BCO1 (beta-carotene oxygenase 1) - Rat Genome Database

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Gene: BCO1 (beta-carotene oxygenase 1) Canis lupus familiaris
Analyze
Symbol: BCO1
Name: beta-carotene oxygenase 1
RGD ID: 12082325
Description: ENCODES a protein that exhibits beta-carotene 15,15'-dioxygenase activity (ortholog); INVOLVED IN beta-carotene metabolic process (ortholog); retinal metabolic process (ortholog); PARTICIPATES IN retinol metabolic pathway; vitamin A deficiency pathway; ASSOCIATED WITH genetic disease (ortholog); giant axonal neuropathy 1 (ortholog); Hypercarotenemia and Vitamin A Deficiency, Autosomal Dominant (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: BCMO1; beta,beta-carotene 15,15'-dioxygenase; beta,beta-carotene 15,15'-monooxygenase; beta-carotene 15,15'-monooxygenase 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1570,598,743 - 70,637,273 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl570,599,284 - 70,637,017 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha570,547,948 - 70,586,427 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0570,903,713 - 70,942,206 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl570,903,715 - 70,942,392 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1570,846,152 - 70,884,642 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0570,681,343 - 70,719,822 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0571,159,198 - 71,197,682 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
BCO1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1570,598,743 - 70,637,273 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl570,599,284 - 70,637,017 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha570,547,948 - 70,586,427 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0570,903,713 - 70,942,206 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl570,903,715 - 70,942,392 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1570,846,152 - 70,884,642 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0570,681,343 - 70,719,822 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0571,159,198 - 71,197,682 (-)NCBIUU_Cfam_GSD_1.0
BCO1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381681,238,689 - 81,291,142 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1681,238,689 - 81,291,142 (+)EnsemblGRCh38hg38GRCh38
GRCh371681,272,294 - 81,324,747 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361679,829,797 - 79,882,248 (+)NCBINCBI36Build 36hg18NCBI36
Build 341679,829,796 - 79,882,248NCBI
Celera1665,569,740 - 65,622,032 (+)NCBICelera
Cytogenetic Map16q23.2NCBI
HuRef1667,027,575 - 67,079,925 (+)NCBIHuRef
CHM1_11682,683,655 - 82,736,052 (+)NCBICHM1_1
T2T-CHM13v2.01687,299,473 - 87,351,905 (+)NCBIT2T-CHM13v2.0
Bco1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398117,822,590 - 117,860,459 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8117,822,593 - 117,860,459 (+)EnsemblGRCm39 Ensembl
GRCm388117,095,851 - 117,133,720 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8117,095,854 - 117,133,720 (+)EnsemblGRCm38mm10GRCm38
MGSCv378119,619,765 - 119,657,620 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368119,981,842 - 120,019,458 (+)NCBIMGSCv36mm8
Celera8121,315,369 - 121,353,295 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map863.61NCBI
Bco1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81962,058,061 - 62,094,923 (+)NCBIGRCr8
mRatBN7.21945,149,250 - 45,186,102 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1945,149,265 - 45,186,101 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1951,959,095 - 51,995,942 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01952,612,116 - 52,648,960 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01954,856,354 - 54,893,189 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01949,637,059 - 49,673,577 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1949,637,016 - 49,673,808 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01960,424,580 - 60,460,636 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41947,202,955 - 47,239,225 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11947,207,835 - 47,244,106 (+)NCBI
Celera1944,421,345 - 44,457,802 (+)NCBICelera
Cytogenetic Map19q12NCBI
Bco1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555223,985,266 - 4,018,886 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555223,985,515 - 4,018,116 (+)NCBIChiLan1.0ChiLan1.0
BCO1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21890,987,587 - 91,047,027 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11696,908,478 - 96,962,121 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01661,843,567 - 61,897,012 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11681,270,957 - 81,323,088 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1681,270,577 - 81,323,088 (+)Ensemblpanpan1.1panPan2
Bco1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934930,698,707 - 30,729,976 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647528,859,318 - 28,889,934 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647528,859,222 - 28,890,407 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BCO1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl67,012,332 - 7,055,305 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.167,008,330 - 7,054,089 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
BCO1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1566,681,756 - 66,730,832 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl566,681,513 - 66,733,604 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660479,105,596 - 9,155,354 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Bco1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247466,143,892 - 6,180,408 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247466,146,338 - 6,181,020 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in BCO1
439 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium 4 4 4
Low 3 2 2 2 5 5 1
Below cutoff 2 5 16 6 1 6 7 8 9 6

