Aliases for SYDE2 Gene

Aliases for SYDE2 Gene

  • Synapse Defective Rho GTPase Homolog 2 2 3 5
  • Synapse Defective Protein 1 Homolog 2 3 4
  • Rho GTPase-Activating Protein SYDE2 3 4
  • Protein Syd-1 Homolog 2 3 4
  • Synapse Defective 1, Rho GTPase, Homolog 2 (C. Elegans) 2
  • Synapse Defective 1, Rho GTPase, Homolog 2 3
  • FLJ13815 2
  • SYDE2 5

External Ids for SYDE2 Gene

Previous GeneCards Identifiers for SYDE2 Gene

  • GC01M085338
  • GC01M085623
  • GC01M083733

Summaries for SYDE2 Gene

GeneCards Summary for SYDE2 Gene

SYDE2 (Synapse Defective Rho GTPase Homolog 2) is a Protein Coding gene. Diseases associated with SYDE2 include Hypophosphatasia, Adult. Among its related pathways are Signaling by GPCR and p75 NTR receptor-mediated signalling. Gene Ontology (GO) annotations related to this gene include GTPase activator activity. An important paralog of this gene is SYDE1.

UniProtKB/Swiss-Prot Summary for SYDE2 Gene

  • GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state.

Additional gene information for SYDE2 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SYDE2 Gene

Genomics for SYDE2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SYDE2 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
GH01J085197 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 605.2 +1.6 1639 7 HNRNPL TEAD4 PRDM10 TFE3 IKZF1 ZNF692 POLR2A JUND FOXA1 ZNF143 SYDE2 lnc-WDR63-6 ENSG00000223653 MCOLN2 lnc-C1orf52-2 MCOLN3
GH01J085224 Enhancer 1.5 Ensembl ENCODE CraniofacialAtlas dbSUPER 9.1 -23.8 -23776 2.6 CEBPG TEAD4 PRDM10 LEF1 IKZF1 TARDBP JUND FOXA1 DDX20 PRDM1 LOC105378821 lnc-WDR63-2 C1orf52 SYDE2 piR-42694-010
GH01J085229 Enhancer 1 Ensembl ENCODE dbSUPER 11.9 -28.2 -28189 0.2 ZSCAN5C OSR2 ZBTB17 PKNOX1 ELF1 WT1 SAP130 ZNF335 ZNF610 ZNF18 SYDE2 LOC105378821 lnc-WDR63-2 C1orf52
GH01J085132 Enhancer 0.9 Ensembl ENCODE 11.3 +67.1 67124 5.6 CEBPG CREB1 GATAD2A FOXA1 RFX1 CEBPA ZBTB44 CEBPB EZH2 ZNF23 MIR4423 SYDE2 SPATA1 DNAI3 MCOLN2 ENSG00000280099 lnc-SYDE2-1 MCOLN3
GH01J085148 Enhancer 0.8 FANTOM5 Ensembl 12.2 +52.6 52624 2.2 JUND RUNX3 BCLAF1 BCL11A JUNB IRF4 BATF EBF1 MTA2 SPI1 SYDE2 MCOLN2 DNAI3 ENSG00000280099 lnc-SYDE2-1 MIR4423 MCOLN3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYDE2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SYDE2

Top Transcription factor binding sites by QIAGEN in the SYDE2 gene promoter:
  • CBF(2)
  • CBF-A
  • CBF-B
  • CP1A
  • GR
  • GR-alpha
  • ISGF-3
  • NF-Y
  • NF-YA
  • Nkx2-5

Genomic Locations for SYDE2 Gene

Genomic Locations for SYDE2 Gene
chr1:85,156,381-85,201,725
(GRCh38/hg38)
Size:
45,345 bases
Orientation:
Minus strand
chr1:85,622,556-85,666,729
(GRCh37/hg19)
Size:
44,174 bases
Orientation:
Minus strand

Genomic View for SYDE2 Gene

Genes around SYDE2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYDE2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYDE2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYDE2 Gene

Proteins for SYDE2 Gene

  • Protein details for SYDE2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5VT97-SYDE2_HUMAN
    Recommended name:
    Rho GTPase-activating protein SYDE2
    Protein Accession:
    Q5VT97
    Secondary Accessions:
    • Q5VT96
    • Q8NDB8
    • Q9H8A6

    Protein attributes for SYDE2 Gene

    Size:
    1194 amino acids
    Molecular mass:
    133230 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB14711.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAB14711.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305};

    Alternative splice isoforms for SYDE2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYDE2 Gene

Post-translational modifications for SYDE2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SYDE2 Gene

No data available for DME Specific Peptides for SYDE2 Gene

Domains & Families for SYDE2 Gene

Gene Families for SYDE2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SYDE2 Gene

InterPro:
Blocks:
  • RhoGAP domain
  • C2 domain
ProtoNet:

Suggested Antigen Peptide Sequences for SYDE2 Gene

GenScript: Design optimal peptide antigens:
  • Synapse defective protein 1 homolog 2 (SYDE2_HUMAN)
genes like me logo Genes that share domains with SYDE2: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SYDE2 Gene

Function for SYDE2 Gene

Molecular function for SYDE2 Gene

UniProtKB/Swiss-Prot Function:
GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state.

