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Aliases for SYNJ2 Gene

Aliases for SYNJ2 Gene

  • Synaptojanin 2 2 3 5
  • Synaptic Inositol 1,4,5-Trisphosphate 5-Phosphatase 2 2 3 4
  • Inositol Polyphosphate-5-Phosphatase H 2 3
  • Phosphoinositide 5-Phosphatase 2 3
  • EC 4 56
  • Inositol Phosphate 5-Phosphatase 2 3
  • Synaptojanin-2 3
  • KIAA0348 4
  • INPP5H 3

External Ids for SYNJ2 Gene

Previous GeneCards Identifiers for SYNJ2 Gene

  • GC06P157842
  • GC06P158276
  • GC06P158312
  • GC06P158373
  • GC06P158322
  • GC06P158402
  • GC06P155875

Summaries for SYNJ2 Gene

Entrez Gene Summary for SYNJ2 Gene

  • 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]

GeneCards Summary for SYNJ2 Gene

SYNJ2 (Synaptojanin 2) is a Protein Coding gene. Among its related pathways are Metabolism and Vesicle-mediated transport. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is SYNJ1.

UniProtKB/Swiss-Prot for SYNJ2 Gene

  • Inositol 5-phosphatase which may be involved in distinct membrane trafficking and signal transduction pathways. May mediate the inhibitory effect of Rac1 on endocytosis.

Additional gene information for SYNJ2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYNJ2 Gene

Genomics for SYNJ2 Gene

GeneHancer (GH) Regulatory Elements for SYNJ2 Gene

Promoters and enhancers for SYNJ2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I157980 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 557.1 +3.0 2952 8.2 HDGF PKNOX1 SMAD1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 SYNJ2 SYNJ2-IT1
GH06I158055 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 45 +77.4 77419 7 NCOA3 JUN ZNF223 MAX SIN3A BMI1 BATF FOSL1 ZNF121 POLR2A GC06M158055 SYNJ2 RNU6-786P SERAC1 SNX9
GH06I158066 Enhancer 1.3 Ensembl ENCODE dbSUPER 46.5 +87.9 87879 6.2 HDAC1 ELF3 FOXA2 RB1 ARNT ARID4B ZNF2 DNMT3B ZNF48 RAD21 SYNJ2 GTF2H5 SERAC1 ENSG00000271040 GC06M158055
GH06I158037 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 18.3 +59.5 59526 7.3 MLX YBX1 FEZF1 IRF4 ZNF213 E2F8 SP3 MEF2D SSRP1 ZNF610 SYNJ2 RNU6-786P LDHAL6FP SNX9 GC06M158055 SYNJ2-IT1
GH06I158029 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 16.5 +49.6 49585 3 PKNOX1 ZFP64 FEZF1 ZNF2 ZNF766 GLIS2 KLF7 FOS ATF7 RUNX3 SYNJ2 SNX9 LDHAL6FP GC06M158055 SYNJ2-IT1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SYNJ2 on UCSC Golden Path with GeneCards custom track

Genomic Locations for SYNJ2 Gene

Genomic Locations for SYNJ2 Gene
117,321 bases
Plus strand

Genomic View for SYNJ2 Gene

Genes around SYNJ2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYNJ2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYNJ2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYNJ2 Gene

Proteins for SYNJ2 Gene

  • Protein details for SYNJ2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q5TA13
    • Q5TA16
    • Q5TA19
    • Q86XK0
    • Q8IZA8
    • Q9H226

    Protein attributes for SYNJ2 Gene

    1496 amino acids
    Molecular mass:
    165538 Da
    Quaternary structure:
    • 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.
    • Sequence=AAH43277.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SYNJ2 Gene

    Alternative splice isoforms for SYNJ2 Gene


neXtProt entry for SYNJ2 Gene

Selected DME Specific Peptides for SYNJ2 Gene


Post-translational modifications for SYNJ2 Gene

  • Ubiquitination at posLast=14321432
  • Modification sites at PhosphoSitePlus

Domains & Families for SYNJ2 Gene

Gene Families for SYNJ2 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for SYNJ2 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the synaptojanin family.
  • Belongs to the synaptojanin family.
  • In the central section; belongs to the inositol 1,4,5-trisphosphate 5-phosphatase family.
genes like me logo Genes that share domains with SYNJ2: view

Function for SYNJ2 Gene

Molecular function for SYNJ2 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate.
UniProtKB/Swiss-Prot 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.

