Aliases for SNRNP40 Gene
Aliases for SNRNP40 Gene
- Small Nuclear Ribonucleoprotein U5 Subunit 40 2 3 5
- Small Nuclear Ribonucleoprotein, U5 40kDa Subunit 2 3
- Small Nuclear Ribonucleoprotein 40kDa (U5) 2 3
- WD Repeat Domain 57 (U5 SnRNP Specific) 2 3
- WD Repeat-Containing Protein 57 3 4
- U5 SnRNP 40 KDa Protein 3 4
- 38 KDa-Splicing Factor 3 4
- Prp8-Binding Protein 3 4
- HPRP8BP 3 4
- PRP8BP 3 4
- U5-40K 3 4
External Ids for SNRNP40 Gene
- HGNC: 30857
- Entrez Gene: 9410
- Ensembl: ENSG00000060688
- OMIM: 607797
- UniProtKB: Q96DI7
Previous HGNC Symbols for SNRNP40 Gene
- WDR57
Previous GeneCards Identifiers for SNRNP40 Gene
- GC01M031506
- GC01M031732
- GC01M029838
Summaries for SNRNP40 Gene
-
This gene encodes a component of the U5 small nuclear ribonucleoprotein (snRNP) particle. The U5 snRNP is part of the spliceosome, a multiprotein complex that catalyzes the removal of introns from pre-messenger RNAs. [provided by RefSeq, Jul 2008]
GeneCards Summary for SNRNP40 Gene
SNRNP40 (Small Nuclear Ribonucleoprotein U5 Subunit 40) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Major Pathway and mRNA Splicing - Minor Pathway. An important paralog of this gene is WDR5B.
UniProtKB/Swiss-Prot for SNRNP40 Gene
-
Component of the U5 small nuclear ribonucleoprotein (snRNP) complex. The U5 snRNP is part of the spliceosome, a multiprotein complex that catalyzes the removal of introns from pre-messenger RNAs.
Additional gene information for SNRNP40 Gene
No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SNRNP40 Gene
Genomics for SNRNP40 Gene
GeneHancer (GH) Regulatory Elements for SNRNP40 Gene
Promoters and enhancers for SNRNP40 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association
Download GeneHancer data dump
GeneHancers around SNRNP40 on UCSC Golden Path with GeneCards custom track
- Top Transcription factor binding sites by QIAGEN in the SNRNP40 gene promoter:
-
- AREB6
- NF-AT4
- NF-AT3
- NF-AT2
- NF-AT1
- NF-AT
- RORalpha2
- HOXA5
- Pax-6
- POU3F2
Regulatory Element Products
Genomic Locations for SNRNP40 Gene
Genomic Locations for SNRNP40 Gene
- chr1:31,259,568-31,296,797
- (GRCh38/hg38)
- Size:
- 37,230 bases
- Orientation:
- Minus strand
- chr1:31,732,415-31,769,662
- (GRCh37/hg19)
- Size:
- 37,248 bases
- Orientation:
- Minus strand
Genomic View for SNRNP40 Gene
Genes around SNRNP40 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 1p35.2 by Entrez Gene
- 1p35.2 by HGNC
- 1p35.2 by Ensembl
SNRNP40 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 SNRNP40 Gene
Proteins for SNRNP40 Gene
-
Protein details for SNRNP40 Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- Q96DI7-SNR40_HUMAN
- Recommended name:
- U5 small nuclear ribonucleoprotein 40 kDa protein
- Protein Accession:
- Q96DI7
- B4DQJ1
- O75938
- O95320
Protein attributes for SNRNP40 Gene
- Size:
- 357 amino acids
- Molecular mass:
- 39311 Da
- Quaternary structure:
-
- Identified in the spliceosome C complex. Part of the U5 snRNP complex. Interacts with PRPF8. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39.
