Ddo (D-aspartate oxidase) - Rat Genome Database

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Gene: Ddo (D-aspartate oxidase) Rattus norvegicus
Analyze
Symbol: Ddo
Name: D-aspartate oxidase
RGD ID: 1595123
Description: Enables D-aspartate oxidase activity and FAD binding activity. Involved in D-amino acid catabolic process. Located in peroxisome. Orthologous to human DDO (D-aspartate oxidase); PARTICIPATES IN Canavan disease pathway; alanine, aspartate and glutamate metabolic pathway; INTERACTS WITH (+)-schisandrin B; acrylamide; alpha-Zearalanol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: D-aspartate oxidase-like; DASOX; DASPO; LOC100911156; LOC685325; similar to D-aspartate oxidase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82045,673,486 - 45,693,056 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2045,675,532 - 45,715,758 (+)EnsemblGRCr8
mRatBN7.22044,090,823 - 44,109,962 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2044,090,914 - 44,133,095 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2045,870,156 - 45,889,246 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02045,529,289 - 45,548,385 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02046,247,362 - 46,266,311 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02048,739,812 - 48,758,958 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2048,739,639 - 48,758,905 (-)Ensemblrn6Rnor6.0
Rnor_5.02050,384,344 - 50,403,396 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42044,766,925 - 44,786,836 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2044,899,117 - 44,918,244 (+)NCBICelera
Cytogenetic Map20q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IEA,ISO)
peroxisomal matrix  (IBA,IEA,ISS)
peroxisome  (IDA,IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat d-aspartate oxidase is more similar to the human enzyme than the mouse enzyme. Katane M, etal., Biochim Biophys Acta Proteins Proteom. 2018 Jul;1866(7):806-812. doi: 10.1016/j.bbapap.2017.12.009. Epub 2017 Dec 29.
3. Biochemical characterization of d-aspartate oxidase from Caenorhabditis elegans: its potential use in the determination of free d-glutamate in biological samples. Katane M, etal., Biochim Biophys Acta Proteins Proteom. 2020 Aug;1868(8):140442. doi: 10.1016/j.bbapap.2020.140442. Epub 2020 May 3.
4. Characterization of the enzymatic and structural properties of human D-aspartate oxidase and comparison with those of the rat and mouse enzymes. Katane M, etal., Biol Pharm Bull. 2015;38(2):298-305. doi: 10.1248/bpb.b14-00690.
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. D-aspartate oxidase, a peroxisomal enzyme in liver of rat and man. Van Veldhoven PP, etal., Biochim Biophys Acta. 1991 Jan 23;1073(1):203-8. doi: 10.1016/0304-4165(91)90203-s.
10. Cellular and subcellular distribution of D-aspartate oxidase in human and rat brain. Zaar K, etal., J Comp Neurol. 2002 Aug 26;450(3):272-82. doi: 10.1002/cne.10320.
Additional References at PubMed
PMID:9163533   PMID:16525061   PMID:20178365   PMID:20603179  


