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This gene encodes a transcriptional regulator of sensory neuronal specification that plays a critical role in pain perception. The encoded protein contains an N-terminal PRDI-BF1 and RIZ homology (PR) domain, a SET domain, and three C-terminal C2H2 zinc finger DNA-binding domains. Naturally occurring mutations in this gene are associated with congenital insensitivity to pain (C... See more...
Aliases for PRDM12 Gene
Aliases for PRDM12 Gene
External Ids for PRDM12 Gene
- HGNC: 13997
- Entrez Gene: 59335
- Ensembl: ENSG00000130711
- OMIM: 616458
- UniProtKB: Q9H4Q4
Previous GeneCards Identifiers for PRDM12 Gene
- GC09P124554
- GC09P125086
- GC09P126893
- GC09P128816
- GC09P130569
- GC09P132529
- GC09P133539
- GC09P103027
Summaries for PRDM12 Gene
-
This gene encodes a transcriptional regulator of sensory neuronal specification that plays a critical role in pain perception. The encoded protein contains an N-terminal PRDI-BF1 and RIZ homology (PR) domain, a SET domain, and three C-terminal C2H2 zinc finger DNA-binding domains. Naturally occurring mutations in this gene are associated with congenital insensitivity to pain (CIP), and hereditary sensory and autonomic neuropathies (HSAN's) affecting peripheral sensory and autonomic neurons. Deregulation of this gene is associated with solid cancers and hematological malignancies including chronic myeloid leukaemia. [provided by RefSeq, Mar 2017]
GeneCards Summary for PRDM12 Gene
PRDM12 (PR/SET Domain 12) is a Protein Coding gene. Diseases associated with PRDM12 include Neuropathy, Hereditary Sensory And Autonomic, Type Viii and Factitious Disorder. Gene Ontology (GO) annotations related to this gene include methyltransferase activity. An important paralog of this gene is ZNF683.
UniProtKB/Swiss-Prot Summary for PRDM12 Gene
-
Involved in the positive regulation of histone H3-K9 dimethylation.
Additional gene information for PRDM12 Gene
- HGNC(13997)
- Entrez Gene(59335)
- Ensembl(ENSG00000130711)
- OMIM(616458)
- UniProtKB(Q9H4Q4)
- Open Targets Platform(ENSG00000130711)
- Monarch Initiative
- Search for PRDM12 at DataMed
- Search for PRDM12 at HumanCyc
No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PRDM12 Gene
Genomics for PRDM12 Gene
GeneHancer (GH) Regulatory Elements Pubs
Promoters and enhancers for PRDM12 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 |
|---|---|---|---|---|---|---|---|---|---|---|
| GH09J130664 | Promoter/Enhancer | 0.9 | Ensembl ENCODE | 600.7 | +0.0 | 7 | 0.4 | PATZ1 EZH2 ZBTB17 ZFHX2 ZNF777 ZNF335 ZNF398 EGR2 EGR1 GLIS2 | PRDM12 piR-58662 EXOSC2 RF00017-7999 | |
| GH09J130665 | Enhancer | 0.8 | VISTA Ensembl | 600.7 | +1.3 | 1290 | 1.4 | EZH2 ZBTB26 YY1 CBX8 | PRDM12 QRFP piR-58662 EXOSC2 RF00017-7999 | |
| GH09J130666 | Promoter | 0.6 | Ensembl | 600.7 | -0.9 | -893 | 0.2 | EZH2 UBTF PCBP1 BCL6 | PRDM12 RF00017-8003 RF00017-7999 FUBP3 | |
| GH09J130663 | Enhancer | 0.4 | ENCODE | 600.7 | -0.6 | -575 | 0.1 | EZH2 UBTF PCBP1 SP1 | PRDM12 RF00017-8003 RF00017-7999 FUBP3 | |
