Aliases for TDRD3 Gene
External Ids for TDRD3 Gene
- HGNC: 20612
- Entrez Gene: 81550
- Ensembl: ENSG00000083544
- OMIM: 614392
- UniProtKB: Q9H7E2
Previous GeneCards Identifiers for TDRD3 Gene
- GC13P054966
- GC13P059907
- GC13P058768
- GC13P058769
- GC13P059868
- GC13P060970
- GC13P041662
Summaries for TDRD3 Gene
GeneCards Summary for TDRD3 Gene
TDRD3 (Tudor Domain Containing 3) is a Protein Coding gene. Diseases associated with TDRD3 include Fragile X Syndrome. Among its related pathways are Translational Control and Chromatin Regulation / Acetylation. GO annotations related to this gene include poly(A) RNA binding and chromatin binding. An important paralog of this gene is RMI1.
UniProtKB/Swiss-Prot for TDRD3 Gene
-
Scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In nucleus, acts as a coactivator: recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In cytoplasm, may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins.
No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TDRD3 Gene
Genomics for TDRD3 Gene
Regulatory Elements for TDRD3 Gene
Enhancers for TDRD3 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 |
|---|---|---|---|---|---|---|---|---|
| GH13G060395 | 1.1 | ENCODE | 33.6 | +1.2 | 1246 | 4.2 | PKNOX1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF143 ZNF207 | TDRD3 DIAPH3 GC13M060411 |
| GH13G060409 | 0.6 | ENCODE | 33.4 | +13.6 | 13571 | 1.1 | SOX13 ZNF766 ZNF133 IKZF1 CEBPG HNF4A | TDRD3 GC13M060411 |
| GH13G060426 | 0.6 | ENCODE | 32.8 | +31.1 | 31060 | 1.3 | MTA2 BHLHE40 TBX21 RELA CBX5 IKZF1 NBN RELB IKZF2 | TDRD3 GC13M060411 GC13P060445 |
| GH13G060161 | 1.3 | Ensembl ENCODE | 13.2 | -232.6 | -232584 | 5.0 | PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 FOS SP3 | TDRD3 DIAPH3 DIAPH3-AS2 |
| GH13G060582 | 1.2 | Ensembl ENCODE | 11.4 | +188.2 | 188169 | 3.8 | PKNOX1 ETS1 ZNF766 ELK1 KLF13 CAVIN1 ZBTB11 HDAC8 ZNF592 POLR2H | TDRD3 RNA5SP31 GC13P060445 |
- Elite enhancer and/or Elite enhancer-gene association
Download GeneHancer data dump
Enhancers around TDRD3 on UCSC Golden Path with GeneCards custom track
- Transcription factor binding sites by QIAGEN in the TDRD3 gene promoter:
Regulatory Element Products
Genomic Location for TDRD3 Gene
- Chromosome:
- 13
- Start:
- 60,396,457 bp from pter
- End:
- 60,573,879 bp from pter
- Size:
- 177,423 bases
- Orientation:
- Plus strand
Genomic View for TDRD3 Gene
Genes around TDRD3 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 13q21.2 by Ensembl
- 13q21.2 by Entrez Gene
- 13q21.2 by HGNC
TDRD3 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene Density
RefSeq DNA sequence for TDRD3 Gene
Proteins for TDRD3 Gene
-
Protein details for TDRD3 Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- Q9H7E2-TDRD3_HUMAN
- Recommended name:
- Tudor domain-containing protein 3
- Protein Accession:
- Q9H7E2
- B2MWP9
- Q53XA6
- Q6P992
Protein attributes for TDRD3 Gene
- Size:
- 651 amino acids
- Molecular mass:
- 73185 Da
- Quaternary structure:
-
- Component of mRNA stress granules. Interacts with FMR1, FXR1, FXR2, EWSR1, FUS, SERBP1, EEF1A1 and DDX3X or DDX3Y, and with the small nuclear ribonucleoprotein-associated proteins SNRPB and SNRPN. Interacts with Lys-48-linked tetra-ubiquitin, but not with monoubiquitin or Lys-63-linked ubiquitin chains. May interact with the exon junction complex (EJC) composed at least of CASC3, EIF4A3, MAGOH and RBM8A. Interacts with POLR2A (via the C-terminal domain (CTD)).
