Aliases for HMGCS2 Gene
Aliases for HMGCS2 Gene
External Ids for HMGCS2 Gene
- HGNC: 5008
- Entrez Gene: 3158
- Ensembl: ENSG00000134240
- OMIM: 600234
- UniProtKB: P54868
Previous GeneCards Identifiers for HMGCS2 Gene
- GC01M120737
- GC01M119128
- GC01M119438
- GC01M119637
- GC01M120003
- GC01M120092
- GC01M120290
- GC01M118149
Summaries for HMGCS2 Gene
-
The protein encoded by this gene belongs to the HMG-CoA synthase family. It is a mitochondrial enzyme that catalyzes the first reaction of ketogenesis, a metabolic pathway that provides lipid-derived energy for various organs during times of carbohydrate deprivation, such as fasting. Mutations in this gene are associated with HMG-CoA synthase deficiency. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]
GeneCards Summary for HMGCS2 Gene
HMGCS2 (3-Hydroxy-3-Methylglutaryl-CoA Synthase 2) is a Protein Coding gene. Diseases associated with HMGCS2 include Hmg-Coa Synthase-2 Deficiency and Smith-Lemli-Opitz Syndrome. Among its related pathways are Validated targets of C-MYC transcriptional repression and Ketone body metabolism. GO annotations related to this gene include hydroxymethylglutaryl-CoA synthase activity. An important paralog of this gene is HMGCS1.
UniProtKB/Swiss-Prot for HMGCS2 Gene
-
This enzyme condenses acetyl-CoA with acetoacetyl-CoA to form HMG-CoA, which is the substrate for HMG-CoA reductase.
No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HMGCS2 Gene
Genomics for HMGCS2 Gene
Regulatory Elements for HMGCS2 Gene
| GeneHancer Identifier | Enhancer Score | Enhancer Sources | Gene-Enhancer Score | TSS distance (kb) | Number of Genes Away | Size (kb) | Transcription Factor Binding Sites within enhancer | Gene Targets for Enhancer |
|---|---|---|---|---|---|---|---|---|
| GH01G119789 | 1 | ENCODE dbSUPER | 27.8 | -21.8 | -21757 | 2.4 | ELF3 SOX13 TFAP4 FOXA2 TAF1 TEAD4 MAX RAD21 RARA YY1 | HMGCS2 REG4 ADAM30 |
| GH01G119778 | 1.5 | Ensembl ENCODE dbSUPER | 15.8 | -10.9 | -10850 | 2.3 | FOXA2 MLX YY1 FOS YY2 ZHX2 REST PPARG ZNF518A KAT8 | HMGCS2 REG4 |
| GH01G119782 | 1.4 | Ensembl ENCODE dbSUPER | 16 | -16.5 | -16546 | 6.9 | PKNOX1 RAD21 RARA YY1 ZNF766 ZNF366 FOS U2AF2 CEBPB REST | PHGDH REG4 HMGCS2 ADAM30 LOC101929147 WARS2 |
| GH01G119772 | 1.3 | Ensembl ENCODE dbSUPER | 15.4 | -5.5 | -5457 | 4.2 | BCOR FOXA2 TAF1 CHD4 ZMYM3 ZNF384 YY1 ZNF664 GATA3 SCRT2 | HMGCS2 ADAM30 REG4 |
| GH01G119793 | 0.5 | dbSUPER | 27.3 | -25.8 | -25844 | 2.0 | ZFHX2 MAZ FOXA2 EGR2 | HMGCS2 ADAM30 PHGDH ZNF697 REG4 |
- Transcription factor binding sites by QIAGEN in the HMGCS2 gene promoter:
Regulatory Element Products
Genomic Location for HMGCS2 Gene
- Chromosome:
- 1
- Start:
- 119,747,996 bp from pter
- End:
- 119,769,125 bp from pter
- Size:
- 21,130 bases
- Orientation:
- Minus strand
Genomic View for HMGCS2 Gene
- Cytogenetic band:
-
- 1p12 by Ensembl
- 1p12 by Entrez Gene
- 1p12 by HGNC
Genomic Neighborhood
• Exon Structure
• Gene Density
RefSeq DNA sequence for HMGCS2 Gene
Proteins for HMGCS2 Gene
-
Protein details for HMGCS2 Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- P54868-HMCS2_HUMAN
- Recommended name:
- Hydroxymethylglutaryl-CoA synthase, mitochondrial
- Protein Accession:
- P54868
- B7Z8R3
- D3Y5K6
- Q5SZU2
- Q6IBF4
Protein attributes for HMGCS2 Gene
- Size:
- 508 amino acids
- Molecular mass:
- 56635 Da
- Quaternary structure:
-
- Homodimer.
