Human Gene FBXL4 (ENST00000369244.7) from GENCODE V44
  Description: Homo sapiens F-box and leucine rich repeat protein 4 (FBXL4), transcript variant 3, non-coding RNA. (from RefSeq NR_103836)
RefSeq Summary (NM_001278716): This gene encodes a member of the F-box protein family, which are characterized by an approximately 40 amino acid motif, the F-box. F-box proteins constitute one subunit of modular E3 ubiquitin ligase complexes, called SCF complexes, which function in phosphorylation-dependent ubiquitination. The F-box domain mediates protein-protein interactions and binds directly to S-phase kinase-associated protein 1. In addition to an F-box domain, the encoded protein contains at least 9 tandem leucine-rich repeats. The ubiquitin ligase complex containing the encoded protein may function in cell-cycle control by regulating levels of lysine-specific demethylase 4A. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013].
Gencode Transcript: ENST00000369244.7
Gencode Gene: ENSG00000112234.9
Transcript (Including UTRs)
   Position: hg38 chr6:98,868,535-98,947,946 Size: 79,412 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg38 chr6:98,874,278-98,926,988 Size: 52,711 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:98,868,535-98,947,946)mRNA (may differ from genome)Protein (621 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGImyGene2
neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: FBXL4_HUMAN
DESCRIPTION: RecName: Full=F-box/LRR-repeat protein 4; AltName: Full=F-box and leucine-rich repeat protein 4; AltName: Full=F-box protein FBL4/FBL5;
SUBUNIT: Part of a SCF (SKP1-cullin-F-box) protein ligase complex (By similarity).
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
TISSUE SPECIFICITY: Expressed in heart, kidney, liver, lung, pancreas, and placenta, but not in skeletal muscle.
SIMILARITY: Contains 1 F-box domain.
SIMILARITY: Contains 9 LRR (leucine-rich) repeats.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: FBXL4
Diseases sorted by gene-association score: mitochondrial dna depletion syndrome 13* (1600), fbxl4-related mitochondrial dna depletion syndrome, encephalomyopathic form* (500), fbxl4-related encephalomyopathic mitochondrial dna depletion syndrome* (400), mitochondrial encephalomyopathy (7)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.43 RPKM in Nerve - Tibial
Total median expression: 140.79 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -149.30449-0.333 Picture PostScript Text
3' UTR -1400.905743-0.244 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001810 - F-box_dom_cyclin-like
IPR006553 - Leu-rich_rpt_Cys-con_subtyp

Pfam Domains:
PF00646 - F-box domain

ModBase Predicted Comparative 3D Structure on Q9UKA2
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004842 ubiquitin-protein transferase activity

Biological Process:
GO:0000209 protein polyubiquitination
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0043687 post-translational protein modification

