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    Synj2 synaptojanin 2 [ Mus musculus (house mouse) ]

    Gene ID: 20975, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Synj2provided by MGI
    Official Full Name
    synaptojanin 2provided by MGI
    Primary source
    MGI:MGI:1201671
    See related
    Ensembl:ENSMUSG00000023805 AllianceGenome:MGI:1201671
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    SJ2; mKIAA0348
    Summary
    Enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity. Predicted to be involved in inositol phosphate catabolic process; phosphatidylinositol dephosphorylation; and synaptic vesicle endocytosis. Predicted to be located in axon terminus; cytoplasmic microtubule; and ruffle membrane. Predicted to be active in membrane; perinuclear region of cytoplasm; and presynapse. Is expressed in several structures, including alimentary system; genitourinary system; nose; spleen; and submandibular gland primordium. Orthologous to human SYNJ2 (synaptojanin 2). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in testis adult (RPKM 5.1), cortex adult (RPKM 4.6) and 27 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Synj2 in Genome Data Viewer
    Location:
    17 A1; 17 3.59 cM
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (5991555..6106041)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (5941280..6055766)

    Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene sorting nexin 9 Neighboring gene STARR-positive B cell enhancer mm9_chr17:5934164-5934465 Neighboring gene STARR-positive B cell enhancer mm9_chr17:5934996-5935297 Neighboring gene STARR-seq mESC enhancer starr_41704 Neighboring gene predicted gene, 46599 Neighboring gene STARR-seq mESC enhancer starr_41705 Neighboring gene mRNA turnover 4 pseudogene Neighboring gene STARR-seq mESC enhancer starr_41707 Neighboring gene predicted gene, 52312 Neighboring gene predicted gene, 35525 Neighboring gene STARR-seq mESC enhancer starr_41712 Neighboring gene predicted gene, 46591 Neighboring gene serine active site containing 1 Neighboring gene STARR-positive B cell enhancer ABC_E9051 Neighboring gene STARR-positive B cell enhancer ABC_E8652 Neighboring gene general transcription factor IIH, polypeptide 5 Neighboring gene TUB like protein 4 Neighboring gene fibrillarin, pseudogene 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Synaptojanin2 Mutation Causes Progressive High-frequency Hearing Loss in Mice. Martelletti E, et al. Front Cell Neurosci, 2020. PMID 33100973, Free PMC Article
    2. Analysis of an intronic promoter within Synj2. Planchart A. Biochem Biophys Res Commun, 2013 Nov 1. PMID 24103750, Free PMC Article
    3. Molecular cloning of multiple isoforms of synaptojanin 2 and assignment of the gene to mouse chromosome 17A2-3.1. Seet LF, et al. Biochem Biophys Res Commun, 1998 Jun 9. PMID 9636665
    4. The Synaptojanins in the murine small and large intestine. Vázquez-Carretero MD, et al. J Bioenerg Biomembr, 2016 Dec. PMID 27878645
    5. A mutation in synaptojanin 2 causes progressive hearing loss in the ENU-mutagenised mouse strain Mozart. Manji SS, et al. PLoS One, 2011 Mar 15. PMID 21423608, Free PMC Article

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. report showing expression, location and isoforms of Synj1 and Synj2 in the small and large intestine and that they might participate in intestinal pathology.
      Title: The Synaptojanins in the murine small and large intestine.
    2. Clustering all known mouse Synj2 transcripts led to uncover a novel subset of transcripts that appears to derive from a region located within intron 7.
      Title: Analysis of an intronic promoter within Synj2.
    3. These results reveal Synj2 as a critical regulator of hair cell survival that is essential for hair cell maintenance and hearing function.
      Title: A mutation in synaptojanin 2 causes progressive hearing loss in the ENU-mutagenised mouse strain Mozart.
    4. role in proximal t-haplotype mediated mouse sterility
      Title: Mutations in Serac1 or Synj2 cause proximal t haplotype-mediated male mouse sterility but not transmission ratio distortion.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Chemically induced (ENU) (1)  1 citation
    • Endonuclease-mediated (4) 
    • Gene trapped (1) 
    • Targeted (2)  1 citation

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables PDZ domain binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables SH3 domain binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables inositol-1,4,5-trisphosphate 5-phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables inositol-1,4,5-trisphosphate 5-phosphatase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylinositol monophosphate phosphatase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in inositol phosphate catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in phosphatidylinositol dephosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylinositol dephosphorylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in synaptic vesicle endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptic vesicle endocytosis ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in axon terminus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasmic microtubule ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane raft IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in perinuclear region of cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in presynapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in presynapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in ruffle membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    synaptojanin-2
    Names
    synaptic inositol-1,4,5-trisphosphate 5-phosphatase 2
    NP_001106822.1
    NP_001106823.1
    NP_001106824.1
    NP_001277627.1
    NP_001344594.1
    NP_001344596.1
    NP_035653.2
    XP_006523265.1
    XP_006523266.1
    XP_006523267.1
    XP_006523268.1
    XP_006523269.1
    XP_006523271.1
    XP_017172861.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001113351.1 → NP_001106822.1  synaptojanin-2 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has multiple differences in the coding region but maintains the reading frame compared to variant 1. This variant encodes isoform d which is shorter than isoform a.
      Source sequence(s)
      AF041862, AK163512, BC060214
      UniProtKB/Swiss-Prot
      Q9D2G5
      Related
      ENSMUST00000115788.8
      Conserved Domains (3) summary
      pfam02383
      Location:3 → 257
      Syja_N; SacI homology domain
      pfam08952
      Location:787 → 923
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:445 → 776
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    2. NM_001113352.2 → NP_001106823.1  synaptojanin-2 isoform b

      See identical proteins and their annotated locations for NP_001106823.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1 that results in a shorter protein (isoform b).
      Source sequence(s)
      AF041857, AK142919, BC060214
      Consensus CDS
      CCDS49932.1
      UniProtKB/Swiss-Prot
      O35404, O88399, O88400, O88401, O88402, O88403, O88404, Q9D2G5
      Related
      ENSMUSP00000079164.7, ENSMUST00000080283.13
      Conserved Domains (4) summary
      pfam02383
      Location:61 → 342
      Syja_N; SacI homology domain
      pfam08952
      Location:872 → 1008
      DUF1866; Domain of unknown function (DUF1866)
      pfam15677
      Location:1245 → 1360
      CEND1; Cell cycle exit and neuronal differentiation protein 1
      cl00490
      Location:530 → 861
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    3. NM_001113353.2 → NP_001106824.1  synaptojanin-2 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AF041857, AF041859, AK142919, AK148053, BC058749
      Consensus CDS
      CCDS49931.1
      UniProtKB/TrEMBL
      F8WHD8
      Related
      ENSMUSP00000111457.3, ENSMUST00000115791.10
      Conserved Domains (4) summary
      pfam02383
      Location:61 → 342
      Syja_N; SacI homology domain
      pfam08952
      Location:872 → 1008
      DUF1866; Domain of unknown function (DUF1866)
      pfam15677
      Location:1290 → 1405
      CEND1; Cell cycle exit and neuronal differentiation protein 1
      cl00490
      Location:530 → 861
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    4. NM_001290698.1 → NP_001277627.1  synaptojanin-2 isoform e

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) has multiple differences compared to variant 1 and initiates translation at an alternate start codon. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AK019694, AK142919, AK161467
      Consensus CDS
      CCDS70757.1
      UniProtKB/TrEMBL
      E9Q4P5, Q3TTB3
      Related
      ENSMUSP00000111451.2, ENSMUST00000115785.8
      Conserved Domains (3) summary
      pfam08952
      Location:556 → 692
      DUF1866; Domain of unknown function (DUF1866)
      pfam15677
      Location:929 → 1044
      CEND1; Cell cycle exit and neuronal differentiation protein 1
      cl00490
      Location:214 → 545
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    5. NM_001357665.1 → NP_001344594.1  synaptojanin-2 isoform f

      Status: VALIDATED

      Source sequence(s)
      AC154650, BU701096
      UniProtKB/TrEMBL
      F7BI35
      Conserved Domains (3) summary
      pfam08952
      Location:497 → 633
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:155 → 486
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
      cl27434
      Location:2 → 110
      Syja_N; SacI homology domain

    6. NM_001357667.1 → NP_001344596.1  synaptojanin-2 isoform g

      Status: VALIDATED

      Source sequence(s)
      AC154650, AK142919, BC060214, BU610521, BU701096, CJ113008
      UniProtKB/TrEMBL
      Q3TTB3
      Conserved Domains (3) summary
      pfam08952
      Location:787 → 923
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:445 → 776
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
      cl27434
      Location:2 → 400
      Syja_N; SacI homology domain

    7. NM_011523.2 → NP_035653.2  synaptojanin-2 isoform c

      See identical proteins and their annotated locations for NP_035653.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has multiple differences in the coding region but maintains the reading frame compared to variant 1. This variant encodes isoform c which is shorter than isoform a.
      Source sequence(s)
      AF041859, AF041862, AK163512, BC058749
      Consensus CDS
      CCDS28365.1
      UniProtKB/Swiss-Prot
      Q9D2G5
      Related
      ENSMUSP00000060382.8, ENSMUST00000061091.14
      Conserved Domains (3) summary
      pfam02383
      Location:3 → 257
      Syja_N; SacI homology domain
      pfam08952
      Location:787 → 923
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:445 → 776
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    RNA

    1. NR_151772.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC154650, AF041857, AK142919, BU610521, BU701096
      Related
      ENSMUST00000134767.8

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000083.7 Reference GRCm39 C57BL/6J

      Range
      5991555..6106041
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006523203.2 → XP_006523266.1  synaptojanin-2 isoform X2

      Conserved Domains (3) summary
      COG5329
      Location:30 → 485
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam08952
      Location:872 → 1008
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:530 → 861
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    2. XM_006523204.2 → XP_006523267.1  synaptojanin-2 isoform X3

      Conserved Domains (3) summary
      COG5329
      Location:30 → 485
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam08952
      Location:872 → 1008
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:530 → 861
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    3. XM_006523205.4 → XP_006523268.1  synaptojanin-2 isoform X4

      UniProtKB/Swiss-Prot
      Q9D2G5
      Conserved Domains (3) summary
      COG5329
      Location:30 → 485
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam08952
      Location:872 → 1008
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:530 → 861
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    4. XM_006523208.3 → XP_006523271.1  synaptojanin-2 isoform X6

      Conserved Domains (3) summary
      COG5329
      Location:30 → 485
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam08952
      Location:872 → 1008
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:530 → 861
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    5. XM_006523206.3 → XP_006523269.1  synaptojanin-2 isoform X5

      UniProtKB/TrEMBL
      Q3TTB3
      Conserved Domains (4) summary
      COG5329
      Location:7 → 245
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam08952
      Location:632 → 768
      DUF1866; Domain of unknown function (DUF1866)
      pfam15677
      Location:1050 → 1165
      CEND1; Cell cycle exit and neuronal differentiation protein 1
      cl00490
      Location:290 → 621
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    6. XM_006523202.5 → XP_006523265.1  synaptojanin-2 isoform X1

      UniProtKB/TrEMBL
      D3YZB2, Q3TTB3
      Related
      ENSMUSP00000111456.2, ENSMUST00000115790.8
      Conserved Domains (4) summary
      COG5329
      Location:2 → 400
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam08952
      Location:787 → 923
      DUF1866; Domain of unknown function (DUF1866)
      pfam15677
      Location:1205 → 1320
      CEND1; Cell cycle exit and neuronal differentiation protein 1
      cl00490
      Location:445 → 776
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    7. XM_017317372.2 → XP_017172861.1  synaptojanin-2 isoform X7

      UniProtKB/TrEMBL
      Q3TTB3
      Conserved Domains (4) summary
      COG5329
      Location:2 → 110
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam08952
      Location:497 → 633
      DUF1866; Domain of unknown function (DUF1866)
      pfam15677
      Location:915 → 1030
      CEND1; Cell cycle exit and neuronal differentiation protein 1
      cl00490
      Location:155 → 486
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    RNA

    1. XR_385128.2 RNA Sequence

    2. XR_004939486.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9D2G5.2 GenPept UniProtKB/Swiss-Prot:Q9D2G5

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