Protein Expression for HMGCS2 Gene
Selected DME Specific Peptides for HMGCS2 Gene
- P54868:
-
- RPTGGAGAVAML
- VVCGDIA
- LAGSRIGAFSYGSGLAASF
- EVYFPAQYVDQT
- SYGSGLAASFFSF
- VDGKLSIQCYL
- VQKSLAR
- GNARPTGG
- YGCLASLL
- ESSSWDGRYA
- EDINSLCLTVV
- TNACYGGTA
- MGFCSVQED
- CYLRALD
- MIFHTPFCK
Post-translational modifications for HMGCS2 Gene
- Succinylated. Desuccinylated by SIRT5. Succinylation, at least at Lys-83 and Lys-310, inhibits the enzymatic activity.
- Modification sites at PhosphoSitePlus
- Modification sites at neXtProt
Other Protein References for HMGCS2 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
-
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-
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-
Santa Cruz Biotechnology (SCBT) Antibodies for HMGCS2
Protein Products
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Assay Products
- antibodies-online Kits for HMGCS2: See all 10
Domains & Families for HMGCS2 Gene
Protein Domains for HMGCS2 Gene
- InterPro:
- Blocks:
- ProtoNet:
Suggested Antigen Peptide Sequences for HMGCS2 Gene
- GenScript: Design optimal peptide antigens:
Graphical View of Domain Structure for InterPro Entry
P54868- Family:
-
- Belongs to the HMG-CoA synthase family.
No data available for Gene Families for HMGCS2 Gene
Function for HMGCS2 Gene
Molecular function for HMGCS2 Gene
- GENATLAS Biochemistry:
- 3-hydroxy-3-methylglutaryl-CoA synthase 2,mitochondrial,first and regulating enzyme of ketogenic pathway,through association with PPARA
- UniProtKB/Swiss-Prot CatalyticActivity:
- Acetyl-CoA + H(2)O + acetoacetyl-CoA = (S)-3-hydroxy-3-methylglutaryl-CoA + CoA.
- UniProtKB/Swiss-Prot Function:
- This enzyme condenses acetyl-CoA with acetoacetyl-CoA to form HMG-CoA, which is the substrate for HMG-CoA reductase.
Enzyme Numbers (IUBMB) for HMGCS2 Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0004421 | hydroxymethylglutaryl-CoA synthase activity | TAS | -- |
| GO:0016740 | transferase activity | IEA | -- |
Phenotypes for HMGCS2 Gene
- GenomeRNAi human phenotypes for HMGCS2:
-
- Increased vaccinia virus (VACV) infection
- Decreased viability in esophageal squamous lineage
- Decreased viability ratio
- Decreased human papilloma virus 16 (HPV16) pseudovirus infection
- Increased shRNA abundance (Z-score > 2)
- Decreased shRNA abundance (Z-score < -2)
- Increased shRNA abundance
- Downregulation of Wnt pathway after Wnt3A stimulation
Animal Model Products
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-
ViGene Biosciences lentiviral particle packaged cDNA for HMGCS2 gene
-
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CRISPR Products
-
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-
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miRNA Products
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Inhibitory RNA Products
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Clone Products
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Cell Line Products
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-
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Flow Cytometry Products
No data available for Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for HMGCS2 Gene
Localization for HMGCS2 Gene
Subcellular locations from UniProtKB/Swiss-Prot for HMGCS2 Gene
- Mitochondrion.
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005739 | mitochondrion | TAS,IDA | -- |
| GO:0005743 | mitochondrial inner membrane | IEA | -- |
| GO:0005759 | mitochondrial matrix | TAS | -- |
Pathways & Interactions for HMGCS2 Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | Terpenoid backbone biosynthesis | ||
| 2 | Ketone body metabolism |
.01
|
|
| 3 | Metabolism |
.37
|
|
| 4 | Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha) | ||
| 5 | Butanoate metabolism | ||
Pathways by source for HMGCS2 Gene
7 BioSystems pathways for HMGCS2 Gene
7 Reactome pathways for HMGCS2 Gene
6 KEGG pathways for HMGCS2 Gene
UniProtKB/Swiss-Prot P54868-HMCS2_HUMAN
- Pathway: Metabolic intermediate biosynthesis; (R)-mevalonate biosynthesis; (R)-mevalonate from acetyl-CoA: step 2/3.
