Aliases for RFX1 Gene
Aliases for RFX1 Gene
External Ids for RFX1 Gene
- HGNC: 9982
- Entrez Gene: 5989
- Ensembl: ENSG00000132005
- OMIM: 600006
- UniProtKB: P22670
Previous GeneCards Identifiers for RFX1 Gene
- GC19M014429
- GC19M013917
- GC19M014072
- GC19M013643
Summaries for RFX1 Gene
-
This gene encodes a member of the regulatory factor X (RFX) family of transcription factors, which are characterized by a winged-helix DNA-binding domain. The encoded transcription factor contains an N-terminal activation domain and a C-terminal repression domain, and may activate or repress target gene expression depending on cellular context. This transcription factor has been shown to regulate a wide variety of genes involved in immunity and cancer, including the MHC class II genes and genes that may be involved in cancer progression. This gene exhibits altered expression in glioblastoma and the autoimmune disease systemic lupus erythematosis (SLE). [provided by RefSeq, Jul 2016]
GeneCards Summary for RFX1 Gene
RFX1 (Regulatory Factor X1) is a Protein Coding gene. Diseases associated with RFX1 include Bare Lymphocyte Syndrome, Type Ii and Hemopneumothorax. Gene Ontology (GO) annotations related to this gene include RNA polymerase II proximal promoter sequence-specific DNA binding and transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding. An important paralog of this gene is RFX3.
UniProtKB/Swiss-Prot for RFX1 Gene
-
Regulatory factor essential for MHC class II genes expression. Binds to the X boxes of MHC class II genes. Also binds to an inverted repeat (ENH1) required for hepatitis B virus genes expression and to the most upstream element (alpha) of the RPL30 promoter.
No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RFX1 Gene
Genomics for RFX1 Gene
GeneHancer (GH) Regulatory Elements for RFX1 Gene
Promoters and enhancers for RFX1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association
Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)
GeneHancers around RFX1 on UCSC Golden Path with GeneCards custom track
- Top Transcription factor binding sites by QIAGEN in the RFX1 gene promoter:
-
- E2F-4
- E2F-3a
- E2F-2
- E2F-1
- E2F
- E2F-5
- HOXA5
- CBF-C
- CBF-A
Regulatory Element Products
Genomic Locations for RFX1 Gene
Genomic Locations for RFX1 Gene
- chr19:13,961,530-14,007,514
- (GRCh38/hg38)
- Size:
- 45,985 bases
- Orientation:
- Minus strand
- chr19:14,072,342-14,117,851
- (GRCh37/hg19)
- Size:
- 45,510 bases
- Orientation:
- Minus strand
Genomic View for RFX1 Gene
Genes around RFX1 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 19p13.12 by Entrez Gene
- 19p13.12 by HGNC
- 19p13.12 by Ensembl
RFX1 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 RFX1 Gene
Proteins for RFX1 Gene
-
Protein details for RFX1 Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- P22670-RFX1_HUMAN
- Recommended name:
- MHC class II regulatory factor RFX1
- Protein Accession:
- P22670
Protein attributes for RFX1 Gene
- Size:
- 979 amino acids
- Molecular mass:
- 104758 Da
- Quaternary structure:
-
- Homodimer; binds DNA as a homodimer (PubMed:10706293). Heterodimer; heterodimerizes with RFX2 and RFX3 (PubMed:10330134).
Protein Expression for RFX1 Gene
Post-translational modifications for RFX1 Gene
Other Protein References for RFX1 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
- Novus Biologicals Antibodies for RFX1
-
Abcam antibodies for RFX1
- Invitrogen Antibodies for RFX1 (AFLGC-RFX1)
- GeneTex RFX1 Antibody for RFX1
-
Boster Bio Antibodies for RFX1
-
Custom Antibody ServicesProSci Antibodies for RFX1
-
Santa Cruz Biotechnology (SCBT) Antibodies for RFX1
Protein Products
-
OriGene Purified Proteins for RFX1
- Search Origene for MassSpec and Protein Over-expression Lysates for RFX1
- Origene Custom Protein Services for RFX1
- Novus Biologicals proteins for RFX1
- antibodies-online: Search results for 4 available RFX1 Proteins ranked by validation data
- Compare Top RFX1 Proteins
-
Quality Products:
- Search GeneTex for Proteins for RFX1
-
Abcam proteins for RFX1
Assay Products
- antibodies-online: Search results for available RFX1 related products ranked by validation data
No data available for DME Specific Peptides for RFX1 Gene
Domains & Families for RFX1 Gene
Gene Families for RFX1 Gene
- HGNC:
- Human Protein Atlas (HPA):
-
- Predicted intracellular proteins
- Transcription factors
Protein Domains for RFX1 Gene
- InterPro:
- Blocks:
- ProtoNet:
Suggested Antigen Peptide Sequences for RFX1 Gene
- GenScript: Design optimal peptide antigens:
Graphical View of Domain Structure for InterPro Entry
P22670- Family:
-
- Belongs to the RFX family.
