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    Synj2 synaptojanin 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 84018, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Synj2provided by RGD
    Official Full Name
    synaptojanin 2provided by RGD
    Primary source
    RGD:69436
    See related
    EnsemblRapid:ENSRNOG00000017114 AllianceGenome:RGD:69436
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Enables inositol-polyphosphate 5-phosphatase activity; phosphatidylinositol monophosphate phosphatase activity; and protein domain specific binding activity. Involved in inositol phosphate catabolic process and phosphatidylinositol dephosphorylation. Located in axon terminus; cytoplasmic microtubule; and ruffle membrane. Is active in presynapse. Orthologous to human SYNJ2 (synaptojanin 2). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Heart (RPKM 117.1), Lung (RPKM 78.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Synj2 in Genome Data Viewer
    Location:
    1q11
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (48923742..49027153)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (46518594..46621919)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (46835922..46932544)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134484994 Neighboring gene sorting nexin 9 Neighboring gene mRNA turnover 4, ribosome maturation factor, pseudogene 2 Neighboring gene uncharacterized LOC134482645 Neighboring gene uncharacterized LOC134482650 Neighboring gene uncharacterized LOC120099116 Neighboring gene serine active site containing 1 Neighboring gene general transcription factor IIH subunit 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Localization of mRNAs for synaptojanin isoforms in the brain of developing and mature rats. Kudo M, et al. Brain Res Mol Brain Res, 1999 Feb 5. PMID 9931483
    2. Developmentally regulated alternative splicing in a novel synaptojanin. Khvotchev M, et al. J Biol Chem, 1998 Jan 23. PMID 9442075
    3. Synaptojanin 2, a novel synaptojanin isoform with a distinct targeting domain and expression pattern. Nemoto Y, et al. J Biol Chem, 1997 Dec 5. PMID 9388224
    4. Recruitment of an alternatively spliced form of synaptojanin 2 to mitochondria by the interaction with the PDZ domain of a mitochondrial outer membrane protein. Nemoto Y, et al. EMBO J, 1999 Jun 1. PMID 10357812, Free PMC Article
    5. Identification and characterization of a synaptojanin 2 splice isoform predominantly expressed in nerve terminals. Nemoto Y, et al. J Biol Chem, 2001 Nov 2. PMID 11498538

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 RGD

    Function Evidence Code Pubs
    NOT enables PDZ domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables PDZ domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables SH3 domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables inositol phosphate phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol monophosphate phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in inositol phosphate catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in phosphatidylinositol dephosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in phosphatidylinositol dephosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synaptic vesicle endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptic vesicle endocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synaptic vesicle endocytosis ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in axon terminus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasmic microtubule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane raft IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in perinuclear region of cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in presynapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in presynapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in ruffle membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    synaptojanin-2
    Names
    synaptic inositol 1,4,5-trisphosphate 5-phosphatase 2
    NP_001106842.1
    NP_001106843.1
    NP_114460.2
    XP_038948605.1
    XP_038948607.1
    XP_038948608.1
    XP_038948612.1
    XP_038948615.1
    XP_063131749.1
    XP_063131753.1
    XP_063131756.1
    XP_063131758.1
    XP_063131769.1
    XP_063131777.1
    XP_063131784.1
    XP_063131788.1
    XP_063131789.1
    XP_063131792.1
    XP_063131795.1
    XP_063131798.1
    XP_063131802.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001113371.1 → NP_001106842.1  synaptojanin-2 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AY034051, BI290811, CK653289, U90312
      UniProtKB/Swiss-Prot
      O55207, Q91ZD8, Q91ZD9
      UniProtKB/TrEMBL
      A6KNZ4
      Related
      ENSRNOP00000104494.1, ENSRNOT00000149366.1
      Conserved Domains (3) summary
      pfam02383
      Location:61 → 342
      Syja_N; SacI homology domain
      pfam08952
      Location:889 → 1025
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:547 → 878
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    2. NM_001113372.1 → NP_001106843.1  synaptojanin-2 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an internal coding exon, as compared to variant 1. The resulting isoform (2) lacks an internal segment, as compared to isoform 1.
      Source sequence(s)
      AY034050, BI290811, CK653289, U90312
      UniProtKB/TrEMBL
      A6KNZ5
      Conserved Domains (3) summary
      pfam02383
      Location:61 → 342
      Syja_N; SacI homology domain
      pfam08952
      Location:889 → 1025
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:547 → 878
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    3. NM_032071.3 → NP_114460.2  synaptojanin-2 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an internal coding exon and has an additional exon in the 3' region, as compared to variant 1. The resulting isoform (3) lacks an internal segment and has a shorter and distinct C-terminus, as compared to isoform 1.
      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      A6KNZ5, A6KNZ7, F1M2D6
      Related
      ENSRNOP00000063385.4, ENSRNOT00000068476.6
      Conserved Domains (3) summary
      COG5329
      Location:28 → 485
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam08952
      Location:889 → 1025
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:547 → 878
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      48923742..49027153
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063275683.1 → XP_063131753.1  synaptojanin-2 isoform X3

