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Aliases for SYDE1 Gene

Aliases for SYDE1 Gene

  • Synapse Defective Rho GTPase Homolog 1 2 3 5
  • Synapse Defective Protein 1 Homolog 1 3 4
  • Protein Syd-1 Homolog 1 3 4
  • Synapse Defective 1, Rho GTPase, Homolog 1 (C. Elegans) 2
  • Synapse Defective 1, Rho GTPase, Homolog 1 3
  • Rho GTPase-Activating Protein SYDE1 3
  • EC 2.4.1.25 58
  • EC 2.6.1.9 58
  • SYD1 3
  • 7h3 3

External Ids for SYDE1 Gene

Previous GeneCards Identifiers for SYDE1 Gene

  • GC19P015080
  • GC19P015218
  • GC19P014786

Summaries for SYDE1 Gene

Entrez Gene Summary for SYDE1 Gene

  • The protein encoded by this gene is a Rho GTPase-activating protein highly expressed in placenta. The encoded protein is involved in cytoskeletal remodeling and trophoblast cell migration. Decreased expression of this gene has been associated with intrauterine growth restriction (IUGR). [provided by RefSeq, Feb 2017]

GeneCards Summary for SYDE1 Gene

SYDE1 (Synapse Defective Rho GTPase Homolog 1) is a Protein Coding gene. Among its related pathways are p75 NTR receptor-mediated signalling and Signaling by Rho GTPases. GO annotations related to this gene include GTPase activator activity and protein complex binding. An important paralog of this gene is SYDE2.

UniProtKB/Swiss-Prot for SYDE1 Gene

  • GTPase activator for the Rho-type GTPases. As a GCM1 downstream effector, it is involved in placental development and positively regulates trophoblast cells migration. It regulates cytoskeletal remodeling by controlling the activity of Rho GTPases including RHOA, CDC42 and RAC1 (PubMed:27917469).

Additional gene information for SYDE1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYDE1 Gene

Genomics for SYDE1 Gene

Regulatory Elements for SYDE1 Gene

Enhancers for SYDE1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19H014512 1.8 FANTOM5 ENCODE dbSUPER 12.3 -588.8 -588835 12 HDGF PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 BRD4 AKAP8 TECR NOTCH3 DNAJB1 SYDE1 SNRPGP15 ENSG00000273218 GIPC1 IL27RA
GH19H016063 1.9 FANTOM5 ENCODE dbSUPER 9.9 +965.6 965550 18 FEZF1 DMAP1 ZNF143 SP3 MCM3 MEF2D SSRP1 GLIS1 RCOR2 NBN AKAP8 CHERP ENSG00000269578 BRD4 C19orf44 ENSG00000267904 ENSG00000268087 TPM4 SMIM7 OR10H5
GH19H015416 1.4 ENCODE dbSUPER 12.3 +311.0 311048 3 HDGF PKNOX1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B YY1 AKAP8 ZNF333 TPM4 BRD4 OR10H2 OR10H5 LINC00905 LINC01855 OR1AB1P DDX39A
GH19H014378 1.7 FANTOM5 ENCODE dbSUPER 9.9 -724.8 -724788 7 HDGF PKNOX1 ARNT SIN3A FEZF1 YBX1 ZNF2 ZNF302 ZNF416 ZNF143 AKAP8 CCDC130 MRI1 ZNF333 BRD4 DDX39A LOC284454 ADGRE5 SYDE1 PKN1
GH19H014227 1.1 ENCODE dbSUPER 12.3 -879.1 -879115 0 ZNF493 ZNF138 ZNF354C ZNF202 ZNF680 SMAD5 ZC3H11A OVOL3 REST ZNF623 CCDC130 MRI1 ZNF333 RFX1 DCAF15 NOTCH3 DDX39A SYDE1 SNRPGP15 C19orf67
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SYDE1 on UCSC Golden Path with GeneCards custom track

Promoters for SYDE1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000107600 136 1401 PKNOX1 ZFP64 ZNF384 ZIC2 ZEB1 TEAD3 ETS1 E2F1 ZFHX2 GLIS2

Genomic Location for SYDE1 Gene

Chromosome:
19
Start:
15,107,364 bp from pter
End:
15,114,988 bp from pter
Size:
7,625 bases
Orientation:
Plus strand

Genomic View for SYDE1 Gene

Genes around SYDE1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYDE1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYDE1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYDE1 Gene

Proteins for SYDE1 Gene

  • Protein details for SYDE1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZW31-SYDE1_HUMAN
    Recommended name:
    Rho GTPase-activating protein SYDE1
    Protein Accession:
    Q6ZW31
    Secondary Accessions:
    • Q7L2I8
    • Q8N6J2
    • Q9H8K4

    Protein attributes for SYDE1 Gene

    Size:
    735 amino acids
    Molecular mass:
    79793 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SYDE1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYDE1 Gene

Selected DME Specific Peptides for SYDE1 Gene

Q6ZW31:
  • DFLRLDH
  • YGLGGLR

Post-translational modifications for SYDE1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SYDE1 Gene

Domains & Families for SYDE1 Gene

Gene Families for SYDE1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SYDE1 Gene

Suggested Antigen Peptide Sequences for SYDE1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SYDE1: view

No data available for UniProtKB/Swiss-Prot for SYDE1 Gene

Function for SYDE1 Gene

Molecular function for SYDE1 Gene

UniProtKB/Swiss-Prot Function:
GTPase activator for the Rho-type GTPases. As a GCM1 downstream effector, it is involved in placental development and positively regulates trophoblast cells migration. It regulates cytoskeletal remodeling by controlling the activity of Rho GTPases including RHOA, CDC42 and RAC1 (PubMed:27917469).

