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    FUBP3 far upstream element binding protein 3 [ Homo sapiens (human) ]

    Gene ID: 8939, updated on 3-Nov-2024

    Summary

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    Official Symbol
    FUBP3provided by HGNC
    Official Full Name
    far upstream element binding protein 3provided by HGNC
    Primary source
    HGNC:HGNC:4005
    See related
    Ensembl:ENSG00000107164 MIM:603536; AllianceGenome:HGNC:4005
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    FBP3
    Summary
    Enables single-stranded DNA binding activity. Involved in DNA-templated transcription; positive regulation of DNA-templated transcription; and positive regulation of gene expression. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 15.5), brain (RPKM 11.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FUBP3 in Genome Data Viewer
    Location:
    9q34.11-q34.12
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (130579577..130638352)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (142784549..142843289)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (133454964..133513739)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene Sharpr-MPRA regulatory region 491 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133328870-133329370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133342170-133342798 Neighboring gene argininosuccinate synthase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133346469-133347206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133347207-133347943 Neighboring gene VISTA enhancer hs1328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133355453-133356208 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:133373167-133373668 Neighboring gene Sharpr-MPRA regulatory region 5386 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:133380533-133381032 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:133381216-133382062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133394336-133394851 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133397629-133398376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133401147-133401648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133401649-133402148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133402913-133403413 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:133420171-133420671 Neighboring gene uncharacterized LOC100272217 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20402 Neighboring gene uncharacterized LOC124902286 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:133464766-133465266 Neighboring gene Sharpr-MPRA regulatory region 1186 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133507597-133508347 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133513639-133514234 Neighboring gene microRNA 6856 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133538423-133539264 Neighboring gene ribosomal protein L19 pseudogene 15 Neighboring gene VISTA enhancer hs876 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:133541982-133543181 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133556829-133557504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29155 Neighboring gene PR/SET domain 12

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Interactome analysis of the EV71 5' untranslated region in differentiated neuronal cells SH-SY5Y and regulatory role of FBP3 in viral replication. Huang HI, et al. Proteomics, 2016 Sep. PMID 27291656
    2. FUBP3 regulates chronic myeloid leukaemia progression through PRC2 complex regulated PAK1-ERK signalling. Sharma M, et al. J Cell Mol Med, 2023 Jan. PMID 36478132, Free PMC Article
    3. Protein engineering of a novel constitutively active hormone-receptor complex. Wu C, et al. J Biol Chem, 1996 Dec 6. PMID 8940183
    4. Long noncoding RNA CMPK2 promotes colorectal cancer progression by activating the FUBP3-c-Myc axis. Gao Q, et al. Oncogene, 2020 May. PMID 32203166
    5. FUBP3 Degrades the Porcine Epidemic Diarrhea Virus Nucleocapsid Protein and Induces the Production of Type I Interferon. Dong S, et al. J Virol, 2022 Jul 13. PMID 35695513, Free PMC Article

    See all (161) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FUBP3 regulates chronic myeloid leukaemia progression through PRC2 complex regulated PAK1-ERK signalling.
      Title: FUBP3 regulates chronic myeloid leukaemia progression through PRC2 complex regulated PAK1-ERK signalling.
    2. Long noncoding RNA CMPK2 promotes colorectal cancer progression by activating the FUBP3-c-Myc axis.
      Title: Long noncoding RNA CMPK2 promotes colorectal cancer progression by activating the FUBP3-c-Myc axis.
    3. The redistribution of FBP3 in subcellular compartments was observed after Enterovirus 71 (EV71) infection, and the decreased expression of FBP3 in host neuronal cells markedly inhibited viral replication. The results reveal various host proteins that potentially interact with the EV71 5'UTR in neuronal cells, and study found that FBP3 could serve as a positive regulator in host cells.
      Title: Interactome analysis of the EV71 5' untranslated region in differentiated neuronal cells SH-SY5Y and regulatory role of FBP3 in viral replication.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. study found that FBP1 as well as FBP3 are more frequently expressed in prostate and bladder cancer than in renal cancer; in addition, a positive correlation between levels of FBP1, FBP3 and c-Myc was exclusively detectable in renal cell carcinomas
      Title: The FUSE binding proteins FBP1 and FBP3 are potential c-myc regulators in renal, but not in prostate and bladder cancer.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Identification of ten loci associated with height highlights new biological pathways in human growth.
    EBI GWAS Catalog
    Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ25229

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables single-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in intracellular mRNA localization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in dendritic shaft IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane HDA PubMed 
    located_in neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in ribosome IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    far upstream element-binding protein 3
    Names
    FUSE-binding protein 3
    far upstream element (FUSE) binding protein 3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_003934.2 → NP_003925.1  far upstream element-binding protein 3

      See identical proteins and their annotated locations for NP_003925.1

      Status: VALIDATED

      Source sequence(s)
      AL537190, BC001325, BI461266, U69127
      Consensus CDS
      CCDS43893.1
      UniProtKB/Swiss-Prot
      A3KFK8, A3KFL0, Q92946, Q96I24, Q9BVB6
      Related
      ENSP00000318177.9, ENST00000319725.10
      Conserved Domains (1) summary
      cl00098
      Location:159 → 241
      KH-I; K homology (KH) RNA-binding domain, type I

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      130579577..130638352
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005272232.3 → XP_005272289.1  far upstream element-binding protein 3 isoform X1

      See identical proteins and their annotated locations for XP_005272289.1

      Conserved Domains (1) summary
      cl00098
      Location:159 → 241
      KH-I; K homology (KH) RNA-binding domain, type I

    2. XM_011519172.4 → XP_011517474.1  far upstream element-binding protein 3 isoform X2

      Conserved Domains (2) summary
      smart00322
      Location:161 → 232
      KH; K homology RNA-binding domain
      cd00105
      Location:79 → 141
      KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

    RNA

    1. XR_007061369.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      142784549..142843289
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054364134.1 → XP_054220109.1  far upstream element-binding protein 3 isoform X1

    2. XM_054364135.1 → XP_054220110.1  far upstream element-binding protein 3 isoform X2

    RNA

    1. XR_008488101.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96I24.2 GenPept UniProtKB/Swiss-Prot:Q96I24

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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