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

Gene ID: 83875, updated on 10-Dec-2024

Summary

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
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Genomic context

See BCO2 in Genome Data Viewer
Location:
11q23.1
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (112175512..112218946)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (112185841..112229285)
RS_2024_09 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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Pathways from PubChem

General gene information

Markers

Potential readthrough

Included genes: SDHD, TEX12

Clone Names

  • FLJ34464

Gene Ontology Provided by GOA

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

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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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_001037290.4NP_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:29544
    RPE65; Retinal pigment epithelial membrane protein
  2. NM_001256397.3NP_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:29538
    RPE65; Retinal pigment epithelial membrane protein
  3. NM_001256398.3NP_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:63505
    RPE65; Retinal pigment epithelial membrane protein
  4. NM_001256400.3NP_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:1473
    RPE65; Retinal pigment epithelial membrane protein
  5. NM_031938.7NP_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:74577
    RPE65; Retinal pigment epithelial membrane protein

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_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)