- SequenceCaution:
-
- Sequence=AAC64084.1; Type=Frameshift; Positions=319; Note=An insertion/deletion of a short nucleotide stretch in its cDNA resulting in a frameshift.; Evidence={ECO:0000305};
Three dimensional structures from OCA and Proteopedia for SNRNP40 Gene
Protein Expression for SNRNP40 Gene
Post-translational modifications for SNRNP40 Gene
Other Protein References for SNRNP40 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
-
Custom Antibody ServicesOriGene Antibodies for SNRNP40
- Novus Biologicals Antibodies for SNRNP40
-
Abcam antibodies for SNRNP40
- Invitrogen Antibodies for SNRNP40
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-
Boster Bio Antibodies for SNRNP40
Protein Products
-
OriGene Purified Proteins for SNRNP40
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- antibodies-online: Search results for 5 available SNRNP40 Proteins ranked by validation data
- Compare Top SNRNP40 Proteins
-
Quality Products:
- Search GeneTex for Proteins for SNRNP40
-
Abcam proteins for SNRNP40
Assay Products
No data available for DME Specific Peptides for SNRNP40 Gene
Domains & Families for SNRNP40 Gene
Gene Families for SNRNP40 Gene
- HGNC:
- Human Protein Atlas (HPA):
-
- Predicted intracellular proteins
- Predicted membrane proteins
Protein Domains for SNRNP40 Gene
Suggested Antigen Peptide Sequences for SNRNP40 Gene
Graphical View of Domain Structure for InterPro Entry
No data available for UniProtKB/Swiss-Prot for SNRNP40 Gene
Function for SNRNP40 Gene
Molecular function for SNRNP40 Gene
- UniProtKB/Swiss-Prot Function:
- Component of the U5 small nuclear ribonucleoprotein (snRNP) complex. The U5 snRNP is part of the spliceosome, a multiprotein complex that catalyzes the removal of introns from pre-messenger RNAs.
Phenotypes From GWAS Catalog for SNRNP40 Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0003720 | CONTRIBUTES_TO telomerase activity | IBA | -- |
| GO:0003723 | RNA binding | IBA | -- |
| GO:0005515 | protein binding | IEA,IPI | 9774689 |
Phenotypes for SNRNP40 Gene
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
- Cyagen custom Knockout/knockin (KOKI) mouse models for SNRNP40
-
CRISPR Products
-
OriGene CRISPR knockouts for SNRNP40
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- Overview of 104 available SNRNP40 gene related products
- Applied Biological Materials CRISPR for SNRNP40
-
Vectors and viruses for KO, Activation, Repression, and more
-
Santa Cruz Biotechnology (SCBT) CRISPR for SNRNP40
- GenScript: Design CRISPR guide RNA sequences for SNRNP40
miRNA for SNRNP40 Gene
- miRTarBase miRNAs that target SNRNP40
miRNA Products
Inhibitory RNA Products
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- Overview of 104 available SNRNP40 gene related products
Clone Products
- Sino Biological Human cDNA Clone for SNRNP40
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- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for SNRNP40
-
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
- Addgene plasmids for SNRNP40
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for SNRNP40
- Applied Biological Materials Clones for SNRNP40
-
Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SNRNP40 Gene
Localization for SNRNP40 Gene
Subcellular locations from UniProtKB/Swiss-Prot for SNRNP40 Gene
- Nucleus.
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
| cytosol | 5 |
| extracellular | 1 |
| peroxisome | 1 |
- Nuclear speckles (3)
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005634 | nucleus | IEA | -- |
| GO:0005654 | nucleoplasm | TAS | -- |
| GO:0005681 | spliceosomal complex | IEA | -- |
| GO:0005682 | U5 snRNP | TAS | 9774689 |
| GO:0005697 | telomerase holoenzyme complex | IBA | -- |
Pathways & Interactions for SNRNP40 Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | mRNA Splicing - Major Pathway |
.79
|
.50
.41
|
| 2 | Gene Expression |
.48
|
|
| 3 | mRNA Splicing - Minor Pathway | ||
Pathways by source for SNRNP40 Gene
1 BioSystems pathway for SNRNP40 Gene
5 Reactome pathways for SNRNP40 Gene
1 KEGG pathway for SNRNP40 Gene
Interacting Proteins for SNRNP40 Gene
Selected Interacting proteins:
Q96DI7-SNR40_HUMAN
ENSP00000263694
for SNRNP40 Gene via
UniProtKB
STRING
MINT
IID
GPS-Prot Interaction Network for SNRNP40
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000375 | RNA splicing, via transesterification reactions | TAS | 9774689 |
| GO:0000398 | mRNA splicing, via spliceosome | TAS | -- |
| GO:0000722 | telomere maintenance via recombination | IBA | -- |