Genomics

Comparative Map Data
Ddo
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82045,673,486 - 45,693,056 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2045,675,532 - 45,715,758 (+)EnsemblGRCr8
mRatBN7.22044,090,823 - 44,109,962 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2044,090,914 - 44,133,095 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2045,870,156 - 45,889,246 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02045,529,289 - 45,548,385 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02046,247,362 - 46,266,311 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02048,739,812 - 48,758,958 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2048,739,639 - 48,758,905 (-)Ensemblrn6Rnor6.0
Rnor_5.02050,384,344 - 50,403,396 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42044,766,925 - 44,786,836 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2044,899,117 - 44,918,244 (+)NCBICelera
Cytogenetic Map20q12NCBI
DDO
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386110,388,321 - 110,415,575 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6110,391,771 - 110,415,862 (-)Ensemblhg38GRCh38
GRCh376110,709,524 - 110,736,778 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366110,820,076 - 110,843,446 (-)NCBIBuild 36Build 36hg18NCBI36
Build 346110,820,076 - 110,843,446NCBI
Celera6111,460,002 - 111,483,375 (-)NCBICelera
Cytogenetic Map6q21NCBI
HuRef6108,280,297 - 108,303,682 (-)NCBIHuRef
CHM1_16110,976,574 - 110,999,941 (-)NCBICHM1_1
T2T-CHM13v2.06111,566,803 - 111,594,070 (-)NCBIT2T-CHM13v2.0
Ddo
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391040,505,933 - 40,557,847 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1040,506,007 - 40,557,843 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381040,630,011 - 40,681,847 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1040,630,011 - 40,681,847 (+)Ensemblmm10GRCm38
MGSCv371040,349,817 - 40,369,737 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361040,319,451 - 40,338,387 (+)NCBIMGSCv36mm8
Celera1041,519,749 - 41,540,710 (+)NCBICelera
Cytogenetic Map10B1NCBI
cM Map1022.0NCBI
Ddo
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541135,143,735 - 35,163,276 (-)Ensembl
ChiLan1.0NW_00495541135,142,415 - 35,163,234 (-)NCBIChiLan1.0ChiLan1.0
DDO
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25130,404,773 - 130,429,463 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16128,290,785 - 128,315,497 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06108,199,861 - 108,223,844 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16112,269,271 - 112,292,980 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6112,269,271 - 112,292,980 (-)EnsemblpanPan2panpan1.1
DDO
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11267,080,646 - 67,104,429 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1267,081,329 - 67,104,397 (-)NCBIcanFam3CanFam3.1
CanFam3.1 Ensembl1267,081,329 - 67,104,397 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1266,885,507 - 66,924,087 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01267,950,181 - 67,988,830 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1267,965,688 - 67,988,779 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11267,316,440 - 67,340,123 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01267,163,368 - 67,186,153 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01267,419,791 - 67,458,386 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ddo
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946102,005,153 - 102,025,014 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365646,280,014 - 6,299,856 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365646,280,890 - 6,299,838 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DDO
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl176,391,116 - 76,417,301 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1176,391,112 - 76,417,147 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2185,867,147 - 85,892,926 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DDO
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11363,484,726 - 63,510,181 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604035,777,187 - 35,805,285 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ddo
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249161,490,226 - 1,522,212 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046249161,488,912 - 1,522,175 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ddo
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11840,391,262 - 40,408,485 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ddo
138 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:28
Interacting mature miRNAs:28
Transcripts:ENSRNOT00000000710
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202668936256021148Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)20418947649189476Rat
1598858Cm61Cardiac mass QTL 613.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)20821635953216359Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202679235356021148Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)201224324249189476Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202668936256021148Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202074558556021148Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202668936256021148Rat
1598870Bp289Blood pressure QTL 2892.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)20821635953216359Rat
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203215696745978663Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202668936256021148Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
9 11 54 130 79 78 47 36 47 6 266 122 9 102 80 90 31 6 6

