Aliases for SLITRK1 Gene
Aliases for SLITRK1 Gene
External Ids for SLITRK1 Gene
- HGNC: 20297
- Entrez Gene: 114798
- Ensembl: ENSG00000178235
- OMIM: 609678
- UniProtKB: Q96PX8
Previous HGNC Symbols for SLITRK1 Gene
- LRRC12
Previous GeneCards Identifiers for SLITRK1 Gene
- GC13M082251
- GC13M082249
- GC13M083349
- GC13M084451
- GC13M065151
Summaries for SLITRK1 Gene
-
This gene encodes a member of the SLITRK protein family. Members of this family are integral membrane proteins that are characterized by two N-terminal leucine-rich repeat (LRR) domains and a C-terminal region that shares homology with trk neurotrophin receptors. However, the protein encoded by this gene lacks the region of homology to neurotrophin receptors. This protein is thought to be involved in neurite outgrowth. Mutations in this gene may be associated with Tourette syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
GeneCards Summary for SLITRK1 Gene
SLITRK1 (SLIT And NTRK Like Family Member 1) is a Protein Coding gene. Diseases associated with SLITRK1 include Trichotillomania and Gilles De La Tourette Syndrome. An important paralog of this gene is SLITRK2.
UniProtKB/Swiss-Prot for SLITRK1 Gene
-
It is involved in synaptogenesis and promotes excitatory synapse differentiation (PubMed:27273464, PubMed:27812321). Enhances neuronal dendrite outgrowth (PubMed:16224024, PubMed:19640509).
Additional gene information for SLITRK1 Gene
- Monarch Initiative
- Search for SLITRK1 at DataMed
- Search for SLITRK1 at HumanCyc
No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLITRK1 Gene
Genomics for SLITRK1 Gene
GeneHancer (GH) Regulatory Elements for SLITRK1 Gene
Promoters and enhancers for SLITRK1 Gene
| GeneHancer (GH) Identifier | GH Type | GH Score |
GH Sources | Gene Association Score | Total Score | TSS distance (kb) | Number of Genes Away | Size (kb) | Transcription Factor Binding Sites |
Gene Targets |
|---|---|---|---|---|---|---|---|---|---|---|
| GH13I083881 | Promoter/Enhancer | 1.6 | EPDnew Ensembl ENCODE | 550.8 | +0.3 | 293 | 1.1 | MXI1 BACH1 SIN3A MIER2 REST CTBP1 ZNF512B POLR2A CTBP2 ZNF143 | SLITRK1 LOC105370286 | |
| GH13I083883 | Enhancer | 0.4 | ENCODE | 550.8 | -0.7 | -708 | 0.1 | CTBP1 PKNOX1 L3MBTL2 | SLITRK1 VENTXP2 | |
| GH13I083100 | Enhancer | 0.8 | ENCODE | 8.9 | +780.7 | 780653 | 1.9 | ATF1 TAF9B ARNT NFRKB CHAMP1 POLR2B CREM SMARCA5 SMAD5 REST | SLITRK1 GC13M083079 ENSG00000270400 | |
| GH13I083221 | Enhancer | 0.5 | ENCODE | 5.9 | +660.4 | 660364 | 1.6 | MAFF JUND POLR2A NFE2 | SLITRK1 GC13P083229 GC13P083166 | |
| GH13I083906 | Enhancer | 0.3 | FANTOM5 | 0.3 | -24.2 | -24175 | 0.1 | VENTXP2 SLITRK1 |
- Elite GeneHancer and/or Elite GeneHancer-gene association
Download GeneHancer data dump
GeneHancers around SLITRK1 on UCSC Golden Path with GeneCards custom track
Regulatory Element Products
Genomic Locations for SLITRK1 Gene
Genomic Locations for SLITRK1 Gene
- chr13:83,877,205-83,882,393
- (GRCh38/hg38)
- Size:
- 5,189 bases
- Orientation:
- Minus strand
- chr13:84,451,343-84,456,528
- (GRCh37/hg19)
Genomic View for SLITRK1 Gene
Genes around SLITRK1 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 13q31.1 by Ensembl
- 13q31.1 by Entrez Gene
- 13q31.1 by HGNC
SLITRK1 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 SLITRK1 Gene
Proteins for SLITRK1 Gene
-
Protein details for SLITRK1 Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- Q96PX8-SLIK1_HUMAN
- Recommended name:
- SLIT and NTRK-like protein 1
- Protein Accession:
- Q96PX8
- Q5U5I6
- Q96SF9
Protein attributes for SLITRK1 Gene
- Size:
- 696 amino acids
- Molecular mass:
- 77735 Da
- Quaternary structure:
-
- Can form homodimers; homodimerization requires repeat LRR 2 (PubMed:27273464). Interacts with YWHAB, YWHAE, YWHAG, YWHAH, SFN, YWHAQ and YWHAZ (PubMed:19640509).