Cellular Component:
GO:0000151 ubiquitin ligase complex
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005758 mitochondrial intermembrane space
GO:0005829 cytosol
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  AK055220 - Homo sapiens cDNA FLJ30658 fis, clone DFNES2000432.
JD231020 - Sequence 212044 from Patent EP1572962.
JD208911 - Sequence 189935 from Patent EP1572962.
JD119940 - Sequence 100964 from Patent EP1572962.
JD301320 - Sequence 282344 from Patent EP1572962.
JD300569 - Sequence 281593 from Patent EP1572962.
JD050547 - Sequence 31571 from Patent EP1572962.
JD288703 - Sequence 269727 from Patent EP1572962.
JD497096 - Sequence 478120 from Patent EP1572962.
JD083060 - Sequence 64084 from Patent EP1572962.
JD115308 - Sequence 96332 from Patent EP1572962.
JD139221 - Sequence 120245 from Patent EP1572962.
JD528526 - Sequence 509550 from Patent EP1572962.
JD335050 - Sequence 316074 from Patent EP1572962.
JD083112 - Sequence 64136 from Patent EP1572962.
JD299566 - Sequence 280590 from Patent EP1572962.
JD302968 - Sequence 283992 from Patent EP1572962.
JD531170 - Sequence 512194 from Patent EP1572962.
JD537524 - Sequence 518548 from Patent EP1572962.
JD414668 - Sequence 395692 from Patent EP1572962.
JD069695 - Sequence 50719 from Patent EP1572962.
JD513876 - Sequence 494900 from Patent EP1572962.
JD120365 - Sequence 101389 from Patent EP1572962.
JD379255 - Sequence 360279 from Patent EP1572962.
JD328729 - Sequence 309753 from Patent EP1572962.
JD242586 - Sequence 223610 from Patent EP1572962.
JD489101 - Sequence 470125 from Patent EP1572962.
JD489100 - Sequence 470124 from Patent EP1572962.
JD374528 - Sequence 355552 from Patent EP1572962.
JD148915 - Sequence 129939 from Patent EP1572962.
JD348073 - Sequence 329097 from Patent EP1572962.
JD268834 - Sequence 249858 from Patent EP1572962.
JD109475 - Sequence 90499 from Patent EP1572962.
JD516019 - Sequence 497043 from Patent EP1572962.
JD524914 - Sequence 505938 from Patent EP1572962.
JD352638 - Sequence 333662 from Patent EP1572962.
JD454053 - Sequence 435077 from Patent EP1572962.
JD536118 - Sequence 517142 from Patent EP1572962.
JD274556 - Sequence 255580 from Patent EP1572962.
JD566860 - Sequence 547884 from Patent EP1572962.
JD204615 - Sequence 185639 from Patent EP1572962.
JD089790 - Sequence 70814 from Patent EP1572962.
AJ420594 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1234832.
AF176699 - Homo sapiens F-box protein FBL4 mRNA, complete cds.
BC055010 - Homo sapiens F-box and leucine-rich repeat protein 4, mRNA (cDNA clone MGC:61641 IMAGE:6137889), complete cds.
BC039819 - Homo sapiens F-box and leucine-rich repeat protein 4, mRNA (cDNA clone IMAGE:6066149), containing frame-shift errors.
JD288249 - Sequence 269273 from Patent EP1572962.
BC091484 - Homo sapiens F-box and leucine-rich repeat protein 4, mRNA (cDNA clone MGC:111014 IMAGE:6178874), complete cds.
JD053359 - Sequence 34383 from Patent EP1572962.
AF174590 - Homo sapiens F-box protein Fbl4 (FBL4) mRNA, partial cds.
AF199355 - Homo sapiens F-box protein FBL5 (FBL5) mRNA, complete cds.
AK313076 - Homo sapiens cDNA, FLJ93557, highly similar to Homo sapiens F-box and leucine-rich repeat protein 4 (FBXL4), mRNA.
KJ893542 - Synthetic construct Homo sapiens clone ccsbBroadEn_02936 FBXL4 gene, encodes complete protein.
AK308736 - Homo sapiens cDNA, FLJ98777.
BC032641 - Homo sapiens F-box and leucine-rich repeat protein 4, mRNA (cDNA clone IMAGE:5496098), with apparent retained intron.
JD437779 - Sequence 418803 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UKA2 (Reactome details) participates in the following event(s):

R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-983147 Release of E3 from polyubiquitinated substrate
R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2
R-HSA-8952620 NEDD8:AcM-UBE2M binds CRL1 E3 ubiquitin ligase complex
R-HSA-8956200 MyrG-DCUN1D3 binds CRL1 E3 ubiquitin ligase complex
R-HSA-8955241 CAND1 binds cytosolic CRL E3 ubiquitin ligases
R-HSA-8952618 AcM-UBE2M transfers NEDD8 to CRL1 E3 ubiquitin ligase complex
R-HSA-8955289 COMMDs displace CAND1 from cytosolic CRL E3 ubiquitin ligase complexes
R-HSA-8956040 COP9 signalosome deneddylates cytosolic CRL E3 ubiquitin ligase complexes
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-1280218 Adaptive Immune System
R-HSA-8951664 Neddylation
R-HSA-168256 Immune System
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: E1P530, ENST00000369244.1, ENST00000369244.2, ENST00000369244.3, ENST00000369244.4, ENST00000369244.5, ENST00000369244.6, FBL4, FBL5, FBXL4_HUMAN, NR_103836, O95919, Q5BJH0, Q9UJU0, Q9UKA2, uc003ppg.1, uc003ppg.2, uc003ppg.3, uc003ppg.4
UCSC ID: ENST00000369244.7
RefSeq Accession: NM_001278716
Protein: Q9UKA2 (aka FBXL4_HUMAN or FXL4_HUMAN)
CCDS: CCDS5041.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene FBXL4:
fbxl4-mtddepl (FBXL4-Related Encephalomyopathic Mitochondrial DNA Depletion Syndrome)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.