Function for RFX1 Gene
Molecular function for RFX1 Gene
- UniProtKB/Swiss-Prot Function:
- Regulatory factor essential for MHC class II genes expression. Binds to the X boxes of MHC class II genes. Also binds to an inverted repeat (ENH1) required for hepatitis B virus genes expression and to the most upstream element (alpha) of the RPL30 promoter.
- GENATLAS Biochemistry:
- transactivating DNA binding regulator 1,involved in MHC class II expression,binding the MHC promoter box X
Phenotypes From GWAS Catalog for RFX1 Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000978 | RNA polymerase II proximal promoter sequence-specific DNA binding | IBA | -- |
| GO:0000981 | RNA polymerase II transcription factor activity, sequence-specific DNA binding | NAS | 19274049 |
| GO:0003677 | DNA binding | IEA | -- |
| GO:0003700 | DNA binding transcription factor activity | IBA | -- |
| GO:0003705 | transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding | TAS | 8289803 |
Phenotypes for RFX1 Gene
- MGI mutant phenotypes for RFX1:
- inferred from 2 alleles
- GenomeRNAi human phenotypes for RFX1:
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
- Cyagen custom Knockout/knockin (KOKI) mouse models for RFX1
-
CRISPR Products
-
OriGene CRISPR knockouts for RFX1
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- Applied Biological Materials CRISPR for RFX1
-
Vectors and viruses for KO, Activation, Repression, and more
-
Santa Cruz Biotechnology (SCBT) CRISPR for RFX1
- GenScript: Design CRISPR guide RNA sequences for RFX1
miRNA for RFX1 Gene
- miRTarBase miRNAs that target RFX1
-
- hsa-mir-197-3p (MIRT004209)
- hsa-mir-346 (MIRT004241)
- hsa-mir-124-3p (MIRT022998)
- hsa-mir-3978 (MIRT566021)
- hsa-mir-92a-1-5p (MIRT566022)
- hsa-mir-3148 (MIRT566023)
- hsa-mir-6124 (MIRT566024)
- hsa-mir-8069 (MIRT566025)
- hsa-mir-758-5p (MIRT566026)
- hsa-mir-15a-3p (MIRT566027)
- hsa-mir-4753-5p (MIRT566028)
- hsa-mir-548as-3p (MIRT566029)
- hsa-mir-548z (MIRT566030)
- hsa-mir-548h-3p (MIRT566031)
- hsa-mir-548d-3p (MIRT566032)
- hsa-mir-548bb-3p (MIRT566033)
- hsa-mir-548ac (MIRT566034)
- hsa-mir-4776-3p (MIRT641573)
- hsa-mir-578 (MIRT641574)
- hsa-mir-587 (MIRT641575)
- hsa-mir-4659b-5p (MIRT641576)
- hsa-mir-4659a-5p (MIRT641577)
- hsa-mir-6801-5p (MIRT641578)
- hsa-mir-5590-5p (MIRT641579)
- hsa-mir-153-5p (MIRT641580)
- hsa-mir-10b-3p (MIRT641581)
- hsa-mir-6826-5p (MIRT641582)
- hsa-mir-370-5p (MIRT641583)
Transcription Factor Targets for RFX1 Gene
Targeted motifs for RFX1 Gene
HOMER Transcription Factor Regulatory Elements motif RFX1
- Consensus sequence: GGTTGCCATGGCAA Submotif: canonical Cell Type: NPC GEO ID: GSE16256
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for RFX1
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- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RFX1
- genomics-online: shRNA clones - Search results for available RFX1 gene related products
Clone Products
- Sino Biological Human cDNA Clone for RFX1
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for RFX1
- genomics-online: cdna clones - Search results for available RFX1 gene related products
- orf clones - Search results for available RFX1 gene related products
- Applied Biological Materials Clones for RFX1
-
Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
Cell Line Products
-
Horizon Cell Lines for RFX1
No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Animal Models for RFX1 Gene
Localization for RFX1 Gene
Subcellular locations from UniProtKB/Swiss-Prot for RFX1 Gene
- Nucleus.