Enzyme Numbers (IUBMB) for SYDE1 Gene

Phenotypes From GWAS Catalog for SYDE1 Gene

Gene Ontology (GO) - Molecular Function for SYDE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity TAS --
genes like me logo Genes that share ontologies with SYDE1: view
genes like me logo Genes that share phenotypes with SYDE1: view

Animal Models for SYDE1 Gene

MGI Knock Outs for SYDE1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SYDE1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for SYDE1 Gene

Localization for SYDE1 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 SYDE1 gene
Compartment Confidence
cytosol 5
nucleus 2
golgi apparatus 2

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for SYDE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with SYDE1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SYDE1 Gene

Pathways & Interactions for SYDE1 Gene

genes like me logo Genes that share pathways with SYDE1: view

Pathways by source for SYDE1 Gene

Gene Ontology (GO) - Biological Process for SYDE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IEA --
GO:0043087 regulation of GTPase activity IBA --
GO:0051056 regulation of small GTPase mediated signal transduction TAS --
GO:0051493 regulation of cytoskeleton organization IMP 27917469
GO:0090630 activation of GTPase activity ISS --
genes like me logo Genes that share ontologies with SYDE1: view

No data available for SIGNOR curated interactions for SYDE1 Gene

Drugs & Compounds for SYDE1 Gene

No Compound Related Data Available

Transcripts for SYDE1 Gene

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SYDE1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for SYDE1 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9
SP1:
SP2:
SP3: -
SP4: -
SP5:
SP6:

Relevant External Links for SYDE1 Gene

GeneLoc Exon Structure for
SYDE1
ECgene alternative splicing isoforms for
SYDE1

Expression for SYDE1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SYDE1 Gene

Protein differential expression in normal tissues from HIPED for SYDE1 Gene

This gene is overexpressed in Placenta (28.3), Tlymphocyte (21.0), and Bone marrow stromal cell (9.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SYDE1 Gene



NURSA nuclear receptor signaling pathways regulating expression of SYDE1 Gene:

SYDE1

SOURCE GeneReport for Unigene cluster for SYDE1 Gene:

Hs.528701

mRNA Expression by UniProt/SwissProt for SYDE1 Gene:

Q6ZW31-SYDE1_HUMAN
Tissue specificity: Expressed in trophoblast cells of placental villi.

Evidence on tissue expression from TISSUES for SYDE1 Gene

  • Liver(4.1)
  • Muscle(4.1)
genes like me logo Genes that share expression patterns with SYDE1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYDE1 Gene

Orthologs for SYDE1 Gene

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

Orthologs for SYDE1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SYDE1 33 34
  • 99.46 (n)
dog
(Canis familiaris)
Mammalia SYDE1 33 34
  • 87.89 (n)
rat
(Rattus norvegicus)
Mammalia Syde1 33
  • 82.95 (n)
mouse
(Mus musculus)
Mammalia Syde1 33 16 34
  • 82.31 (n)
cow
(Bos Taurus)
Mammalia SYDE1 33 34
  • 81.42 (n)
oppossum
(Monodelphis domestica)
Mammalia SYDE1 34
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SYDE1 34
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves SYDE1 33 34
  • 64.96 (n)
lizard
(Anolis carolinensis)
Reptilia SYDE1 34
  • 52 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii LOC568166 33
  • 58.5 (n)
SYDE1 34
  • 40 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta RhoGAP100F 34
  • 12 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea syd-1 34
  • 15 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BEM2 34
  • 5 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.767 34
  • 28 (a)
OneToMany
Species where no ortholog for SYDE1 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)
  • 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 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 SYDE1 Gene

ENSEMBL:
Gene Tree for SYDE1 (if available)
TreeFam:
Gene Tree for SYDE1 (if available)

Paralogs for SYDE1 Gene

Paralogs for SYDE1 Gene

(4) SIMAP similar genes for SYDE1 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with SYDE1: view

Variants for SYDE1 Gene

Sequence variations from dbSNP and Humsavar for SYDE1 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs772906202 A pancreatic ductal adenocarcinoma sample 15,110,668(+) GGAGC(A/G)GCCCC reference, missense
rs1000107815 -- 15,106,561(+) TTTTC(A/G)TATTT upstream-variant-2KB
rs1000113488 -- 15,114,456(+) GGGGG(A/G)CAGCC utr-variant-3-prime
rs1000297336 -- 15,105,723(+) CCCCA(C/T)GTTGG upstream-variant-2KB
rs1000351539 -- 15,113,092(+) TAGAG(C/T)AGGGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SYDE1 Gene

Variant ID Type Subtype PubMed ID
esv2758746 CNV gain 17122850
esv34154 CNV loss 18971310
nsv9668 CNV gain 18304495

Variation tolerance for SYDE1 Gene

Gene Damage Index Score: 4.28; 62.65% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SYDE1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYDE1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYDE1 Gene

Disorders for SYDE1 Gene

Relevant External Links for SYDE1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SYDE1

No disorders were found for SYDE1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SYDE1 Gene

Publications for SYDE1 Gene

  1. 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 4 60
  2. mSYD1A, a mammalian synapse-defective-1 protein, regulates synaptogenic signaling and vesicle docking. (PMID: 23791195) Wentzel C … Scheiffele P (Neuron 2013) 2 3 60
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  5. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. (PMID: 27173435) Boldt K … UK10K Rare Diseases Group (Nature communications 2016) 3 60

Products for SYDE1 Gene

Sources for SYDE1 Gene

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