| GH09J130467 | Enhancer | 1.2 | FANTOM5 Ensembl CraniofacialAtlas dbSUPER | 21.4 | -197.8 | -197786 | 2.4 | ZIC2 POLR2A SP1 SCRT2 RAD21 CTCF ATF3 YY1 GABPA ZBTB33 | PRDM12 TOR1A lnc-QRFP-1 SNODB1213 ASS1 FUBP3 |
- Elite GeneHancer and/or Elite GeneHancer-gene association
Download GeneHancer data from 2017 publication |
Request up-to-date GeneHancer data (full dataset)
GeneHancers around PRDM12 on the GeneHancer Hub at the UCSC Golden Path
Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PRDM12
- Top Transcription factor binding sites by QIAGEN in the PRDM12 gene promoter:
-
- GATA-1
- GATA-2
- Ik-1
- MZF-1
- NF-AT
- NF-AT1
- NF-AT2
- NF-AT3
- NF-AT4
Genomic Locations for PRDM12 Gene
Genomic Locations for PRDM12 Gene
- chr9:130,664,594-130,682,983
- (GRCh38/hg38)
- Size:
- 18,390 bases
- Orientation:
- Plus strand
- chr9:133,539,981-133,558,384
- (GRCh37/hg19)
- Size:
- 18,404 bases
- Orientation:
- Plus strand
Genomic View for PRDM12 Gene
Genes around PRDM12 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 9q34.12 by HGNC
- 9q34.12 by Entrez Gene
- 9q34.12 by Ensembl
PRDM12 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 PRDM12 Gene
Proteins for PRDM12 Gene
-
Protein details for PRDM12 Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- Q9H4Q4-PRD12_HUMAN
- Recommended name:
- PR domain zinc finger protein 12
- Protein Accession:
- Q9H4Q4
- A3KFK9
Protein attributes for PRDM12 Gene
- Size:
- 367 amino acids
- Molecular mass:
- 40403 Da
- Quaternary structure:
- No Data Available
Protein Expression for PRDM12 Gene
Post-translational modifications for PRDM12 Gene
Other Protein References for PRDM12 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
- Creative Diagnostics Anti-PRDM12 polyclonal antibody
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-
Abcam antibodies for PRDM12
- Invitrogen Antibodies for PRDM12 (AFLGC-PRDM12)
-
Boster Bio Antibodies for PRDM12
Protein Products
-
OriGene Purified Proteins for PRDM12
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- Origene Custom Protein Services for PRDM12
- antibodies-online: Show 3 available PRDM12 Proteins ranked by validation data
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-
Quality Products:
-
Abcam proteins for PRDM12
No data available for DME Specific Peptides for PRDM12 Gene
Domains & Families for PRDM12 Gene
Gene Families for PRDM12 Gene
- HGNC:
- Human Protein Atlas (HPA):
-
- Disease related genes
- Predicted intracellular proteins
Protein Domains for PRDM12 Gene
- InterPro:
- ProtoNet:
Suggested Antigen Peptide Sequences for PRDM12 Gene
- GenScript: Design optimal peptide antigens:
-
- PR domain-containing protein 12 (PRD12_HUMAN)
Graphical View of Domain Structure for InterPro Entry
Q9H4Q4UniProtKB/Swiss-Prot:
PRD12_HUMAN :- Belongs to the class V-like SAM-binding methyltransferase superfamily.
- Family:
-
- Belongs to the class V-like SAM-binding methyltransferase superfamily.
Function for PRDM12 Gene
Molecular function for PRDM12 Gene
- UniProtKB/Swiss-Prot Function:
- Involved in the positive regulation of histone H3-K9 dimethylation.
