Human Gene SYDE1 (ENST00000342784.7_6) from GENCODE V47lift37
  Description: synapse defective Rho GTPase homolog 1, transcript variant 1 (from RefSeq NM_033025.6)
Gencode Transcript: ENST00000342784.7_6
Gencode Gene: ENSG00000105137.13_10
Transcript (Including UTRs)
   Position: hg19 chr19:15,218,212-15,225,785 Size: 7,574 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr19:15,218,245-15,224,774 Size: 6,530 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:15,218,212-15,225,785)mRNA (may differ from genome)Protein (735 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SYDE1_HUMAN
DESCRIPTION: RecName: Full=Rho GTPase-activating protein SYDE1; AltName: Full=Synapse defective protein 1 homolog 1; Short=Protein syd-1 homolog 1;
FUNCTION: GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state (By similarity).
SIMILARITY: Contains 1 Rho-GAP domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.69 RPKM in Cells - Cultured fibroblasts
Total median expression: 332.73 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -16.8033-0.509 Picture PostScript Text
3' UTR -396.301011-0.392 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008973 - C2_Ca/lipid-bd_dom_CaLB
IPR008936 - Rho_GTPase_activation_prot
IPR000198 - RhoGAP_dom

Pfam Domains:
PF00620 - RhoGAP domain

SCOP Domains:
48350 - GTPase activation domain, GAP
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)

ModBase Predicted Comparative 3D Structure on Q6ZW31
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005096 GTPase activator activity

Biological Process:
GO:0007165 signal transduction
GO:0043087 regulation of GTPase activity
GO:0051056 regulation of small GTPase mediated signal transduction
GO:0051493 regulation of cytoskeleton organization
GO:0090630 activation of GTPase activity
GO:1901165 positive regulation of trophoblast cell migration

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  LF208803 - JP 2014500723-A/16306: Polycomb-Associated Non-Coding RNAs.
AK123686 - Homo sapiens cDNA FLJ41692 fis, clone HCHON2000028, highly similar to Homo sapiens 7h3 protein mRNA.
AK315453 - Homo sapiens cDNA, FLJ96511.
BC029926 - Homo sapiens synapse defective 1, Rho GTPase, homolog 1 (C. elegans), mRNA (cDNA clone MGC:34690 IMAGE:5106728), complete cds.
CU688794 - Synthetic construct Homo sapiens gateway clone IMAGE:100019996 5' read SYDE1 mRNA.
KJ903516 - Synthetic construct Homo sapiens clone ccsbBroadEn_12910 SYDE1 gene, encodes complete protein.
AK128870 - Homo sapiens cDNA FLJ46850 fis, clone UTERU3006720.
LF323034 - JP 2014500723-A/130537: Polycomb-Associated Non-Coding RNAs.
BC018942 - Homo sapiens synapse defective 1, Rho GTPase, homolog 1 (C. elegans), mRNA (cDNA clone IMAGE:4139438), partial cds.
JD422520 - Sequence 403544 from Patent EP1572962.
AK023573 - Homo sapiens cDNA FLJ13511 fis, clone PLACE1005331, highly similar to Homo sapiens 7h3 protein mRNA.
AF209931 - Homo sapiens 7h3 protein mRNA, partial cds.
JD269865 - Sequence 250889 from Patent EP1572962.
JD565382 - Sequence 546406 from Patent EP1572962.
JD548910 - Sequence 529934 from Patent EP1572962.
JD141118 - Sequence 122142 from Patent EP1572962.
JD416174 - Sequence 397198 from Patent EP1572962.
JD564613 - Sequence 545637 from Patent EP1572962.
JD059771 - Sequence 40795 from Patent EP1572962.
JD180773 - Sequence 161797 from Patent EP1572962.
JD077521 - Sequence 58545 from Patent EP1572962.
JD392400 - Sequence 373424 from Patent EP1572962.
JD336945 - Sequence 317969 from Patent EP1572962.
JD211773 - Sequence 192797 from Patent EP1572962.
JD114943 - Sequence 95967 from Patent EP1572962.
JD368755 - Sequence 349779 from Patent EP1572962.
JD065638 - Sequence 46662 from Patent EP1572962.
JD066382 - Sequence 47406 from Patent EP1572962.
MA558611 - JP 2018138019-A/130537: Polycomb-Associated Non-Coding RNAs.
MA444380 - JP 2018138019-A/16306: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q6ZW31 (Reactome details) participates in the following event(s):

R-HSA-194922 GAPs inactivate Rho GTPase:GTP by hydrolysis
R-HSA-194840 Rho GTPase cycle
R-HSA-194315 Signaling by Rho GTPases
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000342784.1, ENST00000342784.2, ENST00000342784.3, ENST00000342784.4, ENST00000342784.5, ENST00000342784.6, NM_033025, Q6ZW31, Q7L2I8, Q8N6J2, Q9H8K4, SYDE1_HUMAN, uc317wlo.1, uc317wlo.2
UCSC ID: ENST00000342784.7_6
RefSeq Accession: NM_033025.6
Protein: Q6ZW31 (aka SYDE1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.