- SequenceCaution:
-
- Sequence=BAB67803.1; Type=Erroneous initiation; Evidence={ECO:0000305};
Protein Expression for SLITRK1 Gene
Post-translational modifications for SLITRK1 Gene
- Undergoes proteolytic cleavage that results in shedding of the ectodomain and cleavage of the C-terminal cytoplasmic tail. Glycosylated. Phosphorylation at Ser-695 is necessary for proper function in promoting neurite outgrowth.
Other Protein References for SLITRK1 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
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No data available for DME Specific Peptides for SLITRK1 Gene
Domains & Families for SLITRK1 Gene
Gene Families for SLITRK1 Gene
- Human Protein Atlas (HPA):
-
- Disease related genes
- Plasma proteins
- Predicted membrane proteins
Protein Domains for SLITRK1 Gene
- InterPro:
- Blocks:
- ProtoNet:
Suggested Antigen Peptide Sequences for SLITRK1 Gene
- GenScript: Design optimal peptide antigens:
Graphical View of Domain Structure for InterPro Entry
Q96PX8- Family:
-
- Belongs to the SLITRK family.
Function for SLITRK1 Gene
Molecular function for SLITRK1 Gene
- UniProtKB/Swiss-Prot Function:
- It is involved in synaptogenesis and promotes excitatory synapse differentiation (PubMed:27273464, PubMed:27812321). Enhances neuronal dendrite outgrowth (PubMed:16224024, PubMed:19640509).
Phenotypes From GWAS Catalog for SLITRK1 Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005515 | protein binding | IPI | 19640509 |
Phenotypes for SLITRK1 Gene
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miRNA for SLITRK1 Gene
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No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SLITRK1 Gene
Localization for SLITRK1 Gene
Subcellular locations from UniProtKB/Swiss-Prot for SLITRK1 Gene
- Membrane; Single-pass type I membrane protein. Secreted. Cell junction, synapse.
| Compartment | Confidence |
|---|---|
| plasma membrane | 5 |
| extracellular | 4 |
| endoplasmic reticulum | 1 |
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005576 | extracellular region | IEA | -- |
| GO:0005886 | plasma membrane | TAS | -- |
| GO:0016020 | membrane | IEA | -- |
| GO:0016021 | integral component of membrane | IEA | -- |
| GO:0030054 | cell junction | IEA | -- |
No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLITRK1 Gene
Pathways & Interactions for SLITRK1 Gene
No Data Available
Interacting Proteins for SLITRK1 Gene
Selected Interacting proteins:
Q96PX8-SLIK1_HUMAN
ENSP00000366288
for SLITRK1 Gene via
IID
STRING
MINT
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0007399 | nervous system development | IEA | -- |
| GO:0007409 | axonogenesis | IEA | -- |
| GO:0007416 | synapse assembly | IMP | 27273464 |
| GO:0030534 | adult behavior | IEA | -- |
| GO:0035264 | multicellular organism growth | IEA | -- |
No data available for Pathways by source and SIGNOR curated interactions for SLITRK1 Gene
Transcripts for SLITRK1 Gene
mRNA/cDNA for SLITRK1 Gene
- (2) REFSEQ mRNAs :
- (4) Additional mRNA sequences :
- (26) Selected AceView cDNA sequences:
- (1) Ensembl transcripts including schematic representations, and UCSC links where relevant :
Unigene Clusters for SLITRK1 Gene
CRISPR Products
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Clone Products
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-
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- 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
- genomics-online: cdna clones - Search results for available SLITRK1 gene related products
- orf clones - Search results for available SLITRK1 gene related products
- Applied Biological Materials Clones for SLITRK1
-
Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
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Expression for SLITRK1 Gene
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
mRNA differential expression in normal tissues according to GTEx for SLITRK1 Gene
This gene is overexpressed in Brain - Frontal Cortex (BA9) (x8.8), Brain - Anterior cingulate cortex (BA24) (x7.8), Brain - Cortex (x7.5), Brain - Hippocampus (x5.0), and Brain - Amygdala (x4.9).
