromosome 16q is associated with tumors of favorable prognosis.
    Disease 16q22-qter LOH is detected in bilateral breast cancer and ductal lavage, in rare inflammatory breast cancer, and in several other cancers, including central nervous system neuroectodermal ependymoma and primary ependymomas, colorectal liver metastases, gastric tumor cancer, head and neck squamous cell carcinoma, hepatocellular carcinoma, lung tumor, nasopharyngeal tumor, ovarian tumor, rhabdomyosarcoma, and Wilms' tumor. 16q22-qter LOH in ovarian, hepatocellular and particularly breast and prostate cancers, exhibit similar SROs, suggesting common molecular pathways are affected.
      

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    Citation

    This paper should be referenced as such :
    Bais, AJ
    FBXO31 (F-box protein 31)
    Atlas Genet Cytogenet Oncol Haematol. 2009;13(5):338-342.
    Free journal version : [ pdf ]   [ DOI ]
    On line version : http://AtlasGeneticsOncology.org/Genes/FBXO31ID44280ch16q24.html

    Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
      DEF8/FBXO31 (16q24)

    External links

    Nomenclature
    HGNC (Hugo)FBXO31   16510
    Cards
    AtlasFBXO31ID44280ch16q24
    Entrez_Gene (NCBI)FBXO31  79791  F-box protein 31
    AliasesFBX14; FBXO14; Fbx31; MRT45; 
    pp2386
    GeneCards (Weizmann)FBXO31
    Ensembl hg19 (Hinxton)ENSG00000103264 [Gene_View]
    Ensembl hg38 (Hinxton)ENSG00000103264 [Gene_View]  ENSG00000103264 [Sequence]  chr16:87326987-87383793 [Contig_View]  FBXO31 [Vega]
    ICGC DataPortalENSG00000103264
    TCGA cBioPortalFBXO31
    AceView (NCBI)FBXO31
    Genatlas (Paris)FBXO31
    WikiGenes79791
    SOURCE (Princeton)FBXO31
    Genetics Home Reference (NIH)FBXO31
    Genomic and cartography
    GoldenPath hg38 (UCSC)FBXO31  -     chr16:87326987-87383793 -  16q24.2   [Description]    (hg38-Dec_2013)
    GoldenPath hg19 (UCSC)FBXO31  -     16q24.2   [Description]    (hg19-Feb_2009)
    GoldenPathFBXO31 - 16q24.2 [CytoView hg19]  FBXO31 - 16q24.2 [CytoView hg38]
    ImmunoBaseENSG00000103264
    Mapping of homologs : NCBIFBXO31 [Mapview hg19]  FBXO31 [Mapview hg38]
    OMIM609102   615979   
    Gene and transcription
    Genbank (Entrez)AF318348 AF428140 AK311122 AL117444 AL576585
    RefSeq transcript (Entrez)NM_001282683 NM_024735
    RefSeq genomic (Entrez)
    Consensus coding sequences : CCDS (NCBI)FBXO31
    Cluster EST : UnigeneHs.733212 [ NCBI ]
    CGAP (NCI)Hs.733212
    Alternative Splicing GalleryENSG00000103264
    Gene ExpressionFBXO31 [ NCBI-GEO ]   FBXO31 [ EBI - ARRAY_EXPRESS ]   FBXO31 [ SEEK ]   FBXO31 [ MEM ]
    Gene Expression Viewer (FireBrowse)FBXO31 [ Firebrowse - Broad ]
    SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
    GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
    BioGPS (Tissue expression)79791
    GTEX Portal (Tissue expression)FBXO31
    Human Protein AtlasENSG00000103264-FBXO31 [pathology]   [cell]   [tissue]
    Protein : pattern, domain, 3D structure
    UniProt/SwissProtQ5XUX0   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
    NextProtQ5XUX0  [Sequence]  [Exons]  [Medical]  [Publications]
    With graphics : InterProQ5XUX0
    Splice isoforms : SwissVarQ5XUX0
    PhosPhoSitePlusQ5XUX0
    Domaine pattern : Prosite (Expaxy)FBOX (PS50181)   
    Domains : Interpro (EBI)F-box-like_dom_sf    F-box_dom    FBXO31   
    Domain families : Pfam (Sanger)F-box-like (PF12937)   
    Domain families : Pfam (NCBI)pfam12937   
    Domain families : Smart (EMBL)FBOX (SM00256)  
    Conserved Domain (NCBI)FBXO31
    DMDM Disease mutations79791
    Blocks (Seattle)FBXO31
    PDB (RSDB)5VZT    5VZU   
    PDB Europe5VZT    5VZU   
    PDB (PDBSum)5VZT    5VZU   
    PDB (IMB)5VZT    5VZU   
    Structural Biology KnowledgeBase5VZT    5VZU   
    SCOP (Structural Classification of Proteins)5VZT    5VZU   
    CATH (Classification of proteins structures)5VZT    5VZU   
    SuperfamilyQ5XUX0
    Human Protein Atlas [tissue]ENSG00000103264-FBXO31 [tissue]
    Peptide AtlasQ5XUX0
    HPRD10954
    IPIIPI00028347   IPI00930569   
    Protein Interaction databases
    DIP (DOE-UCLA)Q5XUX0
    IntAct (EBI)Q5XUX0
    FunCoupENSG00000103264
    BioGRIDFBXO31
    STRING (EMBL)FBXO31
    ZODIACFBXO31
    Ontologies - Pathways
    QuickGOQ5XUX0