Interacting Proteins for HMGCS2 Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0006629 | lipid metabolic process | IEA | -- |
| GO:0006694 | steroid biosynthetic process | IEA | -- |
| GO:0006695 | cholesterol biosynthetic process | IEA | -- |
| GO:0008152 | metabolic process | IEA | -- |
| GO:0008202 | steroid metabolic process | IEA | -- |
No data available for SIGNOR curated interactions for HMGCS2 Gene
Drugs & Compounds for HMGCS2 Gene
| Name | Synonyms | Role | CAS Number | PubChem IDs | PubMed IDs | |
|---|---|---|---|---|---|---|
| 3-hydroxy-3-methylglutaryl-coa |
|
1553-55-5 | ||||
| 7-dehydrocholesterol |
|
434-16-2 | ||||
| acetyl-coa |
|
72-89-9 |
|
Transcripts for HMGCS2 Gene
mRNA/cDNA for HMGCS2 Gene
- (3) REFSEQ mRNAs :
- (10) Additional mRNA sequences :
- (185) Selected AceView cDNA sequences:
- (4) Ensembl transcripts including schematic representations, and UCSC links where relevant :
Unigene Clusters for HMGCS2 Gene
CRISPR Products
-
OriGene CRISPR knockouts for HMGCS2
-
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miRNA Products
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Inhibitory RNA Products
- Origene RNAi, siRNA, and shRNA products in human, mouse, rat for HMGCS2
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-
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Clone Products
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Flow Cytometry Products
| ExUns: | 1a | · | 1b | ^ | 2 | ^ | 3 | ^ | 4a | · | 4b | ^ | 5 | ^ | 6a | · | 6b | ^ | 7a | · | 7b | ^ | 8a | · | 8b | ^ | 9 | ^ | 10a | · | 10b | ^ | 11a | · | 11b |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SP1: | - | - | |||||||||||||||||||||||||||||||||
| SP2: | - | - | - | ||||||||||||||||||||||||||||||||
| SP3: | - | - | |||||||||||||||||||||||||||||||||
| SP4: | - | - | |||||||||||||||||||||||||||||||||
| SP5: |
Expression for HMGCS2 Gene
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
- Neural Tube (Nervous System)
- Brain (Nervous System)
-
Heart (Cardiovascular System)
- Atrioventricular Node Cells Atrioventricular Node
- Atrioventricular Canal Cells Atrioventricular Canal
- Liver (Hepatobiliary System)
- Kidney (Urinary System)
-
Ovary (Reproductive System)
- Pre-Granulosa Cells Primordial Follicle
- Spleen (Hematopoietic System)
- Gut Tube (Gastrointestinal Tract)
- Intestine (Gastrointestinal Tract)
- Bone (Muscoskeletal System)
- Pancreas (Endocrine System)
- NULL (Uncategorized)
-
Colon (Gastrointestinal Tract)
-
Stomach (Gastrointestinal Tract)
mRNA differential expression in normal tissues according to GTEx for HMGCS2 Gene
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HMGCS2 Gene
NURSA nuclear receptor signaling pathways regulating expression of HMGCS2 Gene:
HMGCS2SOURCE GeneReport for Unigene cluster for HMGCS2 Gene:
Hs.59889mRNA Expression by UniProt/SwissProt for HMGCS2 Gene:
P54868-HMCS2_HUMANEvidence on tissue expression from TISSUES for HMGCS2 Gene
- Liver(4.9)
- Nervous system(4.2)
- Intestine(2.4)
- Stomach(2.3)
Phenotype-based relationships between genes and organs from Gene ORGANizer for HMGCS2 Gene
- ectoderm
- mesoderm
- cardiovascular
- endocrine
- integumentary
- nervous
- brain
- ear
- head
- heart
- adrenal gland
- peripheral nerve
- peripheral nervous system
- skin
- sweat gland
Primer Products
-
OriGene qPCR primer pairs for HMGCS2
-
OriGene qPCR primer pairs and template standards for HMGCS2
