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FERMT3 Gene(Protein Coding)

Fermitin Family Member 3

GCID:
GC11P064206
GIFtS:
50
Genes Participants
UDN Logo

Aliases for FERMT3 Gene

Aliases for FERMT3 Gene

  • Fermitin Family Member 3 2 3 5
  • Unc-112-Related Protein 2 3 4
  • MIG2-Like Protein 3 4
  • Kindlin-3 2 4
  • KIND3 3 4
  • MIG2B 3 4
  • URP2 3 4
  • Fermitin Family Homolog 3 (Drosophila) 2
  • UNC-112 Related Protein 2 3
  • Fermitin Family Homolog 3 3
  • Kindlin 3 3
  • UNC112C 3
  • URP2SF 3
  • MIG-2 3

External Ids for FERMT3 Gene

Previous GeneCards Identifiers for FERMT3 Gene

  • GC11P063731
  • GC11P063975
  • GC11P060302

Summaries for FERMT3 Gene

Entrez Gene Summary for FERMT3 Gene

  • Kindlins are a small family of proteins that mediate protein-protein interactions involved in integrin activation and thereby have a role in cell adhesion, migration, differentiation, and proliferation. The protein encoded by this gene has a key role in the regulation of hemostasis and thrombosis. This protein may also help maintain the membrane skeleton of erythrocytes. Mutations in this gene cause the autosomal recessive leukocyte adhesion deficiency syndrome-III (LAD-III). Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2010]

GeneCards Summary for FERMT3 Gene

FERMT3 (Fermitin Family Member 3) is a Protein Coding gene. Diseases associated with FERMT3 include Leukocyte Adhesion Deficiency, Type Iii and Kindler Syndrome. Among its related pathways are Response to elevated platelet cytosolic Ca2+ and Adhesion. Gene Ontology (GO) annotations related to this gene include integrin binding. An important paralog of this gene is FERMT1.

UniProtKB/Swiss-Prot for FERMT3 Gene

  • Plays a central role in cell adhesion in hematopoietic cells (PubMed:19234463, PubMed:26359933). Acts by activating the integrin beta-1-3 (ITGB1, ITGB2 and ITGB3) (By similarity). Required for integrin-mediated platelet adhesion and leukocyte adhesion to endothelial cells (PubMed:19234460). Required for activation of integrin beta-2 (ITGB2) in polymorphonuclear granulocytes (PMNs) (By similarity).

  • Isoform 2 may act as a repressor of NF-kappa-B and apoptosis.

Gene Wiki entry for FERMT3 Gene

Additional gene information for FERMT3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FERMT3 Gene

Genomics for FERMT3 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for FERMT3 Gene

Promoters and enhancers for FERMT3 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
GH11J064205 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 650.7 +0.9 940 4.4 HDGF PKNOX1 SMAD1 ARNT YY1 POLR2B ZNF766 ZNF143 ZNF592 SMARCA4 FERMT3 TRPT1 ZFPL1 PLCB3 SF1 TRMT112 ENSG00000257086 GPR137 BAD ENSG00000257069
GH11J064204 Enhancer 0.9 ENCODE 650.7 -2.0 -1971 1.2 HDGF ATF1 SMAD1 ARNT ZNF2 POLR2B ARID2 ZNF143 ATF7 RUNX3 FERMT3 TRPT1 NUDT22 DNAJC4 ENSG00000257086 PLCB3 MACROD1 GPR137 BAD STIP1
GH11J064183 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 13.3 -21.0 -20982 4.4 CLOCK MLX ZFP64 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC STIP1 GC11M064182 TRPT1 IMMP1LP1 ENSG00000257086 SF1 FERMT3 C11orf95 ZNHIT2 PLCB3
GH11J064237 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 12.7 +38.7 38664 16.6 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 E2F8 ZNF143 SP3 NFYC PPP1R14B PLCB3 LOC105369340 FKBP2 TRPT1 LOC102723878 VEGFB ENSG00000257086 TRMT112 SF1
GH11J064180 Enhancer 1.2 Ensembl ENCODE 11.8 -25.1 -25098 2.1 HDGF PKNOX1 ATF1 ARNT ARID4B SIN3A ZNF2 IRF4 ZNF48 SLC30A9 PIR58555 PIR62169 TRPT1 FERMT3 ENSG00000257086 PLCB3 ENSG00000256341 NAA40 CCDC88B STIP1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FERMT3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FERMT3 gene promoter:
  • E2F-5
  • E2F-4
  • E2F-3a
  • E2F-2
  • E2F-1
  • E2F
  • POU2F1
  • POU2F1a
  • PPAR-gamma2
  • PPAR-gamma1