Enzyme Numbers (IUBMB) for SYNJ2 Gene

Phenotypes From GWAS Catalog for SYNJ2 Gene

Gene Ontology (GO) - Molecular Function for SYNJ2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0004438 phosphatidylinositol-3-phosphatase activity TAS --
GO:0004439 phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity TAS --
GO:0005515 protein binding IPI 15090612
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with SYNJ2: view
genes like me logo Genes that share phenotypes with SYNJ2: view

Animal Models for SYNJ2 Gene

MGI Knock Outs for SYNJ2:

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SYNJ2 Gene

Localization for SYNJ2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYNJ2 Gene

Cytoplasm. Cell membrane. Membrane raft. Cell projection, axon. Cytoplasm, cytoskeleton. Note=Localizes at nerve terminals in brain and at bundles of microtubules surrounding the nucleus in the elongating spermatids corresponding to the manchette (By similarity). Translocates from the cytoplasm to membrane ruffles in a RAC1-dependent manner (PubMed:11084340). {ECO:0000269 PubMed:11084340}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SYNJ2 gene
Compartment Confidence
plasma membrane 5
cytosol 5
cytoskeleton 4
nucleus 3
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Microtubules (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SYNJ2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton IEA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with SYNJ2: view

Pathways & Interactions for SYNJ2 Gene

genes like me logo Genes that share pathways with SYNJ2: view

Gene Ontology (GO) - Biological Process for SYNJ2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006661 phosphatidylinositol biosynthetic process TAS --
GO:0036092 phosphatidylinositol-3-phosphate biosynthetic process IEA --
GO:0046856 phosphatidylinositol dephosphorylation IEA --
GO:0061024 membrane organization TAS --
genes like me logo Genes that share ontologies with SYNJ2: view

No data available for SIGNOR curated interactions for SYNJ2 Gene

Drugs & Compounds for SYNJ2 Gene

(2) Drugs for SYNJ2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0

(2) Additional Compounds for SYNJ2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (3-Phosphatidyl)-1-D-inositol
  • 1,2-Diacyl-sn-glycero-3-phosphoinositol
  • 1-Phosphatidyl-1D-myo-inositol
  • 1-Phosphatidyl-myo-inositol
  • Phosphatidyl-1D-myo-inositol
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
genes like me logo Genes that share compounds with SYNJ2: view

Transcripts for SYNJ2 Gene

Unigene Clusters for SYNJ2 Gene

Synaptojanin 2:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYNJ2 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b · 8c · 8d ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a ·
SP3: - - - - - -
SP4: - - - - - - - - -
SP5: - - -
SP6: - - - - - -
SP7: - - -
SP8: - -
SP11: - -
SP12: -

ExUns: 17b · 17c ^ 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22a · 22b · 22c ^ 23 ^ 24a · 24b · 24c ^ 25 ^ 26a · 26b ^ 27 ^ 28 ^ 29 ^ 30
SP1: - - -
SP2: -

Relevant External Links for SYNJ2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SYNJ2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SYNJ2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYNJ2 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x9.4) and Brain - Substantia nigra (x4.9).