Phenotypes From GWAS Catalog for SYDE2 Gene

Gene Ontology (GO) - Molecular Function for SYDE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity ISS --
genes like me logo Genes that share ontologies with SYDE2: view

Phenotypes for SYDE2 Gene

genes like me logo Genes that share phenotypes with SYDE2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYDE2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SYDE2 Gene

Localization for SYDE2 Gene

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 SYDE2 gene
Compartment Confidence
cytosol 5
nucleus 2
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SYDE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with SYDE2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SYDE2 Gene

Pathways & Interactions for SYDE2 Gene

genes like me logo Genes that share pathways with SYDE2: view

Pathways by source for SYDE2 Gene

Interacting Proteins for SYDE2 Gene

SIGNOR curated interactions for SYDE2 Gene

Inactivates:

Gene Ontology (GO) - Biological Process for SYDE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IEA --
GO:0016477 cell migration IDA 27917469
GO:0051056 regulation of small GTPase mediated signal transduction TAS --
GO:0090630 activation of GTPase activity ISS --
genes like me logo Genes that share ontologies with SYDE2: view

Drugs & Compounds for SYDE2 Gene

No Compound Related Data Available

Transcripts for SYDE2 Gene

mRNA/cDNA for SYDE2 Gene

1 REFSEQ mRNAs :
3 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYDE2

Alternative Splicing Database (ASD) splice patterns (SP) for SYDE2 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4
SP1: - -
SP2:
SP3: -

Relevant External Links for SYDE2 Gene

GeneLoc Exon Structure for
SYDE2

Expression for SYDE2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SYDE2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYDE2 Gene

This gene is overexpressed in Colon - Sigmoid (x5.9) and Esophagus - Muscularis (x4.8).

Protein differential expression in normal tissues from HIPED for SYDE2 Gene

This gene is overexpressed in Fetal heart (63.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SYDE2 Gene



Protein tissue co-expression partners for SYDE2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SYDE2

SOURCE GeneReport for Unigene cluster for SYDE2 Gene:

Hs.670497

Evidence on tissue expression from TISSUES for SYDE2 Gene

  • Thyroid gland(4.2)
  • Lymph node(4)
  • Lung(3.9)
  • Intestine(3.6)
  • Kidney(2.5)
genes like me logo Genes that share expression patterns with SYDE2: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYDE2 Gene

Orthologs for SYDE2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SYDE2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SYDE2 30 31
  • 99.11 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SYDE2 30 31
  • 88.63 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SYDE2 30 31
  • 88.11 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Syde2 30 17 31
  • 79.38 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Syde2 30
  • 77.85 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia SYDE2 31
  • 72 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SYDE2 31
  • 60 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SYDE2 30 31
  • 68.8 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SYDE2 31
  • 56 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia syde2 30
  • 66.91 (n)
Zebrafish
(Danio rerio)
Actinopterygii SYDE2 31
  • 68 (a)
OneToOne
LOC100333199 30
  • 61.12 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta RhoGAP100F 31
  • 15 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea syd-1 31
  • 17 (a)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BEM2 31
  • 9 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.767 31
  • 27 (a)
OneToMany
Species where no ortholog for SYDE2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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 Vase (Ciona intestinalis)
  • 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 SYDE2 Gene

ENSEMBL:
Gene Tree for SYDE2 (if available)
TreeFam:
Gene Tree for SYDE2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SYDE2: view image

Paralogs for SYDE2 Gene

Paralogs for SYDE2 Gene

genes like me logo Genes that share paralogs with SYDE2: view

Variants for SYDE2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SYDE2 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
711053 Likely Benign: not provided 85,190,219(-) C/T MISSENSE_VARIANT
713881 Benign: not provided 85,190,190(-) C/T SYNONYMOUS_VARIANT
767681 Benign: not provided 85,183,190(-) G/C MISSENSE_VARIANT
781663 Benign: not provided 85,190,726(-) A/G MISSENSE_VARIANT
783290 Benign: not provided 85,190,686(-) A/G MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for SYDE2 Gene

Structural Variations from Database of Genomic Variants (DGV) for SYDE2 Gene

Variant ID Type Subtype PubMed ID
dgv347n54 CNV loss 21841781
dgv348n54 CNV loss 21841781
dgv349n54 CNV gain 21841781
dgv350n54 CNV gain 21841781
dgv351n54 CNV gain 21841781
esv23473 CNV loss 19812545
esv3329522 CNV insertion 20981092
esv34165 CNV loss 18971310
nsv546706 CNV gain+loss 21841781
nsv546709 CNV loss 21841781
nsv830459 CNV loss 17160897

Variation tolerance for SYDE2 Gene

Residual Variation Intolerance Score: 82.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.24; 85.01% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYDE2 Gene

Human Gene Mutation Database (HGMD)
SYDE2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYDE2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYDE2 Gene

Disorders for SYDE2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SYDE2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
hypophosphatasia, adult
  • hypophosphatasia, mild
- elite association - COSMIC cancer census association via MalaCards
Search SYDE2 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with SYDE2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SYDE2 Gene

Publications for SYDE2 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  2. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3
  3. E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins. (PMID: 29676528) Khanna R … Parnaik VK (The FEBS journal 2018) 3
  4. Association of dysfunctional synapse defective 1 (SYDE1) with restricted fetal growth - SYDE1 regulates placental cell migration and invasion. (PMID: 27917469) Lo HF … Chen H (The Journal of pathology 2017) 3
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3

Products for SYDE2 Gene

Sources for SYDE2 Gene