Aliases for LYST Gene
Aliases for LYST Gene
External Ids for LYST Gene
- HGNC: 1968
- Entrez Gene: 1130
- Ensembl: ENSG00000143669
- OMIM: 606897
- UniProtKB: Q99698
Previous HGNC Symbols for LYST Gene
- CHS1
Previous GeneCards Identifiers for LYST Gene
- GC01M232151
- GC01M233890
- GC01M235824
- GC01M206276
Summaries for LYST Gene
-
This gene encodes a protein that regulates intracellular protein trafficking in endosomes, and may be involved in pigmentation. Mutations in this gene are associated with Chediak-Higashi syndrome, a lysosomal storage disorder. Alternative splicing results in multiple transcript variants, though the full-length nature of some of these variants has not been determined. [provided by RefSeq, Apr 2013]
GeneCards Summary for LYST Gene
LYST (Lysosomal Trafficking Regulator) is a Protein Coding gene. Diseases associated with LYST include Chediak-Higashi Syndrome and Attenuated Chédiak-Higashi Syndrome. GO annotations related to this gene include binding and phospholipid binding. An important paralog of this gene is WDFY3.
UniProtKB/Swiss-Prot for LYST Gene
-
May be required for sorting endosomal resident proteins into late multivesicular endosomes by a mechanism involving microtubules.
No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LYST Gene
Genomics for LYST Gene
Regulatory Elements for LYST Gene
Enhancers for LYST Gene
- Elite enhancer and/or Elite enhancer-gene association
Download GeneHancer data dump
Enhancers around LYST on UCSC Golden Path with GeneCards custom track
- Transcription factor binding sites by QIAGEN in the LYST gene promoter:
Regulatory Element Products
Genomic Location for LYST Gene
- Chromosome:
- 1
- Start:
- 235,661,031 bp from pter
- End:
- 235,883,708 bp from pter
- Size:
- 222,678 bases
- Orientation:
- Minus strand
Genomic View for LYST Gene
Genes around LYST on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 1q42.3 by Ensembl
- 1q42.3 by Entrez Gene
- 1q42.3 by HGNC
LYST 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 LYST Gene
Proteins for LYST Gene
-
Protein details for LYST Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- Q99698-LYST_HUMAN
- Recommended name:
- Lysosomal-trafficking regulator
- Protein Accession:
- Q99698
- O43274
- Q5T2U9
- Q96TD7
- Q96TD8
- Q99709
- Q9H133
Protein attributes for LYST Gene
- Size:
- 3801 amino acids
- Molecular mass:
- 429139 Da
- Quaternary structure:
-
- Interacts with CENPJ, LIP8 and ZNF521.
Protein Expression for LYST Gene
Post-translational modifications for LYST Gene
Other Protein References for LYST Gene
Antibody Products
- Novus Biologicals Antibodies for LYST
- Invitrogen Antibodies for LYST
- antibodies-online Antibodies for LYST: See all 4
- Search GeneTex for Antibodies for LYST
Protein Products
- Search Origene for Purified Proteins, MassSpec and Protein Over-expression Lysates for LYST
- Origene Custom Protein Services for LYST
- Novus Biologicals proteins for LYST
- Search GeneTex for Proteins for LYST
Assay Products
- antibodies-online Kits for LYST: See all 4
No data available for DME Specific Peptides for LYST Gene
Domains & Families for LYST Gene
Gene Families for LYST Gene
Protein Domains for LYST Gene
- InterPro:
- Blocks:
- ProtoNet:
Suggested Antigen Peptide Sequences for LYST Gene
- GenScript: Design optimal peptide antigens:
Graphical View of Domain Structure for InterPro Entry
No data available for UniProtKB/Swiss-Prot for LYST Gene
Function for LYST Gene
Molecular function for LYST Gene
- GENATLAS Biochemistry:
- putative lysosomal associated membrane protein,intracellular trafficking regulator,with two alternatively spliced isoforms,homologous to mouse beige and yeast VPS15
- UniProtKB/Swiss-Prot Function:
- May be required for sorting endosomal resident proteins into late multivesicular endosomes by a mechanism involving microtubules.
