Human Gene SYNJ2 (ENST00000640338.1) Description and Page Index
  Description: Inositol 5-phosphatase which may be involved in distinct membrane trafficking and signal transduction pathways. May mediate the inhibitory effect of Rac1 on endocytosis. (from UniProt O15056)
RefSeq Summary (NM_003898): The gene is a member of the inositol-polyphosphate 5-phosphatase family. The encoded protein interacts with the ras-related C3 botulinum toxin substrate 1, which causes translocation of the encoded protein to the plasma membrane where it inhibits clathrin-mediated endocytosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010].
Gencode Transcript: ENST00000640338.1
Gencode Gene: ENSG00000078269.15
Transcript (Including UTRs)
   Position: hg38 chr6:157,981,954-158,094,094 Size: 112,141 Total Exon Count: 27 Strand: +
Coding Region
   Position: hg38 chr6:157,981,962-158,094,010 Size: 112,049 Coding Exon Count: 27 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:157,981,954-158,094,094)mRNA (may differ from genome)Protein (1288 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneCardsHGNCHPRD
LynxMGImyGene2neXtProtPubMedReactome
Stanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SYNJ2_HUMAN
DESCRIPTION: RecName: Full=Synaptojanin-2; EC=3.1.3.36; AltName: Full=Synaptic inositol 1,4,5-trisphosphate 5-phosphatase 2;
FUNCTION: Inositol 5-phosphatase which may be involved in distinct membrane trafficking and signal transduction pathways. May mediate the inhibitory effect of Rac1 on endocytosis.
CATALYTIC ACTIVITY: 1-phosphatidyl-1D-myo-inositol 4,5- bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate.
SUBUNIT: Binds to GRB2. Isoform 2A binds to SYNJ2BP/OMP25. Isoform 2B2 C-terminal proline-rich region binds to a variety of SH3 domain-containing proteins including SH3GL1, SH3GL2, SH3GL3 and GRB2.
INTERACTION: P62993:GRB2; NbExp=2; IntAct=EBI-310513, EBI-401755; P16333:NCK1; NbExp=3; IntAct=EBI-310513, EBI-389883;
SUBCELLULAR LOCATION: Membrane (By similarity). Note=Predominantly associated with the particulate fractions (By similarity).
SIMILARITY: Belongs to the synaptojanin family.
SIMILARITY: In the central section; belongs to the inositol 1,4,5- trisphosphate 5-phosphatase family.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SIMILARITY: Contains 1 SAC domain.
SEQUENCE CAUTION: Sequence=AAH43277.1; Type=Erroneous initiation;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • C006253 pirinixic acid
  • C517041 (4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)
  • C028474 1,4-bis(2-(3,5-dichloropyridyloxy))benzene
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C023035 3,4,5,3',4'-pentachlorobiphenyl
  • C009505 4,4'-diaminodiphenylmethane
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D016604 Aflatoxin B1
  • D000643 Ammonium Chloride
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 39.35 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 233.18 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
3' UTR -19.1084-0.227 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
IPR015047 - DUF1866
IPR005135 - Endo/exonuclease/phosphatase
IPR000300 - IPPc
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom
IPR002013 - Syja_N

Pfam Domains:
PF08952 - Domain of unknown function (DUF1866)
PF03372 - Endonuclease/Exonuclease/phosphatase family
PF02383 - SacI homology domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1UFW
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on O15056
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-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004438 phosphatidylinositol-3-phosphatase activity
GO:0004439 phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0034595 phosphatidylinositol phosphate 5-phosphatase activity
GO:0034596 phosphatidylinositol phosphate 4-phosphatase activity
GO:0042578 phosphoric ester hydrolase activity
GO:0043813 phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity
GO:0052629 phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity

Biological Process:
GO:0006661 phosphatidylinositol biosynthetic process
GO:0036092 phosphatidylinositol-3-phosphate biosynthetic process
GO:0046856 phosphatidylinositol dephosphorylation
GO:0061024 membrane organization

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030424 axon
GO:0042995 cell projection
GO:0045121 membrane raft


