Mlycd (malonyl-CoA decarboxylase) - Rat Genome Database

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Gene: Mlycd (malonyl-CoA decarboxylase) Rattus norvegicus
Analyze
Symbol: Mlycd
Name: malonyl-CoA decarboxylase
RGD ID: 620234
Description: Enables malonyl-CoA decarboxylase activity. Involved in several processes, including acetyl-CoA biosynthetic process; fatty acid metabolic process; and response to ischemia. Located in cytosol; mitochondrial matrix; and peroxisomal matrix. Human ortholog(s) of this gene implicated in cardiomyopathy. Orthologous to human MLYCD (malonyl-CoA decarboxylase); PARTICIPATES IN malonic aciduria pathway; methylmalonic aciduria, cobalamin-related pathway; propanoate metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrotoluene; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: malonyl-CoA decarboxylase, mitochondrial; Mcd
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21947,447,931 - 47,463,794 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1947,447,970 - 47,463,793 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1954,242,309 - 54,258,174 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01954,922,657 - 54,938,880 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01957,137,162 - 57,153,264 (+)NCBIRnor_WKY
Rnor_6.01952,032,950 - 52,048,773 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1952,032,886 - 52,048,753 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01962,781,490 - 62,797,313 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41949,637,193 - 49,653,016 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11949,642,073 - 49,657,896 (+)NCBI
Celera1946,707,681 - 46,723,504 (+)NCBICelera
Cytogenetic Map19q12NCBI
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

Cellular Component
cytoplasm  (IDA,ISO)
cytosol  (IDA)
mitochondrial matrix  (IBA,IDA,ISO)
mitochondrion  (IDA)
mitochondrion  (ISO)
peroxisomal matrix  (IBA,IDA)
peroxisome  (IDA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Malonyl coenzyme a decarboxylase inhibition protects the ischemic heart by inhibiting fatty acid oxidation and stimulating glucose oxidation. Dyck JR, etal., Circ Res. 2004 May 14;94(9):e78-84. Epub 2004 Apr 22.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Regulation of fatty acid oxidation of the heart by MCD and ACC during contractile stimulation. Goodwin GW and Taegtmeyer H, Am J Physiol. 1999 Oct;277(4 Pt 1):E772-7.
5. Malonyl-CoA decarboxylase is present in the cytosolic, mitochondrial and peroxisomal compartments of rat hepatocytes. Joly E, etal., FEBS Lett. 2005 Dec 5;579(29):6581-6. Epub 2005 Nov 9.
6. KEGG: Kyoto Encyclopedia of Genes and Genomes KEGG
7. Genomic organization and characterization of the promoter of rat malonyl-CoA decarboxylase gene. Lee GY, etal., Biochim Biophys Acta 2002 Aug 19;1577(1):133-8.
8. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
9. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
10. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
11. Coordinate regulation of malonyl-CoA decarboxylase, sn-glycerol-3-phosphate acyltransferase, and acetyl-CoA carboxylase by AMP-activated protein kinase in rat tissues in response to exercise. Park H, etal., J Biol Chem 2002 Sep 6;277(36):32571-7.
12. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
13. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
14. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
16. MCD encodes peroxisomal and cytoplasmic forms of malonyl-CoA decarboxylase and is mutated in malonyl-CoA decarboxylase deficiency. Sacksteder KA, etal., J Biol Chem. 1999 Aug 27;274(35):24461-8.
17. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
18. Cloning and expression of rat pancreatic beta-cell malonyl-CoA decarboxylase. Voilley N, etal., Biochem J 1999 May 15;340 ( Pt 1):213-7.
19. Assay of the activity of malonyl-coenzyme A decarboxylase by gas chromatography-mass spectrometry. Wang X, etal., Anal Biochem. 2007 Apr 15;363(2):169-74. Epub 2007 Jan 13.
Additional References at PubMed
PMID:9869665   PMID:10417274   PMID:14641110   PMID:14651853   PMID:15003260   PMID:15206948   PMID:15489334   PMID:18314420   PMID:18614015   PMID:20178365   PMID:23746352   PMID:23791943  
PMID:26767982  


Genomics

Comparative Map Data
Mlycd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21947,447,931 - 47,463,794 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1947,447,970 - 47,463,793 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1954,242,309 - 54,258,174 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01954,922,657 - 54,938,880 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01957,137,162 - 57,153,264 (+)NCBIRnor_WKY
Rnor_6.01952,032,950 - 52,048,773 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1952,032,886 - 52,048,753 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01962,781,490 - 62,797,313 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41949,637,193 - 49,653,016 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11949,642,073 - 49,657,896 (+)NCBI
Celera1946,707,681 - 46,723,504 (+)NCBICelera
Cytogenetic Map19q12NCBI
MLYCD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381683,899,115 - 83,927,031 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1683,899,115 - 83,951,445 (+)EnsemblGRCh38hg38GRCh38
GRCh371683,932,720 - 83,960,636 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361682,490,231 - 82,507,288 (+)NCBINCBI36Build 36hg18NCBI36
Build 341682,490,272 - 82,507,277NCBI
Celera1668,233,776 - 68,250,834 (+)NCBICelera
Cytogenetic Map16q23.3NCBI
HuRef1669,684,307 - 69,701,406 (+)NCBIHuRef
CHM1_11685,344,095 - 85,361,152 (+)NCBICHM1_1
T2T-CHM13v2.01689,964,788 - 89,992,706 (+)NCBIT2T-CHM13v2.0
Mlycd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398120,121,591 - 120,148,577 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8120,121,617 - 120,137,841 (+)EnsemblGRCm39 Ensembl
GRCm388119,394,852 - 119,421,838 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8119,394,878 - 119,411,102 (+)EnsemblGRCm38mm10GRCm38
MGSCv378121,918,792 - 121,934,988 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368122,280,869 - 122,297,065 (+)NCBIMGSCv36mm8
MGSCv364123,800,115 - 123,816,910 (+)NCBIMGSCv36mm8
Celera8123,611,072 - 123,627,694 (+)NCBICelera
Cytogenetic Map8E1NCBI
MLYCD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11683,912,793 - 83,929,856 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1683,912,793 - 83,929,162 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01664,520,860 - 64,537,955 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
MLYCD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1568,385,058 - 68,399,965 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl568,384,618 - 68,399,965 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha568,398,888 - 68,413,778 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0568,683,230 - 68,698,120 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl568,683,230 - 68,698,120 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1568,631,023 - 68,645,876 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0568,467,455 - 68,482,348 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0568,883,325 - 68,898,237 (-)NCBIUU_Cfam_GSD_1.0
Mlycd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934928,082,871 - 28,110,598 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049366413,836,418 - 3,846,485 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MLYCD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl64,681,664 - 4,698,661 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.164,683,386 - 4,698,698 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
MLYCD
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1569,312,978 - 69,329,346 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl569,313,062 - 69,329,102 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660476,492,522 - 6,508,731 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Mlycd
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247463,604,773 - 3,619,775 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247463,604,773 - 3,619,790 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Mlycd
96 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:195
Count of miRNA genes:139
Interacting mature miRNAs:154
Transcripts:ENSRNOT00000019923
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194434021455283277Rat