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005515 | protein binding | IPI | 11984006 |
Phenotypes for LYST Gene
- MGI mutant phenotypes for LYST:
-
inferred from 22 alleles
- mortality/aging
- cellular phenotype
- behavior/neurological phenotype
- growth/size/body region phenotype
- immune system phenotype
- nervous system phenotype
- homeostasis/metabolism phenotype
- respiratory system phenotype
- neoplasm
- endocrine/exocrine gland phenotype
- vision/eye phenotype
- hearing/vestibular/ear phenotype
- integument phenotype
- limbs/digits/tail phenotype
- pigmentation phenotype
- hematopoietic system phenotype
- renal/urinary system phenotype
- craniofacial phenotype
- no phenotypic analysis
- GenomeRNAi human phenotypes for LYST:
Animal Models for LYST Gene
- MGI Knock Outs for LYST:
-
- Lyst tm1b(EUCOMM)Wtsi
Animal Model Products
-
Taconic Biosciences Mouse Models for LYST
- Cyagen custom Knockout/knockin (KOKI) mouse models for LYST
-
-
ViGene Biosciences lentiviral particle packaged cDNA for LYST gene
-
ViGene Biosciences ready-to-package AAV shRNAs for LYST gene
- Search ViGene Biosciences for LYST
CRISPR Products
-
OriGene CRISPR knockouts for LYST
-
Santa Cruz Biotechnology (SCBT) CRISPR for LYST
- GenScript: Design CRISPR guide RNA sequences for LYST
miRNA for LYST Gene
- miRTarBase miRNAs that target LYST
miRNA Products
- Search ViGene Biosciences for LYST
Inhibitory RNA Products
- Origene shRNA, siRNA, and RNAi products in human, mouse, rat for LYST
- Browse OriGene Inhibitory RNA Products For LYST
-
ViGene Biosciences ready-to-package AAV shRNAs for LYST gene
Clone Products
- VectorBuilder custom plasmid, inducible vectors for LYST
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for LYST
-
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 LYST
-
ViGene Biosciences adenoviral particle packaged cDNA for LYST gene
-
ViGene Biosciences lentiviral particle packaged cDNA for LYST gene
-
ViGene Biosciences ready-to-package AAV shRNAs for LYST gene
No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for LYST Gene
Localization for LYST Gene
Subcellular locations from UniProtKB/Swiss-Prot for LYST Gene
- Cytoplasm.
| Compartment | Confidence |
|---|---|
| cytoskeleton | 5 |
| plasma membrane | 4 |
| nucleus | 3 |
| cytosol | 3 |
| lysosome | 2 |
| endosome | 2 |
| golgi apparatus | 1 |
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005737 | cytoplasm | IEA | -- |
| GO:0015630 | microtubule cytoskeleton | IDA | 9606205 |
Pathways & Interactions for LYST Gene
No Data Available
Interacting Proteins for LYST Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0006810 | transport | IEA | -- |
| GO:0007040 | lysosome organization | IEA | -- |
| GO:0015031 | protein transport | IEA | -- |
| GO:0030595 | leukocyte chemotaxis | ISS | -- |
| GO:0032438 | melanosome organization | ISS | -- |
No data available for Pathways by source and SIGNOR curated interactions for LYST Gene
Transcripts for LYST Gene
mRNA/cDNA for LYST Gene
- (14) REFSEQ mRNAs :
- (13) Additional mRNA sequences :
- (149) Selected AceView cDNA sequences:
- (12) Ensembl transcripts including schematic representations, and UCSC links where relevant :
Unigene Clusters for LYST Gene
CRISPR Products
-
OriGene CRISPR knockouts for LYST
-
Santa Cruz Biotechnology (SCBT) CRISPR for LYST
- GenScript: Design CRISPR guide RNA sequences for LYST
miRNA Products
- Search ViGene Biosciences for LYST
Inhibitory RNA Products
- Origene shRNA, siRNA, and RNAi products in human, mouse, rat for LYST
- Browse OriGene Inhibitory RNA Products For LYST
-
ViGene Biosciences ready-to-package AAV shRNAs for LYST gene
Clone Products
- VectorBuilder custom plasmid, inducible vectors for LYST
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for LYST
-
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
Expression for LYST Gene
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
-
Blood (Hematopoietic System)
- Granulocytes Peripheral Blood
- Double Positive Thymocytes Thymus
-
Thymus (Hematopoietic System)
- Double Positive Thymocytes Thymus
- Bone (Muscoskeletal System)
mRNA differential expression in normal tissues according to GTEx for LYST Gene
This gene is overexpressed in Whole Blood (x5.6).
This gene is overexpressed in Bone marrow mesenchymal stem cell (17.2), Breast (13.6), and Peripheral blood mononuclear cells (8.1).
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for LYST Gene
NURSA nuclear receptor signaling pathways regulating expression of LYST Gene:
LYSTSOURCE GeneReport for Unigene cluster for LYST Gene:
Hs.532411mRNA Expression by UniProt/SwissProt for LYST Gene:
Q99698-LYST_HUMAN
Tissue specificity:
Abundantly expressed in adult and fetal thymus, peripheral blood leukocytes, bone marrow and several regions of the adult brain.
