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    Synj1 synaptojanin 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 85238, updated on 27-Nov-2024

    Summary

    Official Symbol
    Synj1provided by RGD
    Official Full Name
    synaptojanin 1provided by RGD
    Primary source
    RGD:69434
    See related
    EnsemblRapid:ENSRNOG00000002051 AllianceGenome:RGD:69434
    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 phosphatase activity and protein domain specific binding activity. Involved in several processes, including positive regulation of gliogenesis; positive regulation of receptor-mediated endocytosis; and response to retinoic acid. Located in microtubule and synaptic membrane. Part of clathrin coat of coated pit. Is active in parallel fiber to Purkinje cell synapse and presynapse. Human ortholog(s) of this gene implicated in Parkinson's disease; Parkinson's disease 20; and developmental and epileptic encephalopathy 53. Orthologous to human SYNJ1 (synaptojanin 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 382.5), Spleen (RPKM 139.7) and 9 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Synj1 in Genome Data Viewer
    Location:
    11q11
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (43678709..43755526, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (30192629..30269447, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (31105784..31181573, complement)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA2/SNORA34 family Neighboring gene cilia and flagella associated protein 298 Neighboring gene PAX3 and PAX7 binding protein 1 Neighboring gene exosomal polycystin 1 interacting protein

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables EH domain binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables SH3 domain binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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-1,4,5-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 phosphate 5-phosphatase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables phosphatidylinositol phosphate 5-phosphatase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables phosphatidylinositol phosphate phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables phosphatidylinositol-3-phosphate phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables phosphatidylinositol-3-phosphate 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 
    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 phosphatidylinositol-4-phosphate phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables phosphatidylinositol-4-phosphate phosphatase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in learning IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within learning ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in learning ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within neurotransmitter transport ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in phosphatidylinositol dephosphorylation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within phosphatidylinositol dephosphorylation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in phosphatidylinositol dephosphorylation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within phosphatidylinositol metabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of endosome organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of endosome organization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of gliogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of receptor-mediated endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of postsynaptic neurotransmitter receptor internalization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to cytokine IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to retinoic acid IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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
     
    acts_upstream_of_or_within synaptic vesicle endocytosis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in synaptic vesicle endocytosis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in synaptic vesicle endocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within synaptic vesicle priming ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within synaptic vesicle transport ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within synaptic vesicle uncoating ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in synaptic vesicle uncoating ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    is_active_in Schaffer collateral - CA1 synapse ISO
    Inferred from Sequence Orthology
    more info
     
    part_of clathrin coat of coated pit IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of membrane coat ISO
    Inferred from Sequence Orthology
    more info
     
    located_in microtubule IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in parallel fiber to Purkinje cell synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in perinuclear region of cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in perinuclear region of cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in postsynapse IEA
    Inferred from Electronic Annotation
    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 presynapse ISO
    Inferred from Sequence Orthology
    more info
     
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in synaptic membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in terminal bouton ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in vesicle membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    synaptojanin-1
    Names
    synaptic inositol 1,4,5-trisphosphate 5-phosphatase 1
    NP_001401979.1
    NP_445928.3
    XP_038944618.1
    XP_038944619.1
    XP_038944620.1
    XP_038944621.1
    XP_038944622.1
    XP_038944623.1
    XP_038944624.1
    XP_038944625.1
    XP_038944627.1
    XP_038944628.1
    XP_038944630.1
    XP_038944634.1
    XP_063126875.1
    XP_063126876.1
    XP_063126877.1
    XP_063126879.1
    XP_063126880.1
    XP_063126881.1
    XP_063126882.1
    XP_063126883.1
    XP_063126884.1
    XP_063126885.1
    XP_063126886.1
    XP_063126887.1
    XP_063126888.1
    XP_063126889.1
    XP_063126890.1
    XP_063126891.1
    XP_063126892.1
    XP_063126893.1
    XP_063126894.1
    XP_063126895.1
    XP_063126896.1
    XP_063126897.1
    XP_063126898.1