This gene is overexpressed in Cerebrospinal fluid (32.2), Serum (12.7), Lung (11.9), and Kidney (8.5).
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SLITRK1 Gene
NURSA nuclear receptor signaling pathways regulating expression of SLITRK1 Gene:
SLITRK1SOURCE GeneReport for Unigene cluster for SLITRK1 Gene:
Hs.415478mRNA Expression by UniProt/SwissProt for SLITRK1 Gene:
Q96PX8-SLIK1_HUMAN
Tissue specificity:
Expressed predominantly in the frontal lobe of the cerebral cortex of the brain. Also expressed in some astrocytic brain tumors such as astrocytomas, oligodendrogliomas, glioblastomas, gangliogliomas and primitive neuroectodermal tumors.
Evidence on tissue expression from TISSUES for SLITRK1 Gene
- Nervous system(4.7)
Phenotype-based relationships between genes and organs from Gene ORGANizer for SLITRK1 Gene
Germ Layers:
- ectoderm
- endoderm
- mesoderm
Systems:
- cardiovascular
- integumentary
- nervous
- respiratory
- skeletal muscle
Organs:
Head and neck:
- brain
- cerebellum
- cranial nerve
- ear
- head
- larynx
- mouth
- neck
- nose
- pharynx
- scalp
- vocal cord
Thorax:
- heart
General:
- blood vessel
- hair
- peripheral nervous system
- skin
Primer Products
-
OriGene qPCR primer pairs for SLITRK1
-
OriGene qPCR primer pairs and template standards for SLITRK1
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No data available for Protein tissue co-expression partners for SLITRK1 Gene
Orthologs for SLITRK1 Gene
This gene was present in the common ancestor of animals.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | SLITRK1 33 34 |
|
||
| cow (Bos Taurus) |
Mammalia | SLITRK1 33 34 |
|
||
| dog (Canis familiaris) |
Mammalia | SLITRK1 33 34 |
|
||
| mouse (Mus musculus) |
Mammalia | Slitrk1 33 16 34 |
|
||
| rat (Rattus norvegicus) |
Mammalia | Slitrk1 33 |
|
||
| oppossum (Monodelphis domestica) |
Mammalia | SLITRK1 34 |
|
OneToOne | |
| platypus (Ornithorhynchus anatinus) |
Mammalia | -- 34 |
|
ManyToMany | |
| -- 34 |
|
ManyToMany | |||
| chicken (Gallus gallus) |
Aves | SLITRK1 33 34 |
|
||
| lizard (Anolis carolinensis) |
Reptilia | SLITRK1 34 |
|
OneToOne | |
| tropical clawed frog (Silurana tropicalis) |
Amphibia | slitrk1 33 |
|
||
| zebrafish (Danio rerio) |
Actinopterygii | SLITRK1 34 |
|
OneToOne | |
| LOC558743 33 |
|
||||
| fruit fly (Drosophila melanogaster) |
Insecta | sli 34 |
|
OneToMany | |
| worm (Caenorhabditis elegans) |
Secernentea | slt-1 34 |
|
OneToMany | |
| sea squirt (Ciona savignyi) |
Ascidiacea | -- 34 |
|
OneToMany |
- Species where no ortholog for SLITRK1 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)
Paralogs for SLITRK1 Gene
Variants for SLITRK1 Gene
| SNP ID | Clin | Chr 13 pos | Variation | AA Info | Type |
|---|---|---|---|---|---|
| rs1035448844 | (TTM) [MIM:613229] | 83,879,757(-) | C/T | coding_sequence_variant, missense_variant | |
| rs1037756552 | uncertain-significance, Tourette Syndrome | 83,879,187(-) | A/C | 3_prime_UTR_variant | |