No data available for Protein tissue co-expression partners for HMGCS2 Gene
Orthologs for HMGCS2 Gene
This gene was present in the common ancestor of eukaryotes.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | HMGCS2 34 35 |
|
||
| dog (Canis familiaris) |
Mammalia | HMGCS2 34 35 |
|
||
| cow (Bos Taurus) |
Mammalia | HMGCS2 34 35 |
|
||
| mouse (Mus musculus) |
Mammalia | Hmgcs2 34 16 35 |
|
||
| rat (Rattus norvegicus) |
Mammalia | Hmgcs2 34 |
|
||
| oppossum (Monodelphis domestica) |
Mammalia | HMGCS2 35 |
|
OneToOne | |
| platypus (Ornithorhynchus anatinus) |
Mammalia | HMGCS2 35 |
|
OneToOne | |
| chicken (Gallus gallus) |
Aves | HMGCS2 34 35 |
|
||
| lizard (Anolis carolinensis) |
Reptilia | HMGCS2 35 |
|
OneToOne | |
| fruit fly (Drosophila melanogaster) |
Insecta | Hmgs 36 35 |
|
||
| worm (Caenorhabditis elegans) |
Secernentea | F25B4.6 36 |
|
|
|
| hmgs-1 35 |
|
OneToMany | |||
| baker's yeast (Saccharomyces cerevisiae) |
Saccharomycetes | ERG13 35 |
|
OneToMany | |
| rice (Oryza sativa) |
Liliopsida | Os.32782 34 |
|
||
| sea squirt (Ciona savignyi) |
Ascidiacea | CSA.9481 35 |
|
OneToMany |
- Species where no ortholog for HMGCS2 was found in the sources mined by GeneCards:
-
- A. gosspyii yeast (Ashbya gossypii)
- Actinobacteria (Mycobacterium tuberculosis)
- African clawed frog (Xenopus laevis)
- African malaria mosquito (Anopheles gambiae)
- Alicante grape (Vitis vinifera)
- alpha proteobacteria (Wolbachia pipientis)
- amoeba (Dictyostelium discoideum)
- Archea (Pyrococcus horikoshii)
- barley (Hordeum vulgare)
- beta proteobacteria (Neisseria meningitidis)
- bread mold (Neurospora crassa)
- Chromalveolata (Phytophthora infestans)
- common water flea (Daphnia pulex)
- corn (Zea mays)
- E. coli (Escherichia coli)
- filamentous fungi (Aspergillus nidulans)
- Firmicute bacteria (Streptococcus pneumoniae)
- fission yeast (Schizosaccharomyces pombe)
- green algae (Chlamydomonas reinhardtii)
- honey bee (Apis mellifera)
- K. lactis yeast (Kluyveromyces lactis)
- loblloly pine (Pinus taeda)
- malaria parasite (Plasmodium falciparum)
- medicago trunc (Medicago Truncatula)
- moss (Physcomitrella patens)
- orangutan (Pongo pygmaeus)
- pig (Sus scrofa)
- rainbow trout (Oncorhynchus mykiss)
- rice blast fungus (Magnaporthe grisea)
- schistosome parasite (Schistosoma mansoni)
- sea anemone (Nematostella vectensis)
- sea urchin (Strongylocentrotus purpuratus)
- sorghum (Sorghum bicolor)
- soybean (Glycine max)
- stem rust fungus (Puccinia graminis)
- sugarcane (Saccharum officinarum)
- thale cress (Arabidopsis thaliana)
- tomato (Lycopersicon esculentum)
- toxoplasmosis (Toxoplasma gondii)
- Trichoplax (Trichoplax adhaerens)
- tropical clawed frog (Silurana tropicalis)
- wheat (Triticum aestivum)
- zebrafish (Danio rerio)
Paralogs for HMGCS2 Gene
(1) SIMAP similar genes for HMGCS2 Gene using alignment to 1 proteins:
Variants for HMGCS2 Gene
| SNP ID | Clin | Chr 01 pos | Sequence Context | AA Info | Type |
|---|---|---|---|---|---|
| rs137852636 | Pathogenic, 3-hydroxy-3-methylglutaryl-CoA synthase-2 deficiency (HMGCS2D) [MIM:605911] | 119,764,211(-) | CCCTC(C/T)TCAAT | reference, missense | |
| rs137852638 | other, 3-hydroxy-3-methylglutaryl-CoA synthase-2 deficiency (HMGCS2D) [MIM:605911] | 119,759,915(-) | GGGCC(A/G)GAGCT | intron-variant, reference, missense | |