Three dimensional structures from OCA and Proteopedia for TDRD3 Gene
Protein Expression for TDRD3 Gene
Post-translational modifications for TDRD3 Gene
Other Protein References for TDRD3 Gene
Antibody Products
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- antibodies-online Antibodies for TDRD3: See all 14
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Protein Products
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- antibodies-online Proteins for TDRD3: See all 3
- Search antibodies-online for peptides
- Search GeneTex for Proteins for TDRD3
No data available for DME Specific Peptides for TDRD3 Gene
Domains & Families for TDRD3 Gene
Gene Families for TDRD3 Gene
Protein Domains for TDRD3 Gene
Suggested Antigen Peptide Sequences for TDRD3 Gene
- GenScript: Design optimal peptide antigens:
Graphical View of Domain Structure for InterPro Entry
Q9H7E2UniProtKB/Swiss-Prot:
TDRD3_HUMAN :- The Tudor domain specifically recognizes and binds asymmetric dimethylation of histone H3 Arg-17 (H3R17me2a) and histones H4 Arg-3, 2 tags for epigenetic transcriptional activation.
- Domain:
-
- The Tudor domain specifically recognizes and binds asymmetric dimethylation of histone H3 Arg-17 (H3R17me2a) and histones H4 Arg-3, 2 tags for epigenetic transcriptional activation.
Function for TDRD3 Gene
Molecular function for TDRD3 Gene
- UniProtKB/Swiss-Prot Function:
- Scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In nucleus, acts as a coactivator: recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In cytoplasm, may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins.
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0003682 | chromatin binding | IDA | 21172665 |
| GO:0003713 | transcription coactivator activity | IDA | 21172665 |
| GO:0003723 | RNA binding | IDA | 22658674 |
| GO:0005515 | protein binding | IPI | 26700805 |
| GO:0035064 | methylated histone binding | IDA | 21172665 |
Phenotypes for TDRD3 Gene
- MGI mutant phenotypes for TDRD3:
- inferred from 1 alleles
- GenomeRNAi human phenotypes for TDRD3:
Animal Model Products
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-
-
ViGene Biosciences lentiviral particle packaged cDNA for TDRD3 gene
-
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CRISPR Products
-
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-
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miRNA for TDRD3 Gene
- miRTarBase miRNAs that target TDRD3
miRNA Products
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Inhibitory RNA Products
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-
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-
VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Cell Line Products
-
Horizon Cell Lines for TDRD3
-
ViGene Biosciences adenoviral particle packaged cDNA for TDRD3 gene
-
ViGene Biosciences lentiviral particle packaged cDNA for TDRD3 gene
-
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No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TDRD3 Gene
Localization for TDRD3 Gene
Subcellular locations from UniProtKB/Swiss-Prot for TDRD3 Gene
- Cytoplasm. Nucleus. Note=Predominantly cytoplasmic. Associated with actively translating polyribosomes and with mRNA stress granules. {ECO:0000269 PubMed:18632687, ECO:0000269 PubMed:18664458}.