    NCBI Reference Sequences (RefSeq)

    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_001415050.1NP_001401979.1  synaptojanin-1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000011
      Related
      ENSRNOP00000045019.7, ENSRNOT00000052033.8
    2. NM_053476.4NP_445928.3  synaptojanin-1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000011

    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_086029.1 Reference GRCr8

      Range
      43678709..43755526 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063270813.1XP_063126883.1  synaptojanin-1 isoform X16

    2. XM_063270805.1XP_063126875.1  synaptojanin-1 isoform X4

    3. XM_063270811.1XP_063126881.1  synaptojanin-1 isoform X13

    4. XM_063270806.1XP_063126876.1  synaptojanin-1 isoform X6

    5. XM_063270807.1XP_063126877.1  synaptojanin-1 isoform X8

    6. XM_039088691.2XP_038944619.1  synaptojanin-1 isoform X2

      UniProtKB/Swiss-Prot
      O89092, Q62910, Q62911, Q810Z8
      UniProtKB/TrEMBL
      A0A8L2QTB1
      Conserved Domains (4) summary
      cd09098
      Location:573908
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      PHA03247
      Location:10941495
      PHA03247; large tegument protein UL36; Provisional
      COG5329
      Location:100520
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      cl17169
      Location:9071049
      RRM_SF; RNA recognition motif (RRM) superfamily
    7. XM_039088697.2XP_038944625.1  synaptojanin-1 isoform X15

      UniProtKB/TrEMBL
      A0A8I6AHP8
      Conserved Domains (4) summary
      cd09098
      Location:568903
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      COG5329
      Location:100523
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam03154
      Location:10231448
      Atrophin-1; Atrophin-1 family
      cl17169
      Location:9021044
      RRM_SF; RNA recognition motif (RRM) superfamily
    8. XM_063270809.1XP_063126879.1  synaptojanin-1 isoform X10

    9. XM_039088692.2XP_038944620.1  synaptojanin-1 isoform X3

      UniProtKB/Swiss-Prot
      O89092, Q62910, Q62911, Q810Z8
      Conserved Domains (4) summary
      cd09098
      Location:568903
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      PHA03247
      Location:10891490
      PHA03247; large tegument protein UL36; Provisional
      COG5329
      Location:100523
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      cl17169
      Location:9021044
      RRM_SF; RNA recognition motif (RRM) superfamily
    10. XM_039088696.2XP_038944624.1  synaptojanin-1 isoform X12

      UniProtKB/TrEMBL
      A0A8I6AHP8
      Related
      ENSRNOP00000092530.2, ENSRNOT00000113478.2
      Conserved Domains (4) summary
      cd09098
      Location:576911
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      COG5329
      Location:100523
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam03154
      Location:10311456
      Atrophin-1; Atrophin-1 family
      cl17169
      Location:9101052
      RRM_SF; RNA recognition motif (RRM) superfamily
    11. XM_039088695.2XP_038944623.1  synaptojanin-1 isoform X9

      UniProtKB/TrEMBL
      A0A8I6AFG5
      Related
      ENSRNOP00000086242.2, ENSRNOT00000114591.2
      Conserved Domains (4) summary
      cd09098
      Location:576911
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      COG5329
      Location:100523
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam03154
      Location:10311469
      Atrophin-1; Atrophin-1 family
      cl17169
      Location:9101052
      RRM_SF; RNA recognition motif (RRM) superfamily
    12. XM_039088693.2XP_038944621.1  synaptojanin-1 isoform X5

      UniProtKB/TrEMBL
      A0A8I6AFG5
      Conserved Domains (4) summary
      cd09098
      Location:576911
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      PHA03247
      Location:10731304
      PHA03247; large tegument protein UL36; Provisional
      COG5329
      Location:100523
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      cl17169
      Location:9101052
      RRM_SF; RNA recognition motif (RRM) superfamily
    13. XM_039088694.2XP_038944622.1  synaptojanin-1 isoform X7

