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    SYNJ1 synaptojanin 1 [ Homo sapiens (human) ]

    Gene ID: 8867, updated on 3-Apr-2024

    Summary

    Official Symbol
    SYNJ1provided by HGNC
    Official Full Name
    synaptojanin 1provided by HGNC
    Primary source
    HGNC:HGNC:11503
    See related
    Ensembl:ENSG00000159082 MIM:604297; AllianceGenome:HGNC:11503
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DEE53; EIEE53; INPP5G; PARK20
    Summary
    This gene encodes a phosphoinositide phosphatase that regulates levels of membrane phosphatidylinositol-4,5-bisphosphate. As such, expression of this enzyme may affect synaptic transmission and membrane trafficking. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
    Expression
    Broad expression in brain (RPKM 21.4), bone marrow (RPKM 6.6) and 22 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SYNJ1 in Genome Data Viewer
    Location:
    21q22.11
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (32628759..32728394, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (30994760..31094413, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (34001069..34100351, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene CFAP298-TCP10L readthrough Neighboring gene Sharpr-MPRA regulatory region 410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18365 Neighboring gene cilia and flagella associated protein 298 Neighboring gene olfactory receptor family 7 subfamily E member 23 pseudogene Neighboring gene uncharacterized LOC124905011 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:34033532-34033721 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:34099530-34100030 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:34100031-34100531 Neighboring gene PAXBP1 antisense RNA 1 Neighboring gene uncharacterized LOC124905010 Neighboring gene PAX3 and PAX7 binding protein 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:34143733-34144722 Neighboring gene EPCIP antisense RNA 1 Neighboring gene exosomal polycystin 1 interacting protein

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables SH3 domain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables inositol-1,4,5-trisphosphate 5-phosphatase activity TAS
    Traceable Author Statement
    more info
     
    enables phosphatidylinositol phosphate 4-phosphatase activity TAS
    Traceable Author Statement
    more info
     
    enables phosphatidylinositol phosphate 5-phosphatase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity TAS
    Traceable Author Statement
    more info
     
    enables phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity TAS
    Traceable Author Statement
    more info
     
    enables phosphatidylinositol-3-phosphate phosphatase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables phosphatidylinositol-3-phosphate phosphatase activity TAS
    Traceable Author Statement
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity TAS
    Traceable Author Statement
    more info
     
    enables phosphatidylinositol-4-phosphate phosphatase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in inositol phosphate metabolic process TAS
    Traceable Author Statement
    more info
     
    involved_in learning IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in membrane organization TAS
    Traceable Author Statement
    more info
     
    involved_in neurotransmitter transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in phosphatidylinositol biosynthetic process TAS
    Traceable Author Statement
    more info
     
    involved_in phosphatidylinositol dephosphorylation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in phosphatidylinositol dephosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in phosphatidylinositol dephosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in phosphatidylinositol dephosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in phosphatidylinositol metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in phosphatidylinositol-3-phosphate biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of endosome organization 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 IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in synaptic vesicle endocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in synaptic vesicle priming ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in synaptic vesicle transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in synaptic vesicle uncoating ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    part_of clathrin coat of coated pit ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    part_of membrane coat ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    colocalizes_with microtubule ISS
    Inferred from Sequence or Structural Similarity
    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
     
    is_active_in presynapse IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in presynapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in synaptic membrane ISS
    Inferred from Sequence or Structural Similarity
    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
    inositol 5'-phosphatase (synaptojanin 1)
    inositol polyphosphate-5-phosphatase G
    phosphoinositide 5-phosphatase
    synaptic inositol 1,4,5-trisphosphate 5-phosphatase 1
    synaptojanin-1, polyphosphoinositide phosphatase
    NP_001153774.1
    NP_001153778.1
    NP_003886.3
    NP_982271.3
    XP_016883984.1
    XP_016883986.1
    XP_016883988.1
    XP_047296990.1
    XP_047296991.1
    XP_047296992.1
    XP_047296993.1
    XP_047296994.1
    XP_047296995.1
    XP_047296996.1
    XP_047296997.1
    XP_047296998.1
    XP_047296999.1
    XP_047297000.1
    XP_047297001.1
    XP_047297002.1
    XP_047297003.1
    XP_047297004.1
    XP_047297005.1
    XP_047297006.1
    XP_054180906.1
    XP_054180907.1
    XP_054180908.1
    XP_054180909.1
    XP_054180910.1
    XP_054180911.1
    XP_054180912.1
    XP_054180913.1
    XP_054180914.1
    XP_054180915.1
    XP_054180916.1
    XP_054180917.1
    XP_054180918.1
    XP_054180919.1
    XP_054180920.1
    XP_054180921.1
    XP_054180922.1
    XP_054180923.1
    XP_054180924.1
    XP_054180925.1

    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.

    Genomic

    1. NG_030017.2 RefSeqGene

      Range
      5027..104277
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001160302.2NP_001153774.1  synaptojanin-1 isoform c

      See identical proteins and their annotated locations for NP_001153774.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in its 5' UTR, 5' coding region and 3' coding region, and uses a downstream translational start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, a distinct C-terminus, and is shorter than isoform a.
      Source sequence(s)
      AP000275, AP000276, AP000277, AP000278, AP000279
      Consensus CDS
      CCDS54483.1
      UniProtKB/TrEMBL
      J3KPK1
      Related
      ENSP00000349903.3, ENST00000357345.7
      Conserved Domains (5) summary
      cd09098
      Location:533868
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      PRK05641
      Location:10171097
      PRK05641; putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
      pfam02383
      Location:60340
      Syja_N; SacI homology domain
      pfam08952
      Location:8671008
      DUF1866; Domain of unknown function (DUF1866)
      pfam11235
      Location:10