Evidence on tissue expression from TISSUES for LYST Gene
- Liver(4.2)
- Blood(2.6)
- Bone marrow(2.3)
- Skin(2.1)
Phenotype-based relationships between genes and organs from Gene ORGANizer for LYST Gene
Germ Layers:
- ectoderm
- endoderm
- mesoderm
Systems:
- cardiovascular
- digestive
- immune
- integumentary
- lymphatic
- nervous
- respiratory
- skeletal muscle
- skeleton
Organs:
Head and neck:
- brain
- cranial nerve
- eye
- face
- head
- jaw
- mandible
- maxilla
- mouth
- nose
- skull
- tooth
Abdomen:
- liver
- spleen
Limb:
- lower limb
- shin
General:
- blood
- blood vessel
- bone marrow
- coagulation system
- hair
- lymph node
- peripheral nerve
- peripheral nervous system
- red blood cell
- skin
- spinal cord
- white blood cell
Primer Products
-
OriGene qPCR primer pairs for LYST
No data available for Protein tissue co-expression partners for LYST Gene
Orthologs for LYST Gene
This gene was present in the common ancestor of animals.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | LYST 34 35 |
|
||
| dog (Canis familiaris) |
Mammalia | LYST 34 35 |
|
||
| cow (Bos Taurus) |
Mammalia | LYST 34 35 |
|
||
| rat (Rattus norvegicus) |
Mammalia | Lyst 34 |
|
||
| mouse (Mus musculus) |
Mammalia | Lyst 34 16 35 |
|
||
| oppossum (Monodelphis domestica) |
Mammalia | LYST 35 |
|
OneToOne | |
| platypus (Ornithorhynchus anatinus) |
Mammalia | LYST 35 |
|
OneToOne | |
| chicken (Gallus gallus) |
Aves | LYST 34 35 |
|
||
| lizard (Anolis carolinensis) |
Reptilia | LYST 35 |
|
OneToOne | |
| tropical clawed frog (Silurana tropicalis) |
Amphibia | lyst 34 |
|
||
| zebrafish (Danio rerio) |
Actinopterygii | lyst 34 |
|
||
| fruit fly (Drosophila melanogaster) |
Insecta | CG42863 35 |
|
OneToOne | |
| sea squirt (Ciona savignyi) |
Ascidiacea | -- 35 |
|
OneToOne |
- Species where no ortholog for LYST 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)
- 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)
- worm (Caenorhabditis elegans)
Paralogs for LYST Gene
Variants for LYST Gene
| SNP ID | Clin | Chr 01 pos | Sequence Context | AA Info | Type |
|---|---|---|---|---|---|
| rs28942077 | Pathogenic, Chediak-Higashi syndrome (CHS) [MIM:214500] | 235,766,204(-) | AGAAG(A/T)CCTTG | intron-variant, nc-transcript-variant, reference, missense | |
| rs80338657 | Pathogenic, Chediak-Higashi syndrome (CHS) [MIM:214500] | 235,788,701(-) | CTTTC(A/G)GTATT | nc-transcript-variant, reference, missense | |
| VAR_071512 | Chediak-Higashi syndrome (CHS) [MIM:214500] | ||||
| rs370022675 | Pathogenic | 235,809,893(+) | TACTC(A/G/T)ACTCT | nc-transcript-variant, upstream-variant-2KB, reference, synonymous-codon, stop-gained | |
| rs754616030 | Pathogenic | 235,702,776(+) | TTCTC(A/G)GGTCT | intron-variant, reference, stop-gained |
| Variant ID | Type | Subtype | PubMed ID |
|---|---|---|---|
| dgv588n100 | CNV | gain | 25217958 |
| dgv589n100 | CNV | gain | 25217958 |
| esv2661819 | CNV | deletion | 23128226 |
| esv3589199 | CNV | loss | 21293372 |
| nsv1011288 | CNV | gain | 25217958 |
| nsv1012436 | CNV | loss | 25217958 |
| nsv472320 | CNV | novel sequence insertion | 20440878 |
| nsv508701 | CNV | deletion | 20534489 |
| nsv549394 | CNV | gain | 21841781 |
| nsv832936 | CNV | gain | 17160897 |
| nsv832947 | CNV | gain | 17160897 |
| nsv945383 | CNV | duplication | 23825009 |
Residual Variation Intolerance Score:
10.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
7.40;
81.80% of all genes are more intolerant (likely to be disease-causing)
Relevant External Links for LYST Gene
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LYST Gene
Disorders for LYST Gene
(8) MalaCards diseases for LYST Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| chediak-higashi syndrome |
|
|
| attenuated chédiak-higashi syndrome |
|
|
| exfoliation syndrome |
|
|
| hermansky-pudlak syndrome 1 |
|
|
| dyschromatosis symmetrica hereditaria |
|
|
Search LYST in MalaCards
View complete list of genes associated with diseases
UniProtKB/Swiss-Prot
LYST_HUMAN- Chediak-Higashi syndrome (CHS) [MIM:214500]: A rare autosomal recessive disorder characterized by hypopigmentation, severe immunologic deficiency, a bleeding tendency, neurologic abnormalities, abnormal intracellular transport to and from the lysosome, and giant inclusion bodies in a variety of cell types. Most patients die at an early age unless they receive an allogeneic hematopoietic stem cell transplant (SCT). {ECO:0000269 PubMed:11857544, ECO:0000269 PubMed:24521565}. Note=The disease is caused by mutations affecting the gene represented in this entry.
