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
Stanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Synaptojanin-2; EC=; 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


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

-  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
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
AK296242 - Homo sapiens cDNA FLJ60279 complete cds, highly similar to Synaptojanin-2 (EC
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.