Genomic Locations for FERMT3 Gene

Genomic Locations for FERMT3 Gene
chr11:64,206,655-64,223,891
(GRCh38/hg38)
Size:
17,237 bases
Orientation:
Plus strand
chr11:63,974,150-63,991,363
(GRCh37/hg19)
Size:
17,214 bases
Orientation:
Plus strand

Genomic View for FERMT3 Gene

Genes around FERMT3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FERMT3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FERMT3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for FERMT3 Gene

Proteins for FERMT3 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for FERMT3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86UX7-URP2_HUMAN
    Recommended name:
    Fermitin family homolog 3
    Protein Accession:
    Q86UX7
    Secondary Accessions:
    • Q8IUA1
    • Q8N207
    • Q9BT48

    Protein attributes for FERMT3 Gene

    Size:
    667 amino acids
    Molecular mass:
    75953 Da
    Quaternary structure:
    • Interacts with ITGB1, ITGB2 and ITGB3 (via cytoplasmic tails).

    Three dimensional structures from OCA and Proteopedia for FERMT3 Gene

    Alternative splice isoforms for FERMT3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for FERMT3 Gene

Protein Expression for FERMT3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for FERMT3 Gene

  • Ubiquitination at isoforms=2, 2, 1, 2, 1590 and isoforms=2353
  • Modification sites at PhosphoSitePlus

Other Protein References for FERMT3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for FERMT3 Gene

Domains & Families for FERMT3 Gene

Gene Families for FERMT3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for FERMT3 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for FERMT3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q86UX7

UniProtKB/Swiss-Prot:

URP2_HUMAN :
  • The FERM domain is not correctly detected by PROSITE or Pfam techniques because it contains the insertion of a PH domain.
  • Belongs to the kindlin family.
Domain:
  • The FERM domain is not correctly detected by PROSITE or Pfam techniques because it contains the insertion of a PH domain.
Family:
  • Belongs to the kindlin family.
genes like me logo Genes that share domains with FERMT3: view

Function for FERMT3 Gene

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  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
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  6. Cell Line

Molecular function for FERMT3 Gene

UniProtKB/Swiss-Prot Function:
Plays a central role in cell adhesion in hematopoietic cells (PubMed:19234463, PubMed:26359933). Acts by activating the integrin beta-1-3 (ITGB1, ITGB2 and ITGB3) (By similarity). Required for integrin-mediated platelet adhesion and leukocyte adhesion to endothelial cells (PubMed:19234460). Required for activation of integrin beta-2 (ITGB2) in polymorphonuclear granulocytes (PMNs) (By similarity).
UniProtKB/Swiss-Prot Function:
Isoform 2 may act as a repressor of NF-kappa-B and apoptosis.

Phenotypes From GWAS Catalog for FERMT3 Gene

Gene Ontology (GO) - Molecular Function for FERMT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005178 integrin binding IEA,ISS --
genes like me logo Genes that share ontologies with FERMT3: view
genes like me logo Genes that share phenotypes with FERMT3: view

Human Phenotype Ontology for FERMT3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for FERMT3 Gene

MGI Knock Outs for FERMT3:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for FERMT3 Gene

Localization for FERMT3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FERMT3 Gene

Cell projection, podosome. Note=Present in the F-actin surrounding ring structure of podosomes, which are specialized adhesion structures of hematopoietic cells. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for FERMT3 gene
Compartment Confidence
extracellular 5
cytoskeleton 5
cytosol 3
plasma membrane 2
nucleus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for FERMT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002102 podosome ISS --
GO:0005576 extracellular region TAS --
GO:0016020 membrane HDA 19946888
GO:0030054 cell junction IEA --
GO:0031093 platelet alpha granule lumen TAS --
genes like me logo Genes that share ontologies with FERMT3: view