-  Descriptions from all associated GenBank mRNAs
  AF318616 - Homo sapiens synaptojanin 2 mRNA, complete cds.
AY152396 - Homo sapiens synaptojanin 2A mRNA, complete cds.
AB384465 - Synthetic construct DNA, clone: pF1KA0348, Homo sapiens SYNJ2 gene for synaptojanin-2, complete cds, without stop codon, in Flexi system.
BX648749 - Homo sapiens mRNA; cDNA DKFZp686C1268 (from clone DKFZp686C1268).
AB002346 - Homo sapiens KIAA0348 mRNA for KIAA0348 protein.
AF039945 - Homo sapiens synaptojanin 2B mRNA, partial cds.
AL157424 - Homo sapiens mRNA; cDNA DKFZp761E1512 (from clone DKFZp761E1512).
AK296935 - Homo sapiens cDNA FLJ55580 complete cds, highly similar to Synaptojanin-2 (EC 3.1.3.36).
BC043277 - Homo sapiens synaptojanin 2, mRNA (cDNA clone MGC:44422 IMAGE:5297160), complete cds.
AK294480 - Homo sapiens cDNA FLJ60489 complete cds, highly similar to Synaptojanin-2 (EC 3.1.3.36).
AK296242 - Homo sapiens cDNA FLJ60279 complete cds, highly similar to Synaptojanin-2 (EC 3.1.3.36).
AK309018 - Homo sapiens cDNA, FLJ99059.
AK026758 - Homo sapiens cDNA: FLJ23105 fis, clone LNG07677.
AK074294 - Homo sapiens cDNA FLJ23714 fis, clone HEP12851, highly similar to Homo sapiens synaptojanin 2 mRNA.
LF210683 - JP 2014500723-A/18186: Polycomb-Associated Non-Coding RNAs.
MA446260 - JP 2018138019-A/18186: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00562 - Inositol phosphate metabolism
hsa01100 - Metabolic pathways
hsa04070 - Phosphatidylinositol signaling system

BioCarta from NCI Cancer Genome Anatomy Project
h_ndkDynaminPathway - Endocytotic role of NDK, Phosphins and Dynamin

Reactome (by CSHL, EBI, and GO)

Protein O15056 (Reactome details) participates in the following event(s):

R-HSA-8868651 Endophilins recruit synaptojanins to the clathrin-coated pit
R-HSA-8871194 RAB5 and GAPVD1 bind AP-2
R-HSA-8868658 HSPA8-mediated ATP hydrolysis promotes vesicle uncoating
R-HSA-8868659 Clathrin recruits auxilins to the clathrin-coated vesicle
R-HSA-8868661 Dynamin-mediated GTP hydrolysis promotes vesicle scission
R-HSA-8868660 Auxilin recruits HSPA8:ATP to the clathrin-coated vesicle
R-HSA-8868648 SYNJ hydrolyze PI(4,5)P2 to PI(4)P
R-HSA-1675988 PI4P is dephosphorylated to PI by SYNJ at the plasma membrane
R-HSA-1675836 PI(3,5)P2 is dephosphorylated to PI3P by SYNJ at the plasma membrane
R-HSA-1676177 PI(4,5)P2 is dephosphorylated to PI4P by SYNJ/INPP5[1] at the plasma membrane
R-HSA-1676203 PI(3,5)P2 is dephosphorylated to PI5P by SYNJ/MTMs at the plasma membrane
R-HSA-1675994 PI3P is dephosphorylated to PI by SYNJ/MTMs at the plasma membrane
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-199991 Membrane Trafficking
R-HSA-1660499 Synthesis of PIPs at the plasma membrane
R-HSA-5653656 Vesicle-mediated transport
R-HSA-1483255 PI Metabolism
R-HSA-1483257 Phospholipid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: AY152396, KIAA0348, O15056, Q5TA13, Q5TA16, Q5TA19, Q86XK0, Q8IZA8, Q9H226, SYNJ2_HUMAN, uc285zap.1
UCSC ID: uc285zap.1
RefSeq Accession: NM_003898
Protein: O15056 (aka SYNJ2_HUMAN or SYJ2_HUMAN)

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