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
| cytosol | 2 |
| cytoskeleton | 1 |
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005634 | nucleus | IEA,IDA | 21172665 |
| GO:0005737 | cytoplasm | IEA | -- |
| GO:0035145 | colocalizes_with exon-exon junction complex | IDA | 20930030 |
Pathways & Interactions for TDRD3 Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | Chromatin Regulation / Acetylation | ||
| 2 | Translational Control | ||
Pathways by source for TDRD3 Gene
2 Cell Signaling Technology pathways for TDRD3 Gene
Interacting Proteins for TDRD3 Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0016569 | covalent chromatin modification | IEA | -- |
| GO:1903506 | regulation of nucleic acid-templated transcription | IEA | -- |
No data available for SIGNOR curated interactions for TDRD3 Gene
Transcripts for TDRD3 Gene
mRNA/cDNA for TDRD3 Gene
- (8) REFSEQ mRNAs :
- (7) Additional mRNA sequences :
- (250) Selected AceView cDNA sequences:
- (9) Ensembl transcripts including schematic representations, and UCSC links where relevant :
Unigene Clusters for TDRD3 Gene
- Tudor domain containing 3:
- Representative Sequences:
CRISPR Products
-
OriGene CRISPR knockouts for TDRD3
-
Santa Cruz Biotechnology (SCBT) CRISPR for TDRD3
- GenScript: Design CRISPR guide RNA sequences for TDRD3
miRNA Products
- Search ViGene Biosciences for TDRD3
Inhibitory RNA Products
- Origene RNAi, siRNA, and shRNA products in human, mouse, rat for TDRD3
- Browse OriGene Inhibitory RNA Products For TDRD3
-
ViGene Biosciences ready-to-package AAV shRNAs for TDRD3 gene
Clone Products
- Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat
- Addgene plasmids for TDRD3
- VectorBuilder custom plasmid, inducible vectors for TDRD3
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for TDRD3
-
VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
| ExUns: | 1 | ^ | 2 | ^ | 3 | ^ | 4a | · | 4b | ^ | 5 | ^ | 6a | · | 6b | ^ | 7 | ^ | 8 | ^ | 9 | ^ | 10 | ^ | 11 | ^ | 12 | ^ | 13a | · | 13b | ^ | 14a | · | 14b | ^ | 15 | ^ | 16 | ^ | 17 | ^ | 18 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SP1: | - | - | - | - | - | - | |||||||||||||||||||||||||||||||||||||
| SP2: | - | - | - | - | |||||||||||||||||||||||||||||||||||||||
| SP3: | - | - | - | - | |||||||||||||||||||||||||||||||||||||||
| SP4: | |||||||||||||||||||||||||||||||||||||||||||
| SP5: | |||||||||||||||||||||||||||||||||||||||||||
| SP6: | |||||||||||||||||||||||||||||||||||||||||||
| SP7: | |||||||||||||||||||||||||||||||||||||||||||
| SP8: | - |
Expression for TDRD3 Gene
This gene is overexpressed in Fetal gut (28.0) and Fetal Liver (27.6).
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TDRD3 Gene
NURSA nuclear receptor signaling pathways regulating expression of TDRD3 Gene:
TDRD3SOURCE GeneReport for Unigene cluster for TDRD3 Gene:
Hs.525061mRNA Expression by UniProt/SwissProt for TDRD3 Gene:
Q9H7E2-TDRD3_HUMAN
Tissue specificity:
Detected in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas.
Primer Products
-
OriGene qPCR primer pairs for TDRD3
-
OriGene qPCR primer pairs and template standards for TDRD3
No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for TDRD3 Gene
Orthologs for TDRD3 Gene
This gene was present in the common ancestor of animals.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | TDRD3 34 35 |
|
||
| cow (Bos Taurus) |
Mammalia | TDRD3 34 35 |
|
||
| dog (Canis familiaris) |
Mammalia | TDRD3 34 |
|
||
| -- 35 |
|
OneToMany | |||
| -- 35 |
|
OneToMany | |||
| rat (Rattus norvegicus) |
Mammalia | Tdrd3 34 |
|
||
| mouse (Mus musculus) |
Mammalia | Tdrd3 34 16 35 |
|
||
| oppossum (Monodelphis domestica) |
Mammalia | TDRD3 35 |
|
OneToOne | |
| platypus (Ornithorhynchus anatinus) |
Mammalia | TDRD3 35 |
|
OneToOne | |
| chicken (Gallus gallus) |
Aves | TDRD3 34 35 |
|
||
| lizard (Anolis carolinensis) |
Reptilia | TDRD3 35 |
|
OneToOne | |
| tropical clawed frog (Silurana tropicalis) |
Amphibia | tdrd3 34 |
|
||
| MGC76148 34 |
|
||||
| African clawed frog (Xenopus laevis) |