Sequence


Ensembl Acc Id: ENSRNOT00000000710   ⟹   ENSRNOP00000000710
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2045,675,532 - 45,693,632 (+)Ensembl
mRatBN7.2 Ensembl2044,090,914 - 44,110,399 (+)Ensembl
Rnor_6.0 Ensembl2048,739,639 - 48,758,905 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000079308
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2045,675,532 - 45,715,758 (+)Ensembl
mRatBN7.2 Ensembl2044,090,914 - 44,133,095 (+)Ensembl
Rnor_6.0 Ensembl2045,681,159 - 45,684,630 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000085769
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2045,682,816 - 45,684,630 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000102857   ⟹   ENSRNOP00000087688
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2045,675,532 - 45,714,819 (+)Ensembl
mRatBN7.2 Ensembl2044,090,914 - 44,132,156 (+)Ensembl
RefSeq Acc Id: NM_001109465   ⟹   NP_001102935
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82045,673,577 - 45,692,631 (+)NCBI
mRatBN7.22044,090,914 - 44,109,962 (+)NCBI
Rnor_6.02048,739,812 - 48,758,896 (-)NCBI
Rnor_5.02050,384,344 - 50,403,396 (-)NCBI
RGSC_v3.42044,766,925 - 44,786,836 (+)RGD
Celera2044,899,117 - 44,918,244 (+)RGD
Sequence:
RefSeq Acc Id: XM_017601772   ⟹   XP_017457261
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82045,673,486 - 45,693,056 (+)NCBI
mRatBN7.22044,090,823 - 44,109,387 (+)NCBI
Rnor_6.02048,740,386 - 48,758,958 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063279507   ⟹   XP_063135577
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82045,673,579 - 45,693,056 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102935 (Get FASTA)   NCBI Sequence Viewer  
  XP_017457261 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135577 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAP34602 (Get FASTA)   NCBI Sequence Viewer  
  D3ZDM7 (Get FASTA)   NCBI Sequence Viewer  
  EDL83239 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000000710
  ENSRNOP00000000710.3
RefSeq Acc Id: NP_001102935   ⟸   NM_001109465
- UniProtKB: D3ZDM7 (UniProtKB/TrEMBL),   A6KTC0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457261   ⟸   XM_017601772
- Peptide Label: isoform X1
- UniProtKB: A6KTC1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000000710   ⟸   ENSRNOT00000000710
Ensembl Acc Id: ENSRNOP00000087688   ⟸   ENSRNOT00000102857
RefSeq Acc Id: XP_063135577   ⟸   XM_063279507
- Peptide Label: isoform X2
Protein Domains
FAD dependent oxidoreductase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZDM7-F1-model_v2 AlphaFold D3ZDM7 1-341 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595123 AgrOrtholog
BioCyc Gene G2FUF-3420 BioCyc
Ensembl Genes ENSRNOG00000000582 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00000060093 Ensembl
Ensembl Transcript ENSRNOT00000000710 ENTREZGENE
  ENSRNOT00000000710.6 UniProtKB/Swiss-Prot
Gene3D-CATH D-Amino Acid Oxidase, subunit A, domain 2 UniProtKB/Swiss-Prot
  NAD(P)-binding Rossmann-like Domain UniProtKB/Swiss-Prot
InterPro D-amino_acid_oxidase_CS UniProtKB/Swiss-Prot
  DAO UniProtKB/Swiss-Prot
  FAD-dep_OxRdtase UniProtKB/Swiss-Prot
KEGG Report rno:685325 UniProtKB/Swiss-Prot
NCBI Gene 685325 ENTREZGENE
PANTHER D-AMINO ACID OXIDASE UniProtKB/Swiss-Prot
  D-ASPARTATE OXIDASE UniProtKB/Swiss-Prot
Pfam DAO UniProtKB/Swiss-Prot
PhenoGen Ddo PhenoGen
PIRSF D-aa_oxidase UniProtKB/Swiss-Prot
PROSITE DAO UniProtKB/Swiss-Prot
  PROKAR_LIPOPROTEIN UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000000582 RatGTEx
  ENSRNOG00000060093 RatGTEx
Superfamily-SCOP FAD-linked reductases, C-terminal domain UniProtKB/Swiss-Prot
  Nucleotide-binding domain UniProtKB/Swiss-Prot
UniProt A0A8I6A7Q0_RAT UniProtKB/TrEMBL
  A0A8I6AVP8_RAT UniProtKB/TrEMBL
  A6KTC0 ENTREZGENE
  A6KTC1 ENTREZGENE, UniProtKB/TrEMBL
  D3ZDM7 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A6KTC0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Ddo  D-aspartate oxidase  LOC100911156  D-aspartate oxidase-like  Data merged from RGD:6494712 737654 PROVISIONAL
2012-07-05 LOC100911156  D-aspartate oxidase-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-05 Ddo  D-aspartate oxidase  LOC685325  similar to D-aspartate oxidase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC685325  similar to D-aspartate oxidase      Symbol and Name status set to provisional 70820 PROVISIONAL