Protein differential expression in normal tissues from HIPED for SYNJ2 Gene

This gene is overexpressed in Bone marrow stromal cell (27.9) and Breast (10.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SYNJ2 Gene

NURSA nuclear receptor signaling pathways regulating expression of SYNJ2 Gene:


SOURCE GeneReport for Unigene cluster for SYNJ2 Gene:


Evidence on tissue expression from TISSUES for SYNJ2 Gene

  • Nervous system(4.8)
  • Liver(4.2)
  • Eye(2.2)
genes like me logo Genes that share expression patterns with SYNJ2: view

Primer Products

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYNJ2 Gene

Orthologs for SYNJ2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SYNJ2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SYNJ2 33 34
  • 99.44 (n)
(Canis familiaris)
Mammalia SYNJ2 33 34
  • 85.73 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 85 (a)
-- 34
  • 62 (a)
(Bos Taurus)
Mammalia SYNJ2 33 34
  • 84.44 (n)
(Rattus norvegicus)
Mammalia Synj2 33
  • 83.27 (n)
(Mus musculus)
Mammalia Synj2 33 16 34
  • 83.04 (n)
(Monodelphis domestica)
Mammalia SYNJ2 34
  • 81 (a)
(Gallus gallus)
Aves SYNJ2 33 34
  • 71.76 (n)
(Anolis carolinensis)
Reptilia SYNJ2 34
  • 68 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia synj2 33
  • 68.37 (n)
fruit fly
(Drosophila melanogaster)
Insecta synaptojanin 35
  • 47 (a)
synj 34
  • 43 (a)
(Caenorhabditis elegans)
Secernentea unc-26 34
  • 39 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes INP53 34
  • 30 (a)
INP52 34
  • 29 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 47 (a)
Species where no ortholog for SYNJ2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for SYNJ2 Gene

Gene Tree for SYNJ2 (if available)
Gene Tree for SYNJ2 (if available)

Paralogs for SYNJ2 Gene

Paralogs for SYNJ2 Gene

(1) SIMAP similar genes for SYNJ2 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with SYNJ2: view

Variants for SYNJ2 Gene

Sequence variations from dbSNP and Humsavar for SYNJ2 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs869312665 uncertain-significance, not specified 158,078,271(+) T/C coding_sequence_variant, intron_variant, missense_variant
rs1000040832 -- 157,998,996(+) CAAGCAA/CAA genic_upstream_transcript_variant, intron_variant
rs1000041016 -- 158,077,577(+) T/C intron_variant
rs1000066682 -- 157,996,847(+) G/T genic_upstream_transcript_variant, intron_variant
rs1000104651 -- 158,023,707(+) T/C genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SYNJ2 Gene

Variant ID Type Subtype PubMed ID
esv2675122 CNV deletion 23128226
esv2732991 CNV deletion 23290073
esv2732992 CNV deletion 23290073
esv3540731 CNV deletion 23714750
esv3540734 CNV deletion 23714750
esv3611387 CNV loss 21293372
esv3890972 CNV gain 25118596
nsv1124137 CNV deletion 24896259
nsv1137168 CNV deletion 24896259
nsv5559 CNV deletion 18451855
nsv604980 CNV loss 21841781

Variation tolerance for SYNJ2 Gene

Residual Variation Intolerance Score: 6.43% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.09; 61.01% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYNJ2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYNJ2 Gene

Disorders for SYNJ2 Gene

Additional Disease Information for SYNJ2

No disorders were found for SYNJ2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SYNJ2 Gene

Publications for SYNJ2 Gene

  1. Synaptojanin 2, a novel Rac1 effector that regulates clathrin-mediated endocytosis. (PMID: 11084340) Malecz N … Symons M (Current biology : CB 2000) 3 4 22 58
  2. Regulation of synaptojanin 2 5'-phosphatase activity by Src. (PMID: 23076136) Chuang Y … Symons M (Cell adhesion & migration 2012) 2 3 58
  3. Role of the guanine nucleotide exchange factor Ost in negative regulation of receptor endocytosis by the small GTPase Rac1. (PMID: 17562712) Ieguchi K … Satoh T (The Journal of biological chemistry 2007) 3 22 58
  4. Identification of inactivating mutations in the JAK1, SYNJ2, and CLPTM1 genes in prostate cancer cells using inhibition of nonsense-mediated decay and microarray analysis. (PMID: 16102578) Rossi MR … Ionov Y (Cancer genetics and cytogenetics 2005) 3 22 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for SYNJ2 Gene

Sources for SYNJ2 Gene

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