Relevant External Links for LYST
No data available for Genatlas for LYST Gene
Publications for LYST Gene
- Identification of the homologous beige and Chediak-Higashi syndrome genes. (PMID: 8717042) Barbosa M.D.F.S. … Kingsmore S.F. (Nature 1996) 2 3 4 22 64
- Apparent genotype-phenotype correlation in childhood, adolescent, and adult Chediak-Higashi syndrome. (PMID: 11857544) Karim M.A. … Spritz R.A. (Am. J. Med. Genet. 2002) 3 4 22 64
- The Chediak-Higashi protein interacts with SNARE complex and signal transduction proteins. (PMID: 11984006) Tchernev V.T. … Kingsmore S.F. (Mol. Med. 2002) 3 4 22 64
- Identification and mutation analysis of the complete gene for Chediak-Higashi syndrome. (PMID: 8896560) Nagle D.L. … Moore K.J. (Nat. Genet. 1996) 2 3 4 64
- Autosomal-recessive complicated spastic paraplegia with a novel lysosomal trafficking regulator gene mutation. (PMID: 24521565) Shimazaki H. … Takiyama Y. (J. Neurol. Neurosurg. Psych. 2014) 3 4 64
Products for LYST Gene
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- Browse R&D Systems for biochemical assays
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- Find your next knockout model in the Taconic Knockout Repository
- Genetically Engineered Models Available Immediately
- Humanized Mice
- Invitrogen Antibodies for LYST
- antibodies-online Antibodies for LYST: See all 4
- antibodies-online Kits for LYST: See all 4
- Search antibodies-online for proteins
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- ViGene Biosciences adenoviral particle packaged cDNA for LYST gene
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- Horizon Cell Lines for LYST
- Cyagen custom Knockout/knockin (KOKI) mouse models for LYST
- VectorBuilder custom plasmid, inducible vectors for LYST
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for LYST
- 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 LYST 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
- (57) IMGT
- (58) Leiden
- (59) MILLIPORE
- (60) miRBase
- (61) DME
- (62) NCBI
- (63) OriGene
- (64) PubMed
- (65) R&D Systems
- (66) TGDB
- (67) Tocris
- (68) Abcam
- (69) Novus
- (70) ProSpec
- (71) Sino Biological
- (72) GenScript
- (73) Qiagen
- (74) Cloud-Clone Corp.
- (75) Enzo Life Sciences
- (76) OCA
- (77) Proteopedia
- (78) MOPED
- (79) SPIRE
- (80) neXtProt
- (81) Reactome
- (82) GeneGo (Thomson Reuters)
- (83) fRNAdb
- (84) DISEASES
- (85) SIMAP
- (86) GenomeRNAi
- (87) LifeMap
- (88) miRTarBase
- (89) MalaCards
- (90) Invitrogen
- (91) BitterDB
- (92) Vector BioLabs
- (93) ESI-BIO
- (94) RefSeq
- (95) BioSystems
- (96) MaxQB
- (97) IUPHAR
- (98) BioGPS
- (99) Illumina
- (100) COMPARTMENTS
- (101) HOMER
- (102) PaxDb
- (103) ApexBio
- (104) Addgene
- (105) antibodies-online
- (106) CYP
- (107) NONCODE
- (108) SwitchGear Genomics
- (109) TreeFam
- (110) PathCards
- (111) GeneReviews
- (112) GeneTex
- (113) Taconic Biosciences
- (114) GTEx
- (115) ProteomicsDB
- (116) SCBT
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- (136) ViGene Biosciences
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- (141) ENCODE
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- (145) IID
- (146) Cyagen
- (147) VectorBuilder
- (148) SNPedia
- (149) BRCA Exchange
- (150) St John's Lab
- (151) CIViC
- (152) ProteoGenix
- (153) dbSUPER
- (154) TISSUES
- (155) Gene ORGANizer