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    BCO2 beta-carotene oxygenase 2 [ Homo sapiens (human) ]

    Gene ID: 83875, updated on 5-Mar-2024

    Summary

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    Official Symbol
    BCO2provided by HGNC
    Official Full Name
    beta-carotene oxygenase 2provided by HGNC
    Primary source
    HGNC:HGNC:18503
    See related
    Ensembl:ENSG00000197580 MIM:611740; AllianceGenome:HGNC:18503
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BCDO2; B-DIOX-II
    Summary
    This gene encodes an enzyme which oxidizes carotenoids such as beta-carotene during the biosynthesis of vitamin A. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
    Expression
    Broad expression in heart (RPKM 9.3), liver (RPKM 6.3) and 14 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    11q23.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (112175512..112218946)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (112185841..112229285)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (112046235..112089669)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987164 Neighboring gene testis expressed 12 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:112048596-112048762 Neighboring gene potassium channel tetramerization domain containing 9 pseudogene 4 Neighboring gene mitochondrial ribosomal protein S36 pseudogene 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:112090776-112090983 Neighboring gene ribosomal protein S12 pseudogene 21 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3906 Neighboring gene Sharpr-MPRA regulatory region 3969 Neighboring gene 6-pyruvoyltetrahydropterin synthase Neighboring gene ribosomal protein S6 pseudogene 16

    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
    • 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. The human mitochondrial enzyme BCO2 exhibits catalytic activity toward carotenoids and apocarotenoids. Thomas LD, et al. J Biol Chem, 2020 Nov 13. PMID 32873706, Free PMC Article
    2. Mitochondrial β-Carotene 9',10' Oxygenase Modulates Prostate Cancer Growth via NF-κB Inhibition: A Lycopene-Independent Function. Gong X, et al. Mol Cancer Res, 2016 Oct. PMID 27406826
    3. Molecular aspects of β, β-carotene-9', 10'-oxygenase 2 in carotenoid metabolism and diseases. Wu L, et al. Exp Biol Med (Maywood), 2016 Nov. PMID 27390265, Free PMC Article
    4. Inactivity of human β,β-carotene-9',10'-dioxygenase (BCO2) underlies retinal accumulation of the human macular carotenoid pigment. Li B, et al. Proc Natl Acad Sci U S A, 2014 Jul 15. PMID 24982131, Free PMC Article
    5. Towards a better understanding of carotenoid metabolism in animals. von Lintig J, et al. Biochim Biophys Acta, 2005 May 30. PMID 15949678

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The human mitochondrial enzyme BCO2 exhibits catalytic activity toward carotenoids and apocarotenoids.
      Title: The human mitochondrial enzyme BCO2 exhibits catalytic activity toward carotenoids and apocarotenoids.
    2. Evolutionary aspects and enzymology of metazoan carotenoid cleavage oxygenases.
      Title: Evolutionary aspects and enzymology of metazoan carotenoid cleavage oxygenases.
    3. Enzymology of vertebrate carotenoid oxygenases.
      Title: Enzymology of vertebrate carotenoid oxygenases.
    4. Associations for BCO2, PCSK9, and TR1B1 Polymorphism and Lifestyle Factors with Ischemic Stroke
      Title: Associations for BCO2, PCSK9, and TR1B1 Polymorphism and Lifestyle Factors with Ischemic Stroke: A Nested Case-Control Study.
    5. Study identifies BCO2 as a tumor suppressor in prostate cancer which mediates inhibition of NF-kB signaling. Its expression is decreased in human prostate cancer.
      Title: Mitochondrial β-Carotene 9',10' Oxygenase Modulates Prostate Cancer Growth via NF-κB Inhibition: A Lycopene-Independent Function.
    6. review of molecular aspects in carotenoid metabolism and diseases
      Title: Molecular aspects of β, β-carotene-9', 10'-oxygenase 2 in carotenoid metabolism and diseases.
    7. Role of beta-Carotene 9,10-Dioxygenase in Macular Pigment Metabolism
      Title: Characterization of the Role of β-Carotene 9,10-Dioxygenase in Macular Pigment Metabolism.
    8. Inactivity of human beta,beta-carotene-9',10'-dioxygenase (BCO2) underlies retinal accumulation of the human macular carotenoid pigment.
      Title: Inactivity of human β,β-carotene-9',10'-dioxygenase (BCO2) underlies retinal accumulation of the human macular carotenoid pigment.
    9. a stepwise cleavage by BCO2 and BCO1 with APO10ol as an intermediate could provide a mechanism to tailor asymmetric carotenoids such as beta-cryptoxanthin for vitamin A production.
      Title: Two carotenoid oxygenases contribute to mammalian provitamin A metabolism.
    10. The gene encoding beta-carotene-9',10'-oxygenase, which cleaves the 9',10' double bond in beta-carotene into beta-apo-10'-carotenal, was cloned and expressed in Escherichia coli.
      Title: Production of β-apo-10'-carotenal from β-carotene by human β-carotene-9',10'-oxygenase expressed in E. coli.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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
    A genome-wide association study identifies protein quantitative trait loci (pQTLs).
    EBI GWAS Catalog
    Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
    EBI GWAS Catalog
    Genome-wide association study identifies variants at the IL18-BCO2 locus associated with interleukin-18 levels.
    EBI GWAS Catalog
    Novel gene variants predict serum levels of the cytokines IL-18 and IL-1ra in older adults.
    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

