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] See more...

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
  • Synaptojanin-2 3 4
  • EC 3.1.3.36 4 52
  • Inositol Phosphate 5'-Phosphatase 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. Diseases associated with SYNJ2 include Charcot-Marie-Tooth Disease, Type 4J and Frontotemporal Dementia And/Or Amyotrophic Lateral Sclerosis 2. Among its related pathways are superpathway of inositol phosphate compounds and Metabolism. 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 Summary 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 , Rfam classification 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
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J157980 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 507 +2.8 2788 8.5 EP300 FOXK2 CTCF ZSCAN5C SIN3A NRF1 TCF12 POLR2G USF1 NCOR1 SYNJ2 SNX9 HSPE1P26 ENSG00000285642
GH06J158024 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 512.4 +44.6 44644 4.8 CTCF TCF12 POLR2G RBAK JUND FOS ZNF639 ZIC2 REST ZBTB10 SYNJ2 SNX9 LOC100420839 RNU6-786P DYNLT1 LDHAL6FP RF00017-5907 RF00017-5906
GH06J158013 Promoter/Enhancer 1.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 520.8 +36.1 36145 8.8 NCOR1 JUND FOS ZIC2 KDM6A TCF7 ZBTB25 TGIF2 SKI TEAD1 SYNJ2 RF00017-5906 RNU6-786P GTF2H5 RF00017-5907
GH06J157981 Promoter/Enhancer 0.6 Ensembl dbSUPER 500.7 -1.8 -1755 0.2 NCOR1 SYNJ2 HSALNG0054655
GH06J158055 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 45 +77.3 77340 7.2 TCF12 JUND FOS REST RFX1 EP300 NR2F2 SIN3A ZNF592 POLR2A lnc-SERAC1-7 SYNJ2 RNU6-786P SERAC1 SNX9 piR-41195-046
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYNJ2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SYNJ2

Genomic Locations for SYNJ2 Gene

Genomic Locations for SYNJ2 Gene
chr6:157,981,856-158,099,176
(GRCh38/hg38)
Size:
117,321 bases
Orientation:
Plus strand
chr6:158,402,888-158,520,208
(GRCh37/hg19)
Size:
117,321 bases
Orientation:
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:
    O15056-SYNJ2_HUMAN
    Recommended name:
    Synaptojanin-2
    Protein Accession:
    O15056
    Secondary Accessions:
    • Q5TA13
    • Q5TA16
    • Q5TA19
    • Q86XK0
    • Q8IZA8
    • Q9H226

    Protein attributes for SYNJ2 Gene

    Size:
    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.
    SequenceCaution:
    • Sequence=AAH43277.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SYNJ2 Gene

    Alternative splice isoforms for SYNJ2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYNJ2 Gene

Selected DME Specific Peptides for SYNJ2 Gene

O15056:
  • KLKDGARS
  • HKQAKACL
  • FSHDYVFWCGDFNYRIDL
  • EANAPAF
  • DTVKTGMGG
  • DCLDRTN
  • ALEGKAK
  • RGSVPLFW
  • GTWNVNGGKQFRS
  • PFIRDVA
  • KCRTPAWTDRVLW

Post-translational modifications for SYNJ2 Gene

  • Ubiquitination at Lys1432
  • Modification sites at PhosphoSitePlus

Domains & Families for SYNJ2 Gene

Gene Families for SYNJ2 Gene

Protein Domains for SYNJ2 Gene

Blocks:
  • RNA-binding region RNP-1 (RNA recognition motif)
  • Synaptojanin, N-terminal
  • Inositol polyphosphate related phosphatase family
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SYNJ2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ60279, highly similar to Synaptojanin-2 (EC 3.1.3.36) (B4DJU8_HUMAN)
  • Synaptic inositol-1,4,5-trisphosphate 5-phosphatase 2 (SYNJ2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O15056

UniProtKB/Swiss-Prot:

SYNJ2_HUMAN :
  • Belongs to the synaptojanin family.
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 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.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-4,5-bisphosphate) + H2O = 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol 4-phosphate) + phosphate; Xref=Rhea:RHEA:22764, ChEBI:CHEBI:15377, ChEBI:CHEBI:43474, ChEBI:CHEBI:58178, ChEBI:CHEBI:58456; EC=3.1.3.36; Evidence=. ;.