Enzyme Numbers (IUBMB) for PRDM12 Gene
Phenotypes From GWAS Catalog for PRDM12 Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000977 | RNA polymerase II regulatory region sequence-specific DNA binding | IBA | -- |
| GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific | ISM | 19274049 |
| GO:0003676 | nucleic acid binding | IEA | -- |
| GO:0003677 | DNA binding | IEA | -- |
| GO:0003700 | DNA-binding transcription factor activity | IBA | -- |
Phenotypes for PRDM12 Gene
- MGI mutant phenotypes for PRDM12:
- inferred from 3 alleles
- GenomeRNAi human phenotypes for PRDM12:
-
- no effect
- Decreased viability
- shRNA abundance <= 25%
- Increased ionizing radiation sensitivity
- Increased epidermal growth factor (EGF) endocytosis, decreased transferrin (TF) endocytosis
- Decreased shRNA abundance (Z-score < -2)
- Increased shRNA abundance (Z-score > 2)
- Increased cell number in G2M, increased number of polyploid cells, increased number of cells with high perimeter-to-area ratio nuclei
Animal Models for PRDM12 Gene
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
CRISPR Products
- Applied Biological Materials (abm): CRISPR Clones for PRDM12 - Select products 50% OFF >
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-
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-
Santa Cruz Biotechnology (SCBT) CRISPR for PRDM12
miRNA for PRDM12 Gene
- miRTarBase miRNAs that target PRDM12
-
- mmu-miR-466l-5p (MIRT595686)
- mmu-miR-466k (MIRT595687)
- mmu-miR-466i-5p (MIRT595688)
- mmu-miR-466d-5p (MIRT595689)
- mmu-miR-1843b-5p (MIRT595690)
- mmu-miR-1940 (MIRT595691)
- hsa-miR-6834-5p (MIRT719781)
- hsa-miR-4710 (MIRT719782)
- hsa-miR-4632-3p (MIRT719783)
- hsa-miR-6133 (MIRT719784)
- hsa-miR-6130 (MIRT719785)
- hsa-miR-6129 (MIRT719786)
- hsa-miR-6127 (MIRT719787)
- hsa-miR-4510 (MIRT719788)
- hsa-miR-4419a (MIRT719789)
- hsa-miR-6875-5p (MIRT719790)
- hsa-miR-3126-5p (MIRT719791)
- hsa-miR-4302 (MIRT719792)
- hsa-miR-6733-3p (MIRT719793)
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for PRDM12
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Clone Products
- Applied Biological Materials (abm): Clones for PRDM12 - Select products 50% OFF >
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- Addgene plasmids for PRDM12
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Cell Line Products
-
Horizon Cell Lines for PRDM12
No data available for Transcription Factor Targets and HOMER Transcription for PRDM12 Gene
Localization for PRDM12 Gene
Subcellular locations from UniProtKB/Swiss-Prot for PRDM12 Gene
- Nucleus.
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
| cytosol | 2 |
| plasma membrane | 1 |
| cytoskeleton | 1 |
- Nucleoplasm (2)
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005634 | nucleus | IDA | 26005867 |
| GO:0005654 | nucleoplasm | IDA | -- |
Pathways & Interactions for PRDM12 Gene
Interacting Proteins for PRDM12 Gene
GPS-Prot Interaction Network for PRDM12
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000122 | negative regulation of transcription by RNA polymerase II | IEA,ISS | -- |
| GO:0010468 | regulation of gene expression | IBA | 21873635 |
| GO:0019233 | sensory perception of pain | IMP | 26005867 |
| GO:0022008 | neurogenesis | IEA,IBA | 21873635 |
| GO:0031175 | neuron projection development | IMP | 26005867 |
No data available for Pathways by source and SIGNOR curated interactions for PRDM12 Gene
Transcripts for PRDM12 Gene
mRNA/cDNA for PRDM12 Gene
- 1 REFSEQ mRNAs :
- 1 NCBI additional mRNA sequence :
- 1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
-
- ENST00000253008 2478 nts (view in UCSC)
CRISPR Products
- Applied Biological Materials (abm): CRISPR Clones for PRDM12 - Select products 50% OFF >
- * PRDM12 CRISPR as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Protein Vector - Browse All
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-
OriGene CRISPR knockouts for PRDM12
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-
Santa Cruz Biotechnology (SCBT) CRISPR for PRDM12
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for PRDM12
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Clone Products
- Applied Biological Materials (abm): Clones for PRDM12 - Select products 50% OFF >
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- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
- Sino Biological Human cDNA Clone for PRDM12
- Addgene plasmids for PRDM12
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for PRDM12
Relevant External Links for PRDM12 Gene
- GeneLoc Exon Structure for
- PRDM12
Expression for PRDM12 Gene
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
- Brain (Nervous System)
- Neural Tube (Nervous System)
-
Heart (Cardiovascular System)
mRNA differential expression in normal tissues according to GTEx for PRDM12 Gene
This gene is overexpressed in Brain - Hypothalamus (x7.1), Brain - Cortex (x4.6), Brain - Anterior cingulate cortex (BA24) (x4.4), and Brain - Frontal Cortex (BA9) (x4.2).
