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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
  • Rho GTPase-Activating Protein SYDE1 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
  • EC 2.4.1.25 56
  • EC 2.6.1.9 56
  • 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 Signaling by Rho GTPases and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include GTPase activator activity. 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

GeneHancer (GH) Regulatory Elements for SYDE1 Gene

Promoters and enhancers for SYDE1 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
GH19J015106 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 608.8 +0.7 689 3.5 ZNF652 ZNF384 GLIS2 POLR2A PKNOX1 ZBTB8A PRDM10 ZIC2 PATZ1 ZNF341 SYDE1 RNU6-782P GC19P015120
GH19J014512 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 12.3 -588.8 -588834 12 SP1 CC2D1A ELF3 ZFX MNT ZNF148 NKRF POLR2A MLLT1 ZNF121 TECR DNAJB1 AKAP8 BRD4 CCDC130 MRI1 ZNF333 NOTCH3 SYDE1 SNRPGP15
GH19J015416 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 12.3 +311.0 311047 3.4 HDGF MTA3 CC2D1A ZFX SP1 CTCF NKRF POLR2A MLLT1 ZNF121 BRD4 AKAP8L AKAP8 ZNF333 DDX39A NOTCH3 SYDE1 SNRPGP15 TPM4 ENSG00000279716
GH19J016063 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.9 +965.5 965549 18.7 ZNF473 SP1 CC2D1A ELF3 ZFX CTCF ZKSCAN8 CBFA2T2 ZNF148 NKRF TPM4 AKAP8 CHERP ENSG00000269578 BRD4 C19orf44 ENSG00000267904 ENSG00000268087 MED26 ENSG00000268743
GH19J014378 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.9 -724.8 -724788 7.7 SP1 CC2D1A ZFX ZNF148 NKRF MLLT1 ZNF121 GTF2F1 CSDE1 ZNF687 ADGRE5 CCDC130 AKAP8 MRI1 ZNF333 BRD4 DDX39A DCAF15 RFX1 ENSG00000267519
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYDE1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SYDE1 gene promoter:
  • E47
  • GATA-1
  • GATA-3
  • NRSF form 1
  • NRSF form 2
  • RORalpha1
  • Sp1
  • Tal-1
  • USF-1
  • USF1

Genomic Locations for SYDE1 Gene

Genomic Locations for SYDE1 Gene
chr19:15,107,364-15,114,988
(GRCh38/hg38)
Size:
7,625 bases
Orientation:
Plus strand
chr19:15,218,214-15,225,799
(GRCh37/hg19)
Size:
7,586 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:
  • Synapse defective protein 1 homolog 1 (SYDE1_HUMAN)

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 ISS --
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:
  • Syde1 Syde1<tm1.1Hwch>
  • Syde1 Syde1<tm1a(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYDE1

Clone Products

  • Applied Biological Materials (abm): Clones for SYDE1 - Now 50% OFF >
  • * SYDE1 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * SYDE1 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

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 1

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: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:0051056 regulation of small GTPase mediated signal transduction TAS --
GO:0051493 regulation of cytoskeleton organization IMP 27917469
GO:0090630 activation of GTPase activity ISS --
GO:1901165 positive regulation of trophoblast cell migration IMP 27917469
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

mRNA/cDNA for SYDE1 Gene

Unigene Clusters for SYDE1 Gene

Synapse defective 1, Rho GTPase, homolog 1 (C. elegans):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYDE1

Clone Products

  • Applied Biological Materials (abm): Clones for SYDE1 - Now 50% OFF >
  • * SYDE1 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * SYDE1 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

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, 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

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 35 34
  • 99.46 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SYDE1 35 34
  • 87.89 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Syde1 34
  • 82.95 (n)
mouse
(Mus musculus)
Mammalia Syde1 17 35 34
  • 82.31 (n)
cow
(Bos Taurus)
Mammalia SYDE1 35 34
  • 81.42 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SYDE1 35
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SYDE1 35
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves SYDE1 35 34
  • 64.96 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SYDE1 35
  • 52 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii LOC568166 34
  • 58.5 (n)
SYDE1 35
  • 40 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta RhoGAP100F 35
  • 12 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea syd-1 35
  • 15 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BEM2 35
  • 5 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.767 35
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for SYDE1: view image

Paralogs for SYDE1 Gene

Paralogs for SYDE1 Gene

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

  • SYDE1_HUMAN
  • M0QXZ8_HUMAN
  • M0R101_HUMAN
  • M0R3D3_HUMAN
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 Variation AA Info Type
rs772906202 A pancreatic ductal adenocarcinoma sample 15,110,668(+) G/A coding_sequence_variant, missense_variant
rs1000107815 -- 15,106,561(+) A/G upstream_transcript_variant
rs1000113488 -- 15,114,456(+) G/A 3_prime_UTR_variant
rs1000297336 -- 15,105,723(+) T/C upstream_transcript_variant
rs1000351539 -- 15,113,092(+) C/T 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)

Additional Variant Information for SYDE1 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for SYDE1 Gene

Additional Disease Information for 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 58
  2. mSYD1A, a mammalian synapse-defective-1 protein, regulates synaptogenic signaling and vesicle docking. (PMID: 23791195) Wentzel C … Scheiffele P (Neuron 2013) 2 3 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. (PMID: 27173435) Boldt K … UK10K Rare Diseases Group (Nature communications 2016) 3 58

Products for SYDE1 Gene

Sources for SYDE1 Gene

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