Markers in Region
RH144263  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21947,458,178 - 47,458,333 (+)MAPPERmRatBN7.2
Rnor_6.01952,043,158 - 52,043,312NCBIRnor6.0
Rnor_5.01962,791,698 - 62,791,852UniSTSRnor5.0
RGSC_v3.41949,647,401 - 49,647,555UniSTSRGSC3.4
Celera1946,717,889 - 46,718,043UniSTS
RH 3.4 Map19650.4UniSTS
Cytogenetic Map19q12UniSTS
AI044337  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21947,463,485 - 47,463,699 (+)MAPPERmRatBN7.2
Rnor_6.01952,048,465 - 52,048,678NCBIRnor6.0
Rnor_5.01962,797,005 - 62,797,218UniSTSRnor5.0
RGSC_v3.41949,652,708 - 49,652,921UniSTSRGSC3.4
Celera1946,723,196 - 46,723,409UniSTS
RH 3.4 Map19633.5UniSTS
Cytogenetic Map19q12UniSTS
Mlycd  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21947,463,126 - 47,463,196 (+)MAPPERmRatBN7.2
Rnor_6.01952,048,106 - 52,048,175NCBIRnor6.0
Rnor_5.01962,796,646 - 62,796,715UniSTSRnor5.0
RGSC_v3.41949,652,349 - 49,652,418UniSTSRGSC3.4
Celera1946,722,837 - 46,722,906UniSTS
Cytogenetic Map19q12UniSTS


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 renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 17 41 8 11 74 35 36 11 8
Low 2 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019923   ⟹   ENSRNOP00000019923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1947,447,970 - 47,463,793 (+)Ensembl
Rnor_6.0 Ensembl1952,032,886 - 52,048,753 (+)Ensembl
RefSeq Acc Id: NM_053477   ⟹   NP_445929
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21947,447,931 - 47,463,794 (+)NCBI
Rnor_6.01952,032,950 - 52,048,773 (+)NCBI
Rnor_5.01962,781,490 - 62,797,313 (+)NCBI
RGSC_v3.41949,637,193 - 49,653,016 (+)RGD
Celera1946,707,681 - 46,723,504 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_445929   ⟸   NM_053477
- UniProtKB: Q9WUY2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000019923   ⟸   ENSRNOT00000019923

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q920F5-F1-model_v2 AlphaFold Q920F5 1-492 view protein structure

Transcriptome

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

Promoters
RGD ID:13701178
Promoter ID:EPDNEW_R11700
Type:initiation region
Name:Mlycd_1
Description:malonyl-CoA decarboxylase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01952,032,907 - 52,032,967EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620234 AgrOrtholog
BioCyc Gene G2FUF-5521 BioCyc
Ensembl Genes ENSRNOG00000014522 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000019923 ENTREZGENE
  ENSRNOP00000019923.3 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000019923 ENTREZGENE
  ENSRNOT00000019923.6 UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.140.90 UniProtKB/Swiss-Prot
  3.40.630.150 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5621015 IMAGE-MGC_LOAD
InterPro Malonyl_CoA_deC UniProtKB/Swiss-Prot
  Malonyl_CoA_deC_C UniProtKB/Swiss-Prot
  Malonyl_CoA_deC_C_sf UniProtKB/Swiss-Prot
  MCD_N UniProtKB/Swiss-Prot
  MCD_N_sf UniProtKB/Swiss-Prot
KEGG Report rno:85239 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72361 IMAGE-MGC_LOAD
NCBI Gene 85239 ENTREZGENE
PANTHER MALONYL-COA DECARBOXYLASE, MITOCHONDRIAL UniProtKB/Swiss-Prot
  PTHR28641 UniProtKB/Swiss-Prot
Pfam MCD UniProtKB/Swiss-Prot
  MCD_N UniProtKB/Swiss-Prot
PhenoGen Mlycd PhenoGen
UniProt DCMC_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q9WUY2 ENTREZGENE
UniProt Secondary Q9WUY2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Mlycd  malonyl-CoA decarboxylase      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Mlycd  malonyl-CoA decarboxylase      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in liver, skeletal muscle, and adipose tissue 631891
gene_regulation enzyme activity increases in response to exercise 631891