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
| cytosol | 2 |
| cytoskeleton | 1 |
- Nucleoplasm (3)
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005634 | nucleus | IBA | -- |
| GO:0005654 | nucleoplasm | IDA | -- |
| GO:0043231 | intracellular membrane-bounded organelle | IDA | -- |
Pathways & Interactions for RFX1 Gene
No Data Available
Interacting Proteins for RFX1 Gene
Selected Interacting proteins:
P22670-RFX1_HUMAN
ENSP00000254325
for RFX1 Gene via
UniProtKB
MINT
STRING
IID
GPS-Prot Interaction Network for RFX1
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0006351 | transcription, DNA-templated | IEA | -- |
| GO:0006355 | regulation of transcription, DNA-templated | IEA | -- |
| GO:0006357 | regulation of transcription by RNA polymerase II | IEA | -- |
| GO:0006955 | immune response | TAS | 1505960 |
No data available for Pathways by source for RFX1 Gene
Transcripts for RFX1 Gene
mRNA/cDNA for RFX1 Gene
- (7) REFSEQ mRNAs :
- (3) Additional mRNA sequences :
- (88) Selected AceView cDNA sequences:
- (7) Ensembl transcripts including schematic representations, and UCSC links where relevant :
-
- ENST00000254325 4332 bps (uc002mxv.4)
- ENST00000588520 241 bps (uc060ulc.1)
- ENST00000589239 2122 bps (uc010dzi.3)
- ENST00000589937 540 bps (uc060uld.1)
- ENST00000589760 848 bps (uc060ule.1)
Unigene Clusters for RFX1 Gene
- Regulatory factor X, 1 (influences HLA class II expression):
- Representative Sequences:
CRISPR Products
-
OriGene CRISPR knockouts for RFX1
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for RFX1
- genomics-online: gRNA clones - Search results for available RFX1 gene related products
- Applied Biological Materials CRISPR for RFX1
-
Vectors and viruses for KO, Activation, Repression, and more
-
Santa Cruz Biotechnology (SCBT) CRISPR for RFX1
- GenScript: Design CRISPR guide RNA sequences for RFX1
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for RFX1
- Browse OriGene Inhibitory RNA Products For RFX1
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RFX1
- genomics-online: shRNA clones - Search results for available RFX1 gene related products
Clone Products
- Sino Biological Human cDNA Clone for RFX1
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for RFX1
- genomics-online: cdna clones - Search results for available RFX1 gene related products
- orf clones - Search results for available RFX1 gene related products
- Applied Biological Materials Clones for RFX1
-
Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
| ExUns: | 1a | · | 1b | ^ | 2 | ^ | 3 | ^ | 4 | ^ | 5 | ^ | 6 | ^ | 7 | ^ | 8a | · | 8b | ^ | 9a | · | 9b | ^ | 10 | ^ | 11 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SP1: | |||||||||||||||||||||||||||
| SP2: | - | ||||||||||||||||||||||||||
| SP3: | - | - | - | ||||||||||||||||||||||||
| SP4: |
Expression for RFX1 Gene
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
- Skeletal Muscle (Muscoskeletal System)
This gene is overexpressed in CD8 Tcells (11.6), Blymphocyte (8.2), and Placenta (6.7).