| GO:0006396 | RNA processing | TAS | 9774689 |
| GO:0006397 | mRNA processing | IEA | -- |
No data available for SIGNOR curated interactions for SNRNP40 Gene
Transcripts for SNRNP40 Gene
mRNA/cDNA for SNRNP40 Gene
- (1) REFSEQ mRNAs :
- (6) Additional mRNA sequences :
- (184) Selected AceView cDNA sequences:
- (7) Ensembl transcripts including schematic representations, and UCSC links where relevant :
-
- ENST00000263694 1597 bps (uc001bso.4)
- ENST00000486941 743 bps (uc057edm.1)
- ENST00000489853 1928 bps (uc057edn.1)
- ENST00000373720 1087 bps (uc057edo.1)
- ENST00000491106 459 bps (uc057edp.1)
Unigene Clusters for SNRNP40 Gene
- Small nuclear ribonucleoprotein 40kDa (U5):
- Representative Sequences:
CRISPR Products
-
OriGene CRISPR knockouts for SNRNP40
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for SNRNP40
- genomics-online: gRNA clones - Search results for 104 available SNRNP40 gene related products
- Overview of 104 available SNRNP40 gene related products
- Applied Biological Materials CRISPR for SNRNP40
-
Vectors and viruses for KO, Activation, Repression, and more
-
Santa Cruz Biotechnology (SCBT) CRISPR for SNRNP40
- GenScript: Design CRISPR guide RNA sequences for SNRNP40
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for SNRNP40
- Browse OriGene Inhibitory RNA Products For SNRNP40
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SNRNP40
- genomics-online: shRNA clones - Search results for 104 available SNRNP40 gene related products
- Overview of 104 available SNRNP40 gene related products
Clone Products
- Sino Biological Human cDNA Clone for SNRNP40
- VectorBuilder custom plasmid, inducible vectors for SNRNP40
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for SNRNP40
-
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
- Addgene plasmids for SNRNP40
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for SNRNP40
- Applied Biological Materials Clones for SNRNP40
-
Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
Expression for SNRNP40 Gene
This gene is overexpressed in CD8 Tcells (8.1), Monocytes (7.7), and Peripheral blood mononuclear cells (7.4).
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SNRNP40 Gene
- Elite partner
NURSA nuclear receptor signaling pathways regulating expression of SNRNP40 Gene:
SNRNP40SOURCE GeneReport for Unigene cluster for SNRNP40 Gene:
Hs.33962Evidence on tissue expression from TISSUES for SNRNP40 Gene
- Nervous system(2.4)
- Kidney(2.2)
- Pancreas(2.2)
Primer Products
-
OriGene qPCR primer pairs and template standards for SNRNP40
-
OriGene qPCR primer pairs for SNRNP40
- genomics-online: primer clones - Search results for 104 available SNRNP40 gene related products
- Overview of 104 available SNRNP40 gene related products
Gene Expression Assay Products
No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SNRNP40 Gene
Orthologs for SNRNP40 Gene
This gene was present in the common ancestor of eukaryotes.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | SNRNP40 34 33 |
|
OneToOne | |
| oppossum (Monodelphis domestica) |
Mammalia | SNRNP40 34 |
|
OneToOne | |
| platypus (Ornithorhynchus anatinus) |
Mammalia | -- 34 |
|
OneToMany | |
| -- 34 |
|
OneToMany | |||
| dog (Canis familiaris) |
Mammalia | SNRNP40 34 33 |
|
OneToOne | |
| cow (Bos Taurus) |
Mammalia | SNRNP40 34 33 |
|
OneToOne | |
| mouse (Mus musculus) |
Mammalia | Snrnp40 16 34 33 |
|
||
| rat (Rattus norvegicus) |
Mammalia | Snrnp40 33 |
|
||
| chicken (Gallus gallus) |
Aves | SNRNP40 34 33 |
|
OneToOne | |
| lizard (Anolis carolinensis) |
Reptilia | SNRNP40 34 |
|
OneToOne | |
| tropical clawed frog (Silurana tropicalis) |
Amphibia | snrnp40 33 |
|
||
| Str.6725 33 |
|
||||
| zebrafish (Danio rerio) |
Actinopterygii | snrnp40 34 33 |
|
OneToOne | |
| zgc56312 33 |
|
||||
| fruit fly (Drosophila melanogaster) |
Insecta | CG3436 34 33 |
|
OneToOne | |
| African malaria mosquito (Anopheles gambiae) |
Insecta | AgaP_AGAP009506 33 |
|
||
| worm (Caenorhabditis elegans) |
Secernentea | F08G12.2 34 33 |
|
OneToMany | |
| C18E3.5 34 |
|
OneToMany | |||
| thale cress (Arabidopsis thaliana) |
eudicotyledons | AT2G43770 33 |
|
||
| rice (Oryza sativa) |
Liliopsida | Os06g0653800 33 |
|
||
| Os.4736 33 |
|
||||
| corn (Zea mays) |
Liliopsida | Zm.13837 33 |
|
||
| wheat (Triticum aestivum) |
Liliopsida | Ta.7772 33 |
|
||
| fission yeast (Schizosaccharomyces pombe) |
Schizosaccharomycetes | spf38 33 |
|
||
| bread mold (Neurospora crassa) |
Ascomycetes | NCU05797 33 |
|