Amphibia | Xl.8087 34 |
|
||
| zebrafish (Danio rerio) |
Actinopterygii | tdrd3 34 35 |
|
||
| Dr.16828 34 |
|
||||
| fruit fly (Drosophila melanogaster) |
Insecta | CG13472 35 |
|
OneToOne | |
| worm (Caenorhabditis elegans) |
Secernentea | Y50D4C.3 35 |
|
OneToOne | |
| sea squirt (Ciona savignyi) |
Ascidiacea | CSA.3026 35 |
|
OneToOne |
- Species where no ortholog for TDRD3 was found in the sources mined by GeneCards:
-
- A. gosspyii yeast (Ashbya gossypii)
- Actinobacteria (Mycobacterium tuberculosis)
- African malaria mosquito (Anopheles gambiae)
- Alicante grape (Vitis vinifera)
- alpha proteobacteria (Wolbachia pipientis)
- amoeba (Dictyostelium discoideum)
- Archea (Pyrococcus horikoshii)
- baker's yeast (Saccharomyces cerevisiae)
- 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 (Oryza sativa)
- 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)
- wheat (Triticum aestivum)
Paralogs for TDRD3 Gene
Variants for TDRD3 Gene
| SNP ID | Clin | Chr 13 pos | Sequence Context | AA Info | Type |
|---|---|---|---|---|---|
| rs1000013214 | -- | 60,414,576(+) | CAGAA(G/T)TTGTC | intron-variant | |
| rs1000038966 | -- | 60,569,628(+) | CCTGA(A/G)CATAA | intron-variant | |
| rs1000069730 | -- | 60,510,902(+) | TGTTT(C/G/T)TTTAT | intron-variant | |
| rs1000127480 | -- | 60,516,269(+) | TTATG(G/T)CATAT | intron-variant | |
| rs1000135090 | -- | 60,504,832(+) | GCACA(A/G)GGGGT | intron-variant |
| Variant ID | Type | Subtype | PubMed ID |
|---|---|---|---|
| dgv3184n54 | CNV | loss | 21841781 |
| esv29450 | CNV | gain | 19812545 |
| esv3331016 | CNV | insertion | 20981092 |
| esv3580686 | CNV | loss | 25503493 |
| esv3580687 | CNV | loss | 25503493 |
| nsv1070590 | CNV | deletion | 25765185 |
| nsv1144680 | CNV | deletion | 24896259 |
| nsv455903 | CNV | loss | 19166990 |
| nsv523359 | CNV | loss | 19592680 |
Residual Variation Intolerance Score:
35.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
6.15;
75.73% of all genes are more intolerant (likely to be disease-causing)
Relevant External Links for TDRD3 Gene
- SNPedia medical, phenotypic, and genealogical associations of SNPs for
- TDRD3
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TDRD3 Gene
Disorders for TDRD3 Gene
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| fragile x syndrome |
|
|
Search TDRD3 in MalaCards
View complete list of genes associated with diseases
Relevant External Links for TDRD3
No data available for UniProtKB/Swiss-Prot and Genatlas for TDRD3 Gene
Publications for TDRD3 Gene
- SMN and symmetric arginine dimethylation of RNA polymerase II C- terminal domain control termination. (PMID: 26700805) Yanling Zhao D. … Greenblatt J.F. (Nature 2015) 3 4 64
- Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways. (PMID: 22267201) Stolk L. … Lunetta K.L. (Nat. Genet. 2012) 3 46 64
- SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay. (PMID: 20930030) Kashima I. … Izaurralde E. (Genes Dev. 2010) 3 4 64
- TDRD3 is an effector molecule for arginine-methylated histone marks. (PMID: 21172665) Yang Y. … Bedford M.T. (Mol. Cell 2010) 3 4 64
- TDRD3, a novel Tudor domain-containing protein, localizes to cytoplasmic stress granules. (PMID: 18632687) Goulet I. … Cote J. (Hum. Mol. Genet. 2008) 3 4 64
Products for TDRD3 Gene
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- GeneTex Siglec1 antibody for TDRD3
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- ViGene Biosciences adenoviral particle packaged cDNA for TDRD3 gene
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- Cyagen custom Knockout/knockin (KOKI) mouse models for TDRD3
- VectorBuilder custom plasmid, inducible vectors for TDRD3
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for TDRD3
- VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Sources for TDRD3 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
- (50) eBioscience
- (51) Atlas
- (52) Cell Signaling Technology
- (53) GenBank
- (54) H-invDB
- (55) HORDE
- (56) HUGE
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