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RFX1 Gene
- Elite partner
NURSA nuclear receptor signaling pathways regulating expression of RFX1 Gene:
RFX1SOURCE GeneReport for Unigene cluster for RFX1 Gene:
Hs.655215Evidence on tissue expression from TISSUES for RFX1 Gene
- Liver(4.4)
- Blood(2.1)
- Nervous system(2)
Primer Products
-
OriGene qPCR primer pairs for RFX1
- genomics-online: primer clones - Search results for available RFX1 gene related products
Gene Expression Assay Products
No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RFX1 Gene
Orthologs for RFX1 Gene
This gene was present in the common ancestor of animals.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | RFX1 34 33 |
|
OneToOne | |
| dog (Canis familiaris) |
Mammalia | RFX1 34 33 |
|
OneToOne | |
| oppossum (Monodelphis domestica) |
Mammalia | RFX1 34 |
|
OneToOne | |
| mouse (Mus musculus) |
Mammalia | Rfx1 16 34 33 |
|
||
| rat (Rattus norvegicus) |
Mammalia | Rfx1 33 |
|
||
| cow (Bos Taurus) |
Mammalia | RFX1 34 |
|
OneToOne | |
| platypus (Ornithorhynchus anatinus) |
Mammalia | RFX1 34 |
|
OneToOne | |
| lizard (Anolis carolinensis) |
Reptilia | RFX1 34 |
|
OneToOne | |
| tropical clawed frog (Silurana tropicalis) |
Amphibia | rfx1 33 |
|
||
| zebrafish (Danio rerio) |
Actinopterygii | rfx1a 34 33 |
|
OneToMany | |
| rfx1b 34 |
|
OneToMany | |||
| fruit fly (Drosophila melanogaster) |
Insecta | Rfx 34 35 |
|
OneToMany | |
| sea squirt (Ciona savignyi) |
Ascidiacea | -- 34 |
|
OneToMany |
- Species where no ortholog for RFX1 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)
- chicken (Gallus gallus)
- 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)
Evolution for RFX1 Gene
- ENSEMBL:
- Gene Tree for RFX1 (if available)
- TreeFam:
- Gene Tree for RFX1 (if available)
- Aminode:
- Evolutionary constrained regions (ECRs) for RFX1: view image
Paralogs for RFX1 Gene
Variants for RFX1 Gene
| SNP ID | Clin | Chr 19 pos | Variation | AA Info | Type |
|---|---|---|---|---|---|
| rs766888168 | benign, Abnormality of neuronal migration | 13,963,151(-) | C/T | coding_sequence_variant, missense_variant | |
| rs1000005785 | -- | 13,983,709(-) | C/T | intron_variant | |
| rs1000032415 | -- | 14,003,291(-) | CC/C | genic_upstream_transcript_variant, intron_variant | |
| rs1000174432 | -- | 13,988,592(-) | T/C | intron_variant | |
| rs1000199008 | -- | 13,992,824(-) | AAA/A | intron_variant |
Residual Variation Intolerance Score:
23.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
4.70;
66.15% of all genes are more intolerant (likely to be disease-causing)
Additional Variant Information for RFX1 Gene
- SNPedia medical, phenotypic, and genealogical associations of SNPs for
- RFX1
SNP Genotyping and Copy Number Assay Products
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RFX1 Gene
Disorders for RFX1 Gene
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| bare lymphocyte syndrome, type ii |
|
|
| hemopneumothorax |
|
|
| combined immunodeficiency, x-linked |
|
|
Search RFX1 in MalaCards
View complete list of genes associated with diseases
Genatlas disease for RFX1 Gene
immunodeficiency,severe combined with defective expression of MHC class II gene
Additional Disease Information for RFX1
- Human Genome Epidemiology Navigator
- (HuGE)
- ATLAS of Genetics and Cytogenetics in Oncology and Haematology
No data available for UniProtKB/Swiss-Prot for RFX1 Gene
Publications for RFX1 Gene
- Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. (PMID: 10706293) Gajiwala KS … Burley SK (Nature 2000) 3 4 22 58
- RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins. (PMID: 8289803) Reith W … Mach B (Molecular and cellular biology 1994) 2 3 22 58
- The genes for MHC class II regulatory factors RFX1 and RFX2 are located on the short arm of chromosome 19. (PMID: 1505960) Pugliatti L … Mach B (Genomics 1992) 2 3 22 58
- The DNA-binding defect observed in major histocompatibility complex class II regulatory mutants concerns only one member of a family of complexes binding to the X boxes of class II promoters. (PMID: 1508204) Herrero Sanchez C … Mach B (Molecular and cellular biology 1992) 3 4 22 58
- MHC class II regulatory factor RFX has a novel DNA-binding domain and a functionally independent dimerization domain. (PMID: 2253877) Reith W … Mach B (Genes & development 1990) 3 4 22 58
Products for RFX1 Gene
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- Novus Biologicals
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- Invitrogen Antibodies for RFX1 (AFLGC-RFX1)
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- antibodies-online: Search results for 42 available RFX1 Antibodies ranked by validation data
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- antibodies-online: Search results for available RFX1 related products ranked by validation data
- antibodies-online: Search results for 4 available RFX1 Proteins ranked by validation data
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- Quality Products:
- GeneTex RFX1 Antibody for RFX1
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- Horizon Cell Lines for RFX1
- genomics-online: cdna clones - Search results for available RFX1 gene related products
- orf clones - Search results for available RFX1 gene related products
- genomics-online: gRNA clones - Search results for available RFX1 gene related products
- genomics-online: primer clones - Search results for available RFX1 gene related products
- genomics-online: shRNA clones - Search results for available RFX1 gene related products
- Browse GeneCopoeia Cell Lines
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for RFX1
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- Boster Bio Antibodies for RFX1
- Browse Boster Bio ELISA Kits
Sources for RFX1 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
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