      UniProtKB/TrEMBL
      A0A8I6AFG5
      Related
      ENSRNOP00000092411.2, ENSRNOT00000096546.2
      Conserved Domains (4) summary
      cd09098
      Location:576911
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      PHA03247
      Location:10971494
      PHA03247; large tegument protein UL36; Provisional
      COG5329
      Location:100523
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      cl17169
      Location:9101052
      RRM_SF; RNA recognition motif (RRM) superfamily
    14. XM_039088690.2XP_038944618.1  synaptojanin-1 isoform X1

      UniProtKB/Swiss-Prot
      O89092, Q62910, Q62911, Q810Z8
      Conserved Domains (4) summary
      cd09098
      Location:576911
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      PHA03247
      Location:10971498
      PHA03247; large tegument protein UL36; Provisional
      COG5329
      Location:100523
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      cl17169
      Location:9101052
      RRM_SF; RNA recognition motif (RRM) superfamily
    15. XM_063270816.1XP_063126886.1  synaptojanin-1 isoform X19

    16. XM_063270817.1XP_063126887.1  synaptojanin-1 isoform X20

    17. XM_063270814.1XP_063126884.1  synaptojanin-1 isoform X17

      UniProtKB/TrEMBL
      A0A8I6A4X9
    18. XM_063270815.1XP_063126885.1  synaptojanin-1 isoform X18

    19. XM_063270812.1XP_063126882.1  synaptojanin-1 isoform X14

    20. XM_063270810.1XP_063126880.1  synaptojanin-1 isoform X11

    21. XM_039088706.2XP_038944634.1  synaptojanin-1 isoform X33

      UniProtKB/TrEMBL
      A6JLD6
      Conserved Domains (3) summary
      cd09098
      Location:86421
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      PHA03247
      Location:6071008
      PHA03247; large tegument protein UL36; Provisional
      cl17169
      Location:420562
      RRM_SF; RNA recognition motif (RRM) superfamily
    22. XM_063270827.1XP_063126897.1  synaptojanin-1 isoform X31

    23. XM_063270821.1XP_063126891.1  synaptojanin-1 isoform X25

    24. XM_063270825.1XP_063126895.1  synaptojanin-1 isoform X29

    25. XM_063270822.1XP_063126892.1  synaptojanin-1 isoform X26

    26. XM_063270823.1XP_063126893.1  synaptojanin-1 isoform X27

    27. XM_063270819.1XP_063126889.1  synaptojanin-1 isoform X23

    28. XM_063270826.1XP_063126896.1  synaptojanin-1 isoform X30

    29. XM_039088699.2XP_038944627.1  synaptojanin-1 isoform X21

      UniProtKB/TrEMBL
      D4ABN3
      Conserved Domains (4) summary
      cd09098
      Location:576911
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      COG5329
      Location:100523
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      PRK07764
      Location:11101317
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cl17169
      Location:9101052
      RRM_SF; RNA recognition motif (RRM) superfamily
    30. XM_039088700.2XP_038944628.1  synaptojanin-1 isoform X21

      UniProtKB/TrEMBL
      D4ABN3
      Conserved Domains (4) summary
      cd09098
      Location:576911
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      COG5329
      Location:100523
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      PRK07764
      Location:11101317
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cl17169
      Location:9101052
      RRM_SF; RNA recognition motif (RRM) superfamily
    31. XM_039088702.2XP_038944630.1  synaptojanin-1 isoform X22

      UniProtKB/TrEMBL
      D4ABN3
      Conserved Domains (4) summary
      cd09098
      Location:576911
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      COG5329
      Location:100523
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      PRK07764
      Location:11101317
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cl17169
      Location:9101052
      RRM_SF; RNA recognition motif (RRM) superfamily
    32. XM_063270818.1XP_063126888.1  synaptojanin-1 isoform X21

    33. XM_063270828.1XP_063126898.1  synaptojanin-1 isoform X32

      Related
      ENSRNOP00000002812.9, ENSRNOT00000002812.10
    34. XM_063270824.1XP_063126894.1  synaptojanin-1 isoform X28

    35. XM_063270820.1XP_063126890.1  synaptojanin-1 isoform X24