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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
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Genomic context

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See SYDE2 in Genome Data Viewer
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

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