| rs137852639 | Pathogenic, 3-hydroxy-3-methylglutaryl-CoA synthase-2 deficiency (HMGCS2D) [MIM:605911] | 119,750,830(-) | GCATC(A/G)CCGAA | reference, missense | |
| rs137852640 | Pathogenic, 3-hydroxy-3-methylglutaryl-CoA synthase-2 deficiency (HMGCS2D) [MIM:605911] | 119,764,231(-) | CTGCT(A/G)CGGTG | reference, missense | |
| rs28937320 | Pathogenic, 3-hydroxy-3-methylglutaryl-CoA synthase-2 deficiency (HMGCS2D) [MIM:605911] | 119,764,571(-) | AGGAC(A/G)TGGGC | reference, missense |
Relevant External Links for HMGCS2 Gene
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HMGCS2 Gene
Disorders for HMGCS2 Gene
(2) MalaCards diseases for HMGCS2 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| hmg-coa synthase-2 deficiency |
|
|
| smith-lemli-opitz syndrome |
|
|
UniProtKB/Swiss-Prot
HMCS2_HUMAN- 3-hydroxy-3-methylglutaryl-CoA synthase-2 deficiency (HMGCS2D) [MIM:605911]: A metabolic disorder characterized by severe hypoketotic hypoglycemia, encephalopathy, and hepatomegaly. {ECO:0000269 PubMed:11228257, ECO:0000269 PubMed:11479731, ECO:0000269 PubMed:12647205}. Note=The disease is caused by mutations affecting the gene represented in this entry.
Genatlas disease for HMGCS2 Gene
Relevant External Links for HMGCS2
Publications for HMGCS2 Gene
- Genetic basis of mitochondrial HMG-CoA synthase deficiency. (PMID: 11479731) Aledo R. … Hegardt F.G. (Hum. Genet. 2001) 3 4 22 64
- Molecular cloning and tissue expression of human mitochondrial 3- hydroxy-3-methylglutaryl-CoA synthase. (PMID: 7893153) Mascaro C. … Hegardt F.G. (Arch. Biochem. Biophys. 1995) 2 3 4 64
- Human mitochondrial HMG CoA synthase: liver cDNA and partial genomic cloning, chromosome mapping to 1p12-p13, and possible role in vertebrate evolution. (PMID: 7851882) Boukaftane Y. … Mitchell G.A. (Genomics 1994) 2 3 4 64
- Characterization of splice variants of the genes encoding human mitochondrial HMG-CoA lyase and HMG-CoA synthase, the main enzymes of the ketogenesis pathway. (PMID: 21952825) Puisac B. … Pie J. (Mol. Biol. Rep. 2012) 3 4 64
- Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 64
Products for HMGCS2 Gene
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- Addgene plasmids for HMGCS2
- antibodies-online Antibodies for HMGCS2: See all 35
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- antibodies-online Proteins for HMGCS2: See all 10
- Search antibodies-online for peptides
- GeneTex HMGCS2 antibody for HMGCS2
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- ViGene Biosciences adenoviral particle packaged cDNA for HMGCS2 gene
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- Mammalian expression: PiggyBac
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- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Sources for HMGCS2 Gene
- (1) GeneCards
- (2) HGNC
- (3) EntrezGene
- (4) Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) GO
- (12) TrEMBL
- (13) InterPro
- (14) ProtoNet
- (15) Blocks
- (16) MGI
- (17) IUBMB
- (18) KEGG
- (19) MINT
- (20) STRING
- (21) IntAct
- (22) Novoseek
- (23) PharmGKB
- (24) DrugBank
- (25) HMDB
- (26) UniGene
- (27) AceView
- (28) RNAdb
- (29) ASD
- (30) ECgene
- (31) GeneAnnot
- (32) CGAP SAGE
- (33) SOURCE
- (34) HomoloGene
- (35) PanEnsembl
- (36) euGenes
- (37) SGD
- (38) FlyBase
- (39) WormBase
- (40) Pseudogene
- (41) DGV
- (42) dbSNP
- (43) GenAtlas
- (44) GeneTests
- (45) HGMD
- (46) GAD
- (47) LSDB
- (48) BGMUT
- (49) HuGE
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