This gene is overexpressed in Lymph node (69.0).
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PRDM12 Gene
Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PRDM12
SOURCE GeneReport for Unigene cluster for PRDM12 Gene:
Hs.495311mRNA Expression by UniProt/SwissProt for PRDM12 Gene:
Q9H4Q4-PRD12_HUMAN
Tissue specificity:
Not found in adult tissues except in dorsal root ganglia.
Primer Products
-
OriGene qPCR primer pairs for PRDM12
Gene Expression Assay Products
No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRDM12 Gene
Orthologs for PRDM12 Gene
This gene was present in the common ancestor of animals.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| Chimpanzee (Pan troglodytes) |
Mammalia | PRDM12 30 31 |
|
OneToOne | |
| Dog (Canis familiaris) |
Mammalia | PRDM12 31 |
|
OneToOne | |
| LOC608616 30 |
|
||||
| Cow (Bos Taurus) |
Mammalia | PRDM12 30 31 |
|
OneToOne | |
| Oppossum (Monodelphis domestica) |
Mammalia | PRDM12 31 |
|
OneToOne | |
| Platypus (Ornithorhynchus anatinus) |
Mammalia | PRDM12 31 |
|
OneToOne | |
| Mouse (Mus musculus) |
Mammalia | Prdm12 30 17 31 |
|
OneToOne | |
| Rat (Rattus norvegicus) |
Mammalia | Prdm12 30 |
|
||
| Chicken (Gallus gallus) |
Aves | PRDM12 30 31 |
|
OneToOne | |
| Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | prdm12 30 |
|
||
| African clawed frog (Xenopus laevis) |
Amphibia | MGC68944 30 |
|
||
| Zebrafish (Danio rerio) |
Actinopterygii | prdm12b 30 31 |
|
OneToOne | |
| Worm (Caenorhabditis elegans) |
Secernentea | set-17 31 |
|
OneToMany |
- Species where no ortholog for PRDM12 was found in the sources mined by GeneCards:
-
- A. gosspyii yeast (Eremothecium 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)
- Fruit Fly (Drosophila melanogaster)
- Green Algae (Chlamydomonas reinhardtii)
- Honey Bee (Apis mellifera)
- K. Lactis Yeast (Kluyveromyces lactis)
- Lizard (Anolis carolinensis)
- 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 Vase (Ciona intestinalis)
- Sea Squirt (Ciona savignyi)
- 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)
Evolution for PRDM12 Gene
- ENSEMBL:
- Gene Tree for PRDM12 (if available)
- TreeFam:
- Gene Tree for PRDM12 (if available)
- Aminode:
- Evolutionary constrained regions (ECRs) for PRDM12: view image
Paralogs for PRDM12 Gene
Paralogs for PRDM12 Gene
Variants for PRDM12 Gene
Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM12 Gene
- PRD12_HUMAN-Q9H4Q4
- The poly-alanine tract is polymorphic in the general population and contains a maximum of 14 alanines.
Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PRDM12 Gene
| SNP ID | Clinical significance and condition | Chr 09 pos | Variation | AA Info | Type |
|---|---|---|---|---|---|
| 648392 | Uncertain Significance: Neuropathy, hereditary sensory and autonomic, type VIII | 130,681,605(+) | TCGC/T | INFRAME_DELETION | |
| 660300 | Uncertain Significance: Neuropathy, hereditary sensory and autonomic, type VIII | 130,681,544(+) | A/G | MISSENSE_VARIANT | |
| 702870 | Likely Benign: Neuropathy, hereditary sensory and autonomic, type VIII | 130,668,283(+) | C/T | SYNONYMOUS_VARIANT | |
| 706570 | Likely Benign: not provided | 130,668,193(+) | C/T | SYNONYMOUS_VARIANT | |
| 750522 | Likely Benign: not provided | 130,668,178(+) | G/A | SYNONYMOUS_VARIANT |
Residual Variation Intolerance Score:
27.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
0.76;
16.03% of all genes are more intolerant (likely to be disease-causing)
Additional Variant Information for PRDM12 Gene
SNP Genotyping and Copy Number Assay Products
Disorders for PRDM12 Gene
(3) MalaCards diseases for PRDM12 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| neuropathy, hereditary sensory and autonomic, type viii |
|
|
| factitious disorder |
|
|
| neuropathy |
|
|
Search PRDM12 in MalaCards
View complete list of genes associated with diseases
UniProtKB/Swiss-Prot
PRD12_HUMAN- Neuropathy, hereditary sensory and autonomic, 8 (HSAN8) [MIM:616488]: A form of hereditary sensory and autonomic neuropathy, a genetically and clinically heterogeneous group of disorders characterized by degeneration of dorsal root and autonomic ganglion cells, and by sensory and/or autonomic abnormalities. HSAN8 patients manifest congenital insensitivity to pain resulting in ulceration to the fingers, tongue, lips, and other distal appendages. Some patients may also have decreased sweating and tear production. {ECO:0000269 PubMed:26005867}. Note=The disease is caused by mutations affecting the gene represented in this entry.
Additional Disease Information for PRDM12
No data available for Genatlas for PRDM12 Gene
Publications for PRDM12 Gene
- Transcriptional regulator PRDM12 is essential for human pain perception. (PMID: 26005867) Chen YC … Senderek J (Nature genetics 2015) 3 4
- A potential role for PRDM12 in the pathogenesis of chronic myeloid leukaemia with derivative chromosome 9 deletion. (PMID: 14523459) Reid AG … Nacheva EP (Leukemia 2004) 2 3
- Congenital Insensitivity to Pain Overview (PMID: 29419974) Schon KR … Woods CG (GeneReviews® 2018) 3
- Midface toddler excoriation syndrome (MiTES) can be caused by autosomal recessive biallelic mutations in a gene for congenital insensitivity to pain, PRDM12. (PMID: 29949203) Moss C … Woods G (The British journal of dermatology 2018) 3
- Hereditary Sensory Polyneuropathy, Pain Insensitivity and Global Developmental Delay due to Novel Mutation in PRDM12 Gene. (PMID: 28050684) Saini AG … Singhi P (Indian journal of pediatrics 2017) 3
ExternalLinks
Products for PRDM12 Gene
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- antibodies-online: Show 9 available PRDM12 Antibodies ranked by validation data
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- Boster Bio Antibodies for PRDM12
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Sources for PRDM12 Gene
- (1) GeneCards
- (2) HGNC
- (3) NCBI Entrez Gene
- (4) UniProtKB/Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) Cell Signaling Technology
- (12) GO
- (13) UniProtKB/TrEMBL
- (14) InterPro
- (15) ProtoNet
- (16) Blocks
- (17) MGI
- (18) IUBMB
- (19) KEGG
- (20) MINT
- (21) STRING
- (22) IntAct
- (23) Novoseek
- (24) PharmGKB
- (25) DrugBank
- (26) HMDB
- (27) ASD
- (28) SAGE
- (29) SOURCE
- (30) HomoloGene
- (31) PanEnsembl
- (32) euGenes
- (33) SGD
- (34) FlyBase
- (35) WormBase
- (36) Pseudogene
- (37) DGV
- (38) dbSNP
- (39) GenAtlas
- (40) HGMD
- (41) GAD
- (42) BGMUT
- (43) HuGE
- (44) Atlas
- (45) GenBank
- (46) HORDE
- (47) HUGE
- (48) IMGT
- (49) Leiden
- (50) miRBase
- (51) DME
- (52) OriGene
- (53) PubMed
- (54) R&D Systems
- (55) TGDB
- (56) Tocris
- (57) Abcam
- (58) Novus Biologicals
- (59) ProSpec
- (60) Sino Biological
- (61) GenScript
- (62) Qiagen
- (63) OCA
- (64) Proteopedia
- (65) MOPED
- (66) neXtProt
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