| rs1046202 | likely-benign, Tourette Syndrome | 83,877,375(-) | A/T | 3_prime_UTR_variant | |
| rs140472390 | uncertain-significance, Tourette Syndrome | 83,878,104(-) | G/C | 3_prime_UTR_variant | |
| rs140875495 | uncertain-significance, Tourette Syndrome | 83,881,577(-) | C/G | 5_prime_UTR_variant, intron_variant |
| Variant ID | Type | Subtype | PubMed ID |
|---|---|---|---|
| nsv1040716 | CNV | gain | 25217958 |
| nsv562552 | CNV | loss | 21841781 |
Residual Variation Intolerance Score:
15.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
1.22;
24.41% of all genes are more intolerant (likely to be disease-causing)
Additional Variant Information for SLITRK1 Gene
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLITRK1 Gene
Disorders for SLITRK1 Gene
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| trichotillomania |
|
|
| gilles de la tourette syndrome |
|
|
| obsessive-compulsive disorder |
|
|
| body dysmorphic disorder |
|
|
| neurotic excoriation |
|
|
Search SLITRK1 in MalaCards
View complete list of genes associated with diseases
UniProtKB/Swiss-Prot
SLIK1_HUMAN- Trichotillomania (TTM) [MIM:613229]: A neuropsychiatric disorder characterized by chronic, repetitive, or compulsive hair pulling resulting in noticeable hair loss. Affected individuals may develop physical complications and often have overlapping psychological disorders, such as Gilles de la Tourette syndrome or obsessive-compulsive disorder. {ECO:0000269 PubMed:16224024, ECO:0000269 PubMed:17003809, ECO:0000269 PubMed:27812321}. Note=The disease may be caused by mutations affecting the gene represented in this entry.
Additional Disease Information for SLITRK1
- Genetic Association Database
- (GAD)
- Human Genome Epidemiology Navigator
- (HuGE)
- ATLAS of Genetics and Cytogenetics in Oncology and Haematology
No data available for Genatlas for SLITRK1 Gene
Publications for SLITRK1 Gene
- Human SLITRK family genes: genomic organization and expression profiling in normal brain and brain tumor tissue. (PMID: 14557068) Aruga J … Mikoshiba K (Gene 2003) 2 3 4 22 58
- Sequence variants in SLITRK1 are associated with Tourette's syndrome. (PMID: 16224024) Abelson JF … State MW (Science (New York, N.Y.) 2005) 3 4 44 58
- The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4 58
- Slitrk1 is localized to excitatory synapses and promotes their development. (PMID: 27273464) Beaubien F … Cloutier JF (Scientific reports 2016) 3 4 58
- Characterization of SLITRK1 variation in obsessive-compulsive disorder. (PMID: 23990902) Ozomaro U … Grice DE (PloS one 2013) 3 4 58
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- 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
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- Compare Top SLITRK1 Proteins
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- GeneTex SLITRK1 antibody for SLITRK1
- Search GeneTex for Proteins for SLITRK1
- ViGene Biosciences adenoviral particle packaged cDNA for SLITRK1 gene