- Species where no ortholog for SNRNP40 was found in the sources mined by GeneCards:
-
- A. gosspyii yeast (Ashbya gossypii)
- Actinobacteria (Mycobacterium tuberculosis)
- African clawed frog (Xenopus laevis)
- 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)
- Chromalveolata (Phytophthora infestans)
- common water flea (Daphnia pulex)
- E. coli (Escherichia coli)
- filamentous fungi (Aspergillus nidulans)
- Firmicute bacteria (Streptococcus pneumoniae)
- 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 squirt (Ciona intestinalis)
- sea squirt (Ciona savignyi)
- sea urchin (Strongylocentrotus purpuratus)
- sorghum (Sorghum bicolor)
- soybean (Glycine max)
- stem rust fungus (Puccinia graminis)
- sugarcane (Saccharum officinarum)
- tomato (Lycopersicon esculentum)
- toxoplasmosis (Toxoplasma gondii)
- Trichoplax (Trichoplax adhaerens)
Evolution for SNRNP40 Gene
- ENSEMBL:
- Gene Tree for SNRNP40 (if available)
- TreeFam:
- Gene Tree for SNRNP40 (if available)
- Aminode:
- Evolutionary constrained regions (ECRs) for SNRNP40: view image
Paralogs for SNRNP40 Gene
Paralogs for SNRNP40 Gene
(20) SIMAP similar genes for SNRNP40 Gene using alignment to 2 proteins:
- SNR40_HUMAN
- B4DQJ1_HUMAN
Pseudogenes.org Pseudogenes for SNRNP40 Gene
Variants for SNRNP40 Gene
| SNP ID | Clin | Chr 01 pos | Variation | AA Info | Type |
|---|---|---|---|---|---|
| rs1000082214 | -- | 31,288,382(-) | C/T | intron_variant | |
| rs1000186113 | -- | 31,281,591(-) | T/C | intron_variant | |
| rs1000255569 | -- | 31,264,648(-) | C/T | intron_variant | |
| rs1000287439 | -- | 31,293,792(-) | G/A | intron_variant | |
| rs1000309872 | -- | 31,277,775(-) | A/C | intron_variant |
| Variant ID | Type | Subtype | PubMed ID |
|---|---|---|---|
| esv2758930 | CNV | loss | 17122850 |
| esv3585645 | CNV | loss | 21293372 |
| nsv10051 | CNV | gain | 18304495 |
| nsv161067 | CNV | deletion | 16902084 |
| nsv471842 | CNV | novel sequence insertion | 20440878 |
Residual Variation Intolerance Score:
21.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
0.67;
14.37% of all genes are more intolerant (likely to be disease-causing)
Additional Variant Information for SNRNP40 Gene
- SNPedia medical, phenotypic, and genealogical associations of SNPs for
- SNRNP40
SNP Genotyping and Copy Number Assay Products
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SNRNP40 Gene
Disorders for SNRNP40 Gene
Additional Disease Information for SNRNP40
No disorders were found for SNRNP40 Gene.
No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SNRNP40 Gene
Publications for SNRNP40 Gene
- Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. (PMID: 9731529) Neubauer G … Mann M (Nature genetics 1998) 2 3 4 58
- The human U5-220kD protein (hPrp8) forms a stable RNA-free complex with several U5-specific proteins, including an RNA unwindase, a homologue of ribosomal elongation factor EF-2, and a novel WD-40 protein. (PMID: 9774689) Achsel T … Lührmann R (Molecular and cellular biology 1998) 2 3 4 58
- The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
- The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP. (PMID: 16723661) Liu S … Lührmann R (RNA (New York, N.Y.) 2006) 3 4 58
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
Products for SNRNP40 Gene
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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
- Addgene plasmids for SNRNP40
- antibodies-online: Search results for 27 available SNRNP40 Antibodies ranked by validation data
- Compare Top SNRNP40 Antibodies
- antibodies-online: Search results for available SNRNP40 related products ranked by validation data
- antibodies-online: Search results for 5 available SNRNP40 Proteins ranked by validation data
- Compare Top SNRNP40 Proteins
- Quality Products:
- Search GeneTex for Antibodies for SNRNP40
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- genomics-online: cdna clones - Search results for 104 available SNRNP40 gene related products
- Overview of 104 available SNRNP40 gene related products
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- Overview of 104 available SNRNP40 gene related products
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- Overview of 104 available SNRNP40 gene related products
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- Boster Bio Antibodies for SNRNP40
- Browse Boster Bio ELISA Kits
Sources for SNRNP40 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
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