    Ontology : AmiGOprotein polyubiquitination  protein binding  centrosome  cytosol  cellular response to DNA damage stimulus  SCF ubiquitin ligase complex  SCF ubiquitin ligase complex  cyclin binding  anaphase-promoting complex-dependent catabolic process  SCF-dependent proteasomal ubiquitin-dependent protein catabolic process  SCF-dependent proteasomal ubiquitin-dependent protein catabolic process  mitotic G1 DNA damage checkpoint  neuronal cell body  post-translational protein modification  positive regulation of dendrite morphogenesis  positive regulation of neuron migration  
    Ontology : EGO-EBIprotein polyubiquitination  protein binding  centrosome  cytosol  cellular response to DNA damage stimulus  SCF ubiquitin ligase complex  SCF ubiquitin ligase complex  cyclin binding  anaphase-promoting complex-dependent catabolic process  SCF-dependent proteasomal ubiquitin-dependent protein catabolic process  SCF-dependent proteasomal ubiquitin-dependent protein catabolic process  mitotic G1 DNA damage checkpoint  neuronal cell body  post-translational protein modification  positive regulation of dendrite morphogenesis  positive regulation of neuron migration  
    REACTOMEQ5XUX0 [protein]
    REACTOME PathwaysR-HSA-983168 [pathway]   
    NDEx NetworkFBXO31
    Atlas of Cancer Signalling NetworkFBXO31
    Wikipedia pathwaysFBXO31
    Orthology - Evolution
    OrthoDB79791
    GeneTree (enSembl)ENSG00000103264
    Phylogenetic Trees/Animal Genes : TreeFamFBXO31
    HOGENOMQ5XUX0
    Homologs : HomoloGeneFBXO31
    Homology/Alignments : Family Browser (UCSC)FBXO31
    Gene fusions - Rearrangements
    Fusion : MitelmanDEF8/FBXO31 [16q24.3/16q24.2]  [t(16;16)(q24;q24)]  
    Fusion PortalDEF8 16q24.3 FBXO31 16q24.2 LUAD
    Fusion : FusionGDB10610    13156    13157    13158    42187    9690   
    Fusion : Fusion_HubASXL1--FBXO31    ATRX--FBXO31    CTTN--FBXO31    DEF8--FBXO31    DSTN--FBXO31    EPB41L4A--FBXO31    FBXO31--AGPAT6    FBXO31--C16ORF95    FBXO31--PPP1R12C    FBXO31--RPL35    FBXO31--UBE2Q2    FBXO31--WWP2    FBXO31--ZNRF1    GSPT1--FBXO31    PROSC--FBXO31   
    SHANK3--FBXO31    WDR91--FBXO31    XPO6--FBXO31    ZEB1--FBXO31   
    Fusion : QuiverFBXO31
    Polymorphisms : SNP and Copy number variants
    NCBI Variation ViewerFBXO31 [hg38]
    dbSNP Single Nucleotide Polymorphism (NCBI)FBXO31
    dbVarFBXO31
    ClinVarFBXO31
    1000_GenomesFBXO31 
    Exome Variant ServerFBXO31
    ExAC (Exome Aggregation Consortium)ENSG00000103264
    GNOMAD BrowserENSG00000103264
    Varsome BrowserFBXO31
    Genetic variants : HAPMAP79791
    Genomic Variants (DGV)FBXO31 [DGVbeta]
    DECIPHERFBXO31 [patients]   [syndromes]   [variants]   [genes]  
    CONAN: Copy Number AnalysisFBXO31 
    Mutations
    ICGC Data PortalFBXO31 
    TCGA Data PortalFBXO31 
    Broad Tumor PortalFBXO31
    OASIS PortalFBXO31 [ Somatic mutations - Copy number]
    Somatic Mutations in Cancer : COSMICFBXO31  [overview]  [genome browser]  [tissue]  [distribution]  
    Somatic Mutations in Cancer : COSMIC3DFBXO31
    Mutations and Diseases : HGMDFBXO31
    LOVD (Leiden Open Variation Database)Whole genome datasets
    LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
    LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
    BioMutasearch FBXO31
    DgiDB (Drug Gene Interaction Database)FBXO31
    DoCM (Curated mutations)FBXO31 (select the gene name)
    CIViC (Clinical Interpretations of Variants in Cancer)FBXO31 (select a term)
    intoGenFBXO31
    NCG5 (London)FBXO31
    Cancer3DFBXO31(select the gene name)
    Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
    Diseases
    OMIM609102    615979   
    Orphanet11804   
    DisGeNETFBXO31
    MedgenFBXO31
    Genetic Testing Registry FBXO31
    NextProtQ5XUX0 [Medical]
    TSGene79791
    GENETestsFBXO31
    Target ValidationFBXO31
    Huge Navigator FBXO31 [HugePedia]
    snp3D : Map Gene to Disease79791
    BioCentury BCIQFBXO31
    ClinGenFBXO31
    Clinical trials, drugs, therapy
    Chemical/Protein Interactions : CTD79791
    Chemical/Pharm GKB GenePA28042
    Clinical trialFBXO31
    Miscellaneous
    canSAR (ICR)FBXO31 (select the gene name)
    DataMed IndexFBXO31
    Probes
    Litterature
    PubMed42 Pubmed reference(s) in Entrez
    GeneRIFsGene References Into Functions (Entrez)
    CoreMineFBXO31
    EVEXFBXO31
    GoPubMedFBXO31
    iHOPFBXO31
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

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