Pathways & Interactions for FERMT3 Gene

genes like me logo Genes that share pathways with FERMT3: view

Pathways by source for FERMT3 Gene

1 KEGG pathway for FERMT3 Gene
1 Cell Signaling Technology pathway for FERMT3 Gene

Gene Ontology (GO) - Biological Process for FERMT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002576 platelet degranulation TAS --
GO:0007155 cell adhesion IEA --
GO:0007159 leukocyte cell-cell adhesion IEA,IMP 19234460
GO:0007229 integrin-mediated signaling pathway IEA,IMP 19234460
GO:0030335 positive regulation of cell migration IDA 19234463
genes like me logo Genes that share ontologies with FERMT3: view

No data available for SIGNOR curated interactions for FERMT3 Gene

Drugs & Compounds for FERMT3 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for FERMT3 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for FERMT3 Gene

(6) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(151) Selected AceView cDNA sequences:
(9) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for FERMT3 Gene

Fermitin family member 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for FERMT3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16
SP1: -
SP2: -
SP3: -
SP4:
SP5: -
SP6:
SP7:

Relevant External Links for FERMT3 Gene

GeneLoc Exon Structure for
FERMT3
ECgene alternative splicing isoforms for
FERMT3

Expression for FERMT3 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FERMT3 Gene

mRNA expression in normal human tissues for FERMT3 Gene
mRNA expression by GTEx for FERMT3 GenemRNA expression by BioGPS for FERMT3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for FERMT3 Gene

This gene is overexpressed in Whole Blood (x24.0) and Spleen (x4.7).

Protein differential expression in normal tissues from HIPED for FERMT3 Gene

This gene is overexpressed in Platelet (29.6), Peripheral blood mononuclear cells (13.1), and Lymph node (7.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for FERMT3 Gene



Protein tissue co-expression partners for FERMT3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of FERMT3 Gene:

FERMT3

SOURCE GeneReport for Unigene cluster for FERMT3 Gene:

Hs.180535

mRNA Expression by UniProt/SwissProt for FERMT3 Gene:

Q86UX7-URP2_HUMAN
Tissue specificity: Highly expressed in lymph node. Expressed in thymus, spleen and leukocytes. Weakly expressed in placenta, small intestine, stomach, testis and lung. Overexpressed in B-cell malignancies.

Evidence on tissue expression from TISSUES for FERMT3 Gene

  • Blood(4.6)
  • Lung(4.4)
  • Skin(2.9)
  • Bone marrow(2.4)
  • Heart(2.2)
  • Lymph node(2.1)
  • Spleen(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for FERMT3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
Regions:
Head and neck:
  • face
  • head
  • nose
Abdomen:
  • liver
  • spleen
General:
  • blood
  • blood vessel
  • coagulation system
  • red blood cell
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with FERMT3: view

Orthologs for FERMT3 Gene

This gene was present in the common ancestor of animals.

Orthologs for FERMT3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia FERMT3 34 33
  • 99.2 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia FERMT3 34
  • 94 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia FERMT3 34 33
  • 90.55 (n)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia FERMT3 34
  • 87 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Fermt3 16 34 33
  • 86.63 (n)
rat
(Rattus norvegicus)
 Mammalia Fermt3 33
  • 86.02 (n)
oppossum
(Monodelphis domestica)
 Mammalia -- 34
  • 53 (a)
 ManyToMany
lizard
(Anolis carolinensis)
 Reptilia FERMT3 34
  • 70 (a)
 OneToOne
African clawed frog
(Xenopus laevis)
 Amphibia MGC69069 33
zebrafish
(Danio rerio)
 Actinopterygii fermt3b 34 33
  • 64.74 (n)
 OneToMany
FERMT3 (2 of 2) 34
  • 60 (a)
 OneToMany
zgc64101 33
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.9754 33
fruit fly
(Drosophila melanogaster)
 Insecta Fit1 34
  • 39 (a)
 ManyToMany
Fit2 34
  • 38 (a)
 ManyToMany
worm
(Caenorhabditis elegans)
 Secernentea unc-112 34
  • 36 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 43 (a)
 OneToMany
Species where no ortholog for FERMT3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • 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)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for FERMT3 Gene

