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    SYDE1 synapse defective Rho GTPase homolog 1 [ Homo sapiens (human) ]

    Gene ID: 85360, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SYDE1provided by HGNC
    Official Full Name
    synapse defective Rho GTPase homolog 1provided by HGNC
    Primary source
    HGNC:HGNC:25824
    See related
    Ensembl:ENSG00000105137 MIM:617377; AllianceGenome:HGNC:25824
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    7h3; SYD1
    Summary
    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]
    Expression
    Ubiquitous expression in fat (RPKM 9.3), placenta (RPKM 9.2) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SYDE1 in Genome Data Viewer
    Location:
    19p13.12
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (15107401..15114974)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (15232344..15239918)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (15218212..15225785)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene caspase 14 Neighboring gene olfactory receptor family 1 subfamily I member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:15219898-15220448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:15222723-15223250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:15223251-15223776 Neighboring gene ilvB acetolactate synthase like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:15235337-15236102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:15236103-15236866 Neighboring gene ILVBL antisense RNA 1 Neighboring gene olfactory receptor family 10 subfamily B member 1 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Analysis of the placental tissue transcriptome of normal and preeclampsia complicated pregnancies. Trifonova EA, et al. Acta Naturae, 2014 Apr. PMID 25093114, Free PMC Article
    2. Functional relevance of a six mesenchymal gene signature in epithelial-mesenchymal transition (EMT) reversal by the triple angiokinase inhibitor, nintedanib (BIBF1120). Huang RY, et al. Oncotarget, 2015 Sep 8. PMID 26061747, Free PMC Article
    3. Association of dysfunctional synapse defective 1 (SYDE1) with restricted fetal growth - SYDE1 regulates placental cell migration and invasion. Lo HF, et al. J Pathol, 2017 Feb. PMID 27917469
    4. mSYD1A, a mammalian synapse-defective-1 protein, regulates synaptogenic signaling and vesicle docking. Wentzel C, et al. Neuron, 2013 Jun 19. PMID 23791195, Free PMC Article
    5. The shieldin complex mediates 53BP1-dependent DNA repair. Noordermeer SM, et al. Nature, 2018 Aug. PMID 30022168, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. a novel mechanism for GCM1 and SYDE1 in regulation of trophoblast cell migration and invasion during placental development
      Title: Association of dysfunctional synapse defective 1 (SYDE1) with restricted fetal growth - SYDE1 regulates placental cell migration and invasion.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ13511

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTPase activator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables GTPase activator activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables GTPase activator activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables GTPase regulator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables GTPase regulator activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within actin cytoskeleton organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in activation of GTPase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within cell migration IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of trophoblast cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of Ras protein signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in synaptic membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    rho GTPase-activating protein SYDE1
    Names
    protein syd-1 homolog 1
    synapse defective 1, Rho GTPase, homolog 1
    synapse defective protein 1 homolog 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001300910.2 → NP_001287839.1  rho GTPase-activating protein SYDE1 isoform 2

      See identical proteins and their annotated locations for NP_001287839.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AC004794
      Consensus CDS
      CCDS74299.1
      UniProtKB/TrEMBL
      B2RD93
      Related
      ENSP00000470733.1, ENST00000600440.5
      Conserved Domains (1) summary
      cl02570
      Location:329 → 534
      RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...

    2. NM_033025.6 → NP_149014.3  rho GTPase-activating protein SYDE1 isoform 1

      See identical proteins and their annotated locations for NP_149014.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC004794
      Consensus CDS
      CCDS12324.1
      UniProtKB/Swiss-Prot
      Q6ZW31, Q7L2I8, Q8N6J2, Q9H8K4
      UniProtKB/TrEMBL
      A0A2X0SFL9
      Related
      ENSP00000341489.1, ENST00000342784.7
      Conserved Domains (1) summary
      cl02570
      Location:396 → 601
      RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      15107401..15114974
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439579.1 → XP_047295535.1  rho GTPase-activating protein SYDE1 isoform X1

    2. XM_047439580.1 → XP_047295536.1  rho GTPase-activating protein SYDE1 isoform X2

    3. XM_024451750.2 → XP_024307518.1  rho GTPase-activating protein SYDE1 isoform X3

      Conserved Domains (1) summary
      cl02570
      Location:396 → 473
      RhoGAP; GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to ...

    4. XM_047439581.1 → XP_047295537.1  rho GTPase-activating protein SYDE1 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      15232344..15239918
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322456.1 → XP_054178431.1  rho GTPase-activating protein SYDE1 isoform X1

    2. XM_054322457.1 → XP_054178432.1  rho GTPase-activating protein SYDE1 isoform X2

    3. XM_054322458.1 → XP_054178433.1  rho GTPase-activating protein SYDE1 isoform X3

    4. XM_054322459.1 → XP_054178434.1  rho GTPase-activating protein SYDE1 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZW31.1 GenPept UniProtKB/Swiss-Prot:Q6ZW31

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