- ViGene Biosciences lentiviral particle packaged cDNA for SLITRK1 gene
- ViGene Biosciences ready-to-package AAV shRNAs for SLITRK1 gene
- Search ViGene Biosciences for SLITRK1
- Custom Antibody ServicesProSci Antibodies for SLITRK1
- ProSci Proteins for SLITRK1
- Horizon Cell Lines for SLITRK1
- genomics-online: cdna clones - Search results for available SLITRK1 gene related products
- orf clones - Search results for available SLITRK1 gene related products
- genomics-online: gRNA clones - Search results for available SLITRK1 gene related products
- genomics-online: primer clones - Search results for available SLITRK1 gene related products
- genomics-online: shRNA clones - Search results for available SLITRK1 gene related products
Sources for SLITRK1 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) ASD
- (29) ECgene
- (30) GeneAnnot
- (31) CGAP SAGE
- (32) SOURCE
- (33) HomoloGene
- (34) PanEnsembl
- (35) euGenes
- (36) SGD
- (37) FlyBase
- (38) WormBase
- (39) Pseudogene
- (40) DGV
- (41) dbSNP
- (42) GenAtlas
- (43) HGMD
- (44) GAD
- (45) BGMUT
- (46) HuGE
- (47) Atlas
- (48) Cell Signaling Technology
- (49) GenBank
- (50) H-invDB
- (51) HORDE
- (52) HUGE
- (53) IMGT
- (54) Leiden
- (55) miRBase
- (56) DME
- (57) OriGene
- (58) PubMed
- (59) R&D Systems
- (60) TGDB
- (61) Tocris
- (62) Abcam
- (63) Novus Biologicals
- (64) ProSpec
- (65) Sino Biological
- (66) GenScript
- (67) Qiagen
- (68) Cloud-Clone Corp.
- (69) OCA
- (70) Proteopedia
- (71) MOPED
- (72) neXtProt
- (73) Reactome
- (74) GeneGo (Thomson Reuters)
- (75) fRNAdb
- (76) DISEASES
- (77) SIMAP
- (78) GenomeRNAi
- (79) LifeMap
- (80) miRTarBase
- (81) MalaCards
- (82) Invitrogen
- (83) BitterDB
- (84) Vector BioLabs
- (85) ESI-BIO
- (86) RefSeq
- (87) BioSystems
- (88) MaxQB
- (89) IUPHAR
- (90) BioGPS
- (91) Illumina
- (92) COMPARTMENTS
- (93) HOMER
- (94) PaxDb
- (95) ApexBio
- (96) Addgene
- (97) antibodies-online
- (98) CYP
- (99) NONCODE
- (100) SwitchGear Genomics
- (101) TreeFam
- (102) PathCards
- (103) GeneReviews
- (104) GeneTex
- (105) Taconic Biosciences
- (106) GTEx
- (107) ProteomicsDB
- (108) SCBT
- (109) DGIdb
- (110) ClinicalTrials
- (111) FDA Approved Drugs
- (112) RVIS
- (113) SIGNOR
- (114) diseasecard
- (115) NIH Rare Diseases
- (116) Orphanet
- (117) UMLS
- (118) GTR
- (119) Disease Ontology
- (120) Genetics Home Reference
- (121) MeSH
- (122) MedlinePlus
- (123) CDC
- (124) NINDS
- (125) NCBI Bookshelf
- (126) ClinVar
- (127) Gene Damage Index
- (128) ViGene Biosciences
- (129) HPO
- (130) UDN
- (131) VISTA
- (132) FANTOM5
- (133) ENCODE
- (134) ProSci
- (135) Horizon
- (136) NURSA
- (137) IID
- (138) Cyagen
- (139) VectorBuilder
- (140) SNPedia
- (141) BRCA Exchange
- (142) St John's Lab
- (143) CIViC
- (144) ProteoGenix
- (145) dbSUPER
- (146) TISSUES
- (147) Gene ORGANizer
- (148) abm
- (149) CrownBio
- (150) Human Protein Atlas
- (151) GWAS Catalog
- (152) Monarch Initiative
- (153) DataMed
- (154) HumanCyc
- (155) genomics-online
- (156) UCNEbase
- (157) EPDnew