ENSEMBL:
Gene Tree for FERMT3 (if available)
TreeFam:
Gene Tree for FERMT3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for FERMT3: view image

Paralogs for FERMT3 Gene

Paralogs for FERMT3 Gene

(3) SIMAP similar genes for FERMT3 Gene using alignment to 4 proteins:

  • URP2_HUMAN
  • F5H1C6_HUMAN
  • F5H3I6_HUMAN
  • H0YFT5_HUMAN

Pseudogenes.org Pseudogenes for FERMT3 Gene

genes like me logo Genes that share paralogs with FERMT3: view

Variants for FERMT3 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for FERMT3 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs121918295 pathogenic, Leukocyte adhesion deficiency, type III 64,220,649(+) C/T coding_sequence_variant, stop_gained
rs121918296 pathogenic, Leukocyte adhesion deficiency, type III 64,207,412(+) G/A coding_sequence_variant, genic_upstream_transcript_variant, stop_gained, upstream_transcript_variant
rs121918297 pathogenic, Leukocyte adhesion deficiency, type III 64,223,094(+) C/T coding_sequence_variant, stop_gained
rs121918298 pathogenic, Leukocyte adhesion deficiency, type III 64,211,648(+) G/A coding_sequence_variant, stop_gained
rs144256756 uncertain-significance, Leukocyte adhesion deficiency, type III 64,207,450(+) C/T coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for FERMT3 Gene

Variant ID Type Subtype PubMed ID
dgv1963n54 CNV loss 21841781
esv33774 CNV gain 17666407
nsv1159904 CNV deletion 26073780
nsv469961 CNV loss 18288195
nsv555184 CNV loss 21841781
nsv555187 CNV loss 21841781
nsv832186 CNV loss 17160897
nsv951010 CNV deletion 24416366

Variation tolerance for FERMT3 Gene

Residual Variation Intolerance Score: 93.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.51; 43.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FERMT3 Gene

Human Gene Mutation Database (HGMD)
FERMT3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
FERMT3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FERMT3 Gene

Disorders for FERMT3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for FERMT3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

URP2_HUMAN
  • Leukocyte adhesion deficiency 3 (LAD3) [MIM:612840]: A disorder characterized by recurrent bacterial infections without pus formation, leukocytosis and major bleeding disorders. {ECO:0000269 PubMed:18779414, ECO:0000269 PubMed:19064721, ECO:0000269 PubMed:19234460, ECO:0000269 PubMed:19234463, ECO:0000269 PubMed:19617577, ECO:0000269 PubMed:26359933}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for FERMT3

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with FERMT3: view

No data available for Genatlas for FERMT3 Gene

Publications for FERMT3 Gene

  1. LAD-1/variant syndrome is caused by mutations in FERMT3. (PMID: 19064721) Kuijpers TW … Baas F (Blood 2009) 3 4 22 58
  2. A point mutation in KINDLIN3 ablates activation of three integrin subfamilies in humans. (PMID: 19234460) Malinin NL … Byzova TV (Nature medicine 2009) 3 4 22 58
  3. Loss of Kindlin-3 in LAD-III eliminates LFA-1 but not VLA-4 adhesiveness developed under shear flow conditions. (PMID: 19617577) Manevich-Mendelson E … Alon R (Blood 2009) 3 4 22 58
  4. Kindlin-3: a new gene involved in the pathogenesis of LAD-III. (PMID: 18779414) Mory A … Alon R (Blood 2008) 3 4 22 58
  5. URP1: a member of a novel family of PH and FERM domain-containing membrane-associated proteins is significantly over-expressed in lung and colon carcinomas. (PMID: 12697302) Weinstein EJ … Mazzarella R (Biochimica et biophysica acta 2003) 3 4 22 58

Products for FERMT3 Gene

Sources for FERMT3 Gene

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