Sequence


RefSeq Acc Id: ENSCAFT00000031845   ⟹   ENSCAFP00000029650
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl570,599,284 - 70,637,017 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845035136   ⟹   ENSCAFP00845027503
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl570,903,715 - 70,942,392 (-)Ensembl
RefSeq Acc Id: XM_014113991   ⟹   XP_013969466
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1570,598,743 - 70,632,931 (-)NCBI
Dog10K_Boxer_Tasha570,547,948 - 70,579,548 (-)NCBI
Sequence:
RefSeq Acc Id: XM_022419143   ⟹   XP_022274851
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1570,598,743 - 70,637,273 (-)NCBI
Dog10K_Boxer_Tasha570,547,948 - 70,586,427 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038477024   ⟹   XP_038332952
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1570,846,152 - 70,884,642 (-)NCBI
RefSeq Acc Id: XM_038477025   ⟹   XP_038332953
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1570,846,152 - 70,877,763 (-)NCBI
RefSeq Acc Id: XM_038538209   ⟹   XP_038394137
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0571,159,198 - 71,197,682 (-)NCBI
RefSeq Acc Id: XM_038538210   ⟹   XP_038394138
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0571,159,198 - 71,190,803 (-)NCBI
RefSeq Acc Id: XM_038602336   ⟹   XP_038458264
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0570,681,343 - 70,719,822 (-)NCBI
RefSeq Acc Id: XM_038602337   ⟹   XP_038458265
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0570,681,343 - 70,712,943 (-)NCBI
RefSeq Acc Id: XM_038666943   ⟹   XP_038522871
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0570,903,713 - 70,942,206 (-)NCBI
RefSeq Acc Id: XM_038666944   ⟹   XP_038522872
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0570,903,713 - 70,935,325 (-)NCBI
RefSeq Acc Id: XP_013969466   ⟸   XM_014113991
- Peptide Label: isoform X2
- UniProtKB: A0A8P0NL42 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_022274851   ⟸   XM_022419143
- Peptide Label: isoform X1
- UniProtKB: A0A8C0T2J0 (UniProtKB/TrEMBL),   A0A8I3PIC4 (UniProtKB/TrEMBL),   A0A8P0NL42 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000029650   ⟸   ENSCAFT00000031845
RefSeq Acc Id: XP_038332952   ⟸   XM_038477024
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038332953   ⟸   XM_038477025
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038458264   ⟸   XM_038602336
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038458265   ⟸   XM_038602337
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038522871   ⟸   XM_038666943
- Peptide Label: isoform X1
- UniProtKB: A0A8C0T2J0 (UniProtKB/TrEMBL),   A0A8I3PIC4 (UniProtKB/TrEMBL),   A0A8P0NL42 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038522872   ⟸   XM_038666944
- Peptide Label: isoform X2
- UniProtKB: A0A8P0NL42 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038394137   ⟸   XM_038538209
- Peptide Label: isoform X1
- UniProtKB: A0A8P0NL42 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038394138   ⟸   XM_038538210
- Peptide Label: isoform X2
- UniProtKB: A0A8P0NL42 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845027503   ⟸   ENSCAFT00845035136

Promoters
RGD ID:13683412
Promoter ID:EPDNEW_C1482
Type:multiple initiation site
Name:BCO1_1
Description:beta-carotene oxygenase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1570,637,158 - 70,637,218EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000020006 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030001278 UniProtKB/TrEMBL
  ENSCAFG00040018455 UniProtKB/TrEMBL
  ENSCAFG00845019952 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000031845.5 UniProtKB/TrEMBL
  ENSCAFT00000106160.1 UniProtKB/TrEMBL
  ENSCAFT00030002276.1 UniProtKB/TrEMBL
  ENSCAFT00040034178.1 UniProtKB/TrEMBL
  ENSCAFT00845035136 ENTREZGENE
  ENSCAFT00845035136.1 UniProtKB/TrEMBL
InterPro Carotenoid_Oase UniProtKB/TrEMBL
NCBI Gene BCO1 ENTREZGENE
PANTHER BETA,BETA-CAROTENE 15,15'-DIOXYGENASE UniProtKB/TrEMBL
  PTHR10543 UniProtKB/TrEMBL
Pfam RPE65 UniProtKB/TrEMBL
UniProt A0A8C0T2J0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PIC4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0NL42 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:38417 ENTREZGENE