    Pathways from PubChem

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    General gene information

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    Markers

    Potential readthrough

    Included genes: SDHD, TEX12

    Homology

    Clone Names

    • FLJ34464

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 9,10 (9', 10')-carotenoid-cleaving dioxygenase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables beta,beta-carotene-9',10'-cleaving oxygenase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables beta-carotene 15,15'-dioxygenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables carotenoid dioxygenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in carotene catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in carotene catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in carotene metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in carotenoid metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in lutein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in lycopene catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of mitochondrial membrane potential ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in regulation of reactive oxygen species metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in retinal metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retinal metabolic process NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in retinoic acid metabolic process NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in xanthophyll catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in zeaxanthin catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in mitochondrion TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    carotenoid-cleaving dioxygenase, mitochondrial
    Names
    b,b-carotene-9',10'-dioxygenase
    beta,beta-carotene 9',10'-oxygenase
    beta-carotene 9',10' oxygenase
    beta-carotene dioxygenase 2
    carotenoid-9',10'-cleaving dioxygenase
    NP_001032367.3
    NP_001243326.2
    NP_001243327.2
    NP_001243329.2
    NP_114144.5

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001037290.4 → NP_001032367.3  carotenoid-cleaving dioxygenase, mitochondrial isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate segment in the 5' UTR and uses a downstream start codon compared to variant 1. The resulting protein (isoform b) has a shorter N-terminus compared to isoform a.
      Source sequence(s)
      AP002884
      Consensus CDS
      CCDS41716.1
      UniProtKB/TrEMBL
      B0YIX6
      Related
      ENSP00000414843.1, ENST00000438022.5
      Conserved Domains (1) summary
      pfam03055
      Location:29 → 544
      RPE65; Retinal pigment epithelial membrane protein

    2. NM_001256397.3 → NP_001243326.2  carotenoid-cleaving dioxygenase, mitochondrial isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate segment in the 5' UTR, uses a downstream start codon and an alternate in-frame splice site in the 3' coding region compared to variant 1. The resulting protein (isoform c) has a shorter N-terminus compared to isoform a.
      Source sequence(s)
      AP002884
      Consensus CDS
      CCDS58182.1
      UniProtKB/TrEMBL
      B0YIX6
      Related
      ENSP00000436615.1, ENST00000526088.5
      Conserved Domains (1) summary
      pfam03055
      Location:29 → 538
      RPE65; Retinal pigment epithelial membrane protein

    3. NM_001256398.3 → NP_001243327.2  carotenoid-cleaving dioxygenase, mitochondrial isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two alternate in-frame exons compared to variant 1. The resulting protein (isoform d) is shorter compared to isoform a.
      Source sequence(s)
      AP002884
      Consensus CDS
      CCDS58181.1
      UniProtKB/TrEMBL
      B0YIX7
      Related
      ENSP00000354338.4, ENST00000361053.8
      Conserved Domains (1) summary
      pfam03055
      Location:63 → 505
      RPE65; Retinal pigment epithelial membrane protein

    4. NM_001256400.3 → NP_001243329.2  carotenoid-cleaving dioxygenase, mitochondrial isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at downstream start codon compared to variant 1. The encoded protein (isoform e) has a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AP002884
      Consensus CDS
      CCDS58183.1
      UniProtKB/TrEMBL
      B0YIX6
      Related
      ENSP00000431802.1, ENST00000532593.5
      Conserved Domains (1) summary
      pfam03055
      Location:1 → 473
      RPE65; Retinal pigment epithelial membrane protein

    5. NM_031938.7 → NP_114144.5  carotenoid-cleaving dioxygenase, mitochondrial isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform a).
      Source sequence(s)
      AP002884
      Consensus CDS
      CCDS8358.2
      UniProtKB/Swiss-Prot
      B0YIX5, B4DNC3, E9PBI8, E9PJJ1, Q8IUS0, Q96JC8, Q96JY5, Q9BYV7
      UniProtKB/TrEMBL
      B0YIX6
      Related
      ENSP00000350314.5, ENST00000357685.11
      Conserved Domains (1) summary
      pfam03055
      Location:74 → 577
      RPE65; Retinal pigment epithelial membrane protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      112175512..112218946
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      112185841..112229285
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BYV7.5 GenPept UniProtKB/Swiss-Prot:Q9BYV7

    Gene LinkOut

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

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