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    SYDE2 synapse defective Rho GTPase homolog 2 [ Homo sapiens (human) ]

    Gene ID: 84144, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SYDE2provided by HGNC
    Official Full Name
    synapse defective Rho GTPase homolog 2provided by HGNC
    Primary source
    HGNC:HGNC:25841
    See related
    Ensembl:ENSG00000097096 AllianceGenome:HGNC:25841
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to enable GTPase activator activity. Acts upstream of or within cell migration. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in lung (RPKM 2.4), placenta (RPKM 1.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1p22.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (85152491..85201016, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (84997997..85042131, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (85622572..85666699, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:85527645-85528145 Neighboring gene dynein axonemal intermediate chain 3 Neighboring gene microRNA 4423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1266 Neighboring gene NANOG hESC enhancer GRCh37_chr1:85618513-85619014 Neighboring gene uncharacterized LOC124904207 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:85665814-85666425 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1031 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:85690807-85690967 Neighboring gene uncharacterized LOC105378821 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1032 Neighboring gene Sharpr-MPRA regulatory region 4548 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1033 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1267 Neighboring gene chromosome 1 open reading frame 52

    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
    • 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. 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
    2. E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins. Khanna R, et al. FEBS J, 2018 Jun. PMID 29676528
    3. Defining the proximal interaction networks of Arf GTPases reveals a mechanism for the regulation of PLD1 and PI4KB. Li FL, et al. EMBO J, 2022 Sep 1. PMID 35844135, Free PMC Article
    4. A central chaperone-like role for 14-3-3 proteins in human cells. Segal D, et al. Mol Cell, 2023 Mar 16. PMID 36931259
    5. Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions. Müller PM, et al. Nat Cell Biol, 2020 Apr. PMID 32203420

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    • FLJ13815

    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables GTPase activator activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    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 
    involved_in regulation of Ras protein signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of small GTPase mediated signal transduction TAS
    Traceable Author Statement
    more info
    		  
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    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 SYDE2
    Names
    protein syd-1 homolog 2
    synapse defective 1, Rho GTPase, homolog 2
    synapse defective protein 1 homolog 2

    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_032184.2 → NP_115560.1  rho GTPase-activating protein SYDE2

      See identical proteins and their annotated locations for NP_115560.1

      Status: VALIDATED

      Source sequence(s)
      AL603750
      Consensus CDS
      CCDS44169.1
      UniProtKB/Swiss-Prot
      Q5VT96, Q5VT97, Q8NDB8, Q9H8A6
      UniProtKB/TrEMBL
      A0A2X0SFY5
      Related
      ENSP00000340594.5, ENST00000341460.6
      Conserved Domains (2) summary
      cl02570
      Location:814 → 1028
      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 ...
      cl14603
      Location:679 → 794
      C2; C2 domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      85152491..85201016 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017002483.2 → XP_016857972.2  rho GTPase-activating protein SYDE2 isoform X1

    2. XM_017002484.3 → XP_016857973.2  rho GTPase-activating protein SYDE2 isoform X2

    3. XM_047431920.1 → XP_047287876.1  rho GTPase-activating protein SYDE2 isoform X4

    4. XM_006710946.4 → XP_006711009.2  rho GTPase-activating protein SYDE2 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      84997997..85042131 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339085.1 → XP_054195060.1  rho GTPase-activating protein SYDE2 isoform X1

    2. XM_054339086.1 → XP_054195061.1  rho GTPase-activating protein SYDE2 isoform X2

    3. XM_054339088.1 → XP_054195063.1  rho GTPase-activating protein SYDE2 isoform X4

    4. XM_054339087.1 → XP_054195062.1  rho GTPase-activating protein SYDE2 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VT97.2 GenPept UniProtKB/Swiss-Prot:Q5VT97

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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