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:0004439 phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity TAS --
GO:0005515 protein binding IPI 15090612
GO:0016787 hydrolase activity IEA --
GO:0017124 SH3 domain binding IBA 21873635
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:
  • Synj2 Synj2<tm1a(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYNJ2

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 junction, synapse, presynapse. Cytoplasm, cytoskeleton. Note=Localizes at presynapse 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

COMPARTMENTS
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
cytosol 5
plasma membrane 4
cytoskeleton 4
nucleus 3
endosome 2
golgi apparatus 2
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
lysosome 1

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:0007420 brain development IBA 21873635
GO:0046855 inositol phosphate dephosphorylation IBA 21873635
GO:0046856 phosphatidylinositol dephosphorylation IEA,IBA 21873635
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
1-Phosphatidyl-D-myo-inositol
  • (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
Phosphate
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
14066-19-4, 14265-44-2
genes like me logo Genes that share compounds with SYNJ2: view

Transcripts for SYNJ2 Gene

mRNA/cDNA for SYNJ2 Gene

2 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYNJ2

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 ·
SP1:
SP2:
SP3: - - - - - -
SP4: - - - - - - - - -
SP5: - - -
SP6: - - - - - -
SP7: - - -
SP8: - -
SP9:
SP10:
SP11: - -
SP12: -
SP13:
SP14:
SP15:
SP16:

ExUns: 17b · 17c ^ 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22a · 22b · 22c ^ 23 ^ 24a · 24b · 24c ^ 25 ^ 26a · 26b ^ 27 ^ 28 ^ 29 ^ 30
SP1: - - -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:

Relevant External Links for SYNJ2 Gene

GeneLoc Exon Structure for
SYNJ2

Expression for SYNJ2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for SYNJ2 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SYNJ2

SOURCE GeneReport for Unigene cluster for SYNJ2 Gene:

Hs.434494

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

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
chimpanzee
(Pan troglodytes)
Mammalia SYNJ2 31 30
  • 99.44 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SYNJ2 31 30
  • 85.73 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 85 (a)
OneToMany
-- 31
  • 62 (a)
OneToMany
cow
(Bos Taurus)
Mammalia SYNJ2 31 30
  • 84.44 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Synj2 30
  • 83.27 (n)
mouse
(Mus musculus)
Mammalia Synj2 17 31 30
  • 83.04 (n)
oppossum
(Monodelphis domestica)
Mammalia SYNJ2 31
  • 81 (a)
OneToOne
chicken
(Gallus gallus)
Aves SYNJ2 31 30
  • 71.76 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SYNJ2 31
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia synj2 30
  • 68.37 (n)
fruit fly
(Drosophila melanogaster)
Insecta synaptojanin 32
  • 47 (a)
synj 31
  • 43 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea unc-26 31
  • 39 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes INP53 31
  • 30 (a)
ManyToMany
INP52 31
  • 29 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 47 (a)
OneToMany
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

ENSEMBL:
Gene Tree for SYNJ2 (if available)
TreeFam:
Gene Tree for SYNJ2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SYNJ2: view image

Paralogs for SYNJ2 Gene

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

  • SYNJ2_HUMAN
  • B4DJU8_HUMAN
  • E7ER60_HUMAN
  • H0YEV8_HUMAN
  • H7BY56_HUMAN
  • Q5TA15_HUMAN
genes like me logo Genes that share paralogs with SYNJ2: view

Variants for SYNJ2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SYNJ2 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
725882 Likely Benign: not provided 158,069,653(+) A/G SYNONYMOUS_VARIANT
778349 Benign: not provided 158,062,174(+) G/A INTRON_VARIANT
788357 Benign: not provided 158,096,002(+) G/A MISSENSE_VARIANT
rs869312665 Uncertain Significance: not specified 158,078,271(+) T/C MISSENSE_VARIANT
rs2502601 - p.Glu1468Gly

Additional dbSNP identifiers (rs#s) for SYNJ2 Gene

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)
SYNJ2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYNJ2

SNP Genotyping and Copy Number Assay Products

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

Disorders for SYNJ2 Gene

MalaCards: The human disease database

(9) MalaCards diseases for SYNJ2 Gene - From: DISEASES

Additional Disease Information for SYNJ2

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

No data available for 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 23 54
  2. Regulation of synaptojanin 2 5'-phosphatase activity by Src. (PMID: 23076136) Chuang Y … Symons M (Cell adhesion & migration 2012) 2 3 54
  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 23 54
  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 23 54
  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 54

Products for SYNJ2 Gene

Sources for SYNJ2 Gene