      UniProtKB/TrEMBL
      A6KNZ4

    2. XM_039092679.2 → XP_038948607.1  synaptojanin-2 isoform X6

      UniProtKB/TrEMBL
      A6KNZ5
      Conserved Domains (3) summary
      COG5329
      Location:28 → 485
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam08952
      Location:889 → 1025
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:547 → 878
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    3. XM_063275688.1 → XP_063131758.1  synaptojanin-2 isoform X5

      UniProtKB/TrEMBL
      A6KNZ4

    4. XM_063275686.1 → XP_063131756.1  synaptojanin-2 isoform X4

      UniProtKB/TrEMBL
      A6KNZ8, F1M0S5
      Related
      ENSRNOP00000059744.4, ENSRNOT00000066798.6

    5. XM_039092680.2 → XP_038948608.1  synaptojanin-2 isoform X7

      UniProtKB/TrEMBL
      A6KNZ5
      Conserved Domains (3) summary
      COG5329
      Location:28 → 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

    6. XM_063275679.1 → XP_063131749.1  synaptojanin-2 isoform X1

      UniProtKB/TrEMBL
      A6KNZ4, A6KNZ6
      Related
      ENSRNOP00000112432.1, ENSRNOT00000129353.1

    7. XM_039092677.2 → XP_038948605.1  synaptojanin-2 isoform X2

      UniProtKB/TrEMBL
      A6KNZ5
      Conserved Domains (4) summary
      COG5329
      Location:28 → 485
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam08952
      Location:872 → 1008
      DUF1866; Domain of unknown function (DUF1866)
      pfam16014
      Location:1243 → 1288
      SAP130_C; Histone deacetylase complex subunit SAP130 C-terminus
      cl00490
      Location:530 → 861
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    8. XM_063275732.1 → XP_063131802.1  synaptojanin-2 isoform X18

      UniProtKB/TrEMBL
      A6KNZ4

    9. XM_039092684.2 → XP_038948612.1  synaptojanin-2 isoform X8

      UniProtKB/TrEMBL
      A6KNZ5
      Conserved Domains (3) summary
      COG5329
      Location:28 → 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

    10. XM_063275725.1 → XP_063131795.1  synaptojanin-2 isoform X16

      UniProtKB/TrEMBL
      A6KNZ8

    11. XM_063275722.1 → XP_063131792.1  synaptojanin-2 isoform X15

      UniProtKB/TrEMBL
      A6KNZ8

    12. XM_063275719.1 → XP_063131789.1  synaptojanin-2 isoform X14

      UniProtKB/TrEMBL
      A6KNZ8

    13. XM_063275699.1 → XP_063131769.1  synaptojanin-2 isoform X9

      UniProtKB/TrEMBL
      A6KNZ9

    14. XM_039092687.2 → XP_038948615.1  synaptojanin-2 isoform X11

      UniProtKB/TrEMBL
      A6KNZ9
      Conserved Domains (4) summary
      COG5329
      Location:13 → 169
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam08952
      Location:573 → 709
      DUF1866; Domain of unknown function (DUF1866)
      pfam16014
      Location:944 → 989
      SAP130_C; Histone deacetylase complex subunit SAP130 C-terminus
      cl00490
      Location:231 → 562
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    15. XM_063275707.1 → XP_063131777.1  synaptojanin-2 isoform X10

      UniProtKB/TrEMBL
      A6KNZ9

    16. XM_063275718.1 → XP_063131788.1  synaptojanin-2 isoform X13

      UniProtKB/TrEMBL
      A6KNZ9, F1LPP1
      Related
      ENSRNOP00000062564.4, ENSRNOT00000067661.5

    17. XM_063275728.1 → XP_063131798.1  synaptojanin-2 isoform X17

      UniProtKB/TrEMBL
      A6KNZ8

    18. XM_063275714.1 → XP_063131784.1  synaptojanin-2 isoform X12

      UniProtKB/TrEMBL
      A6KNZ9
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O55207.2 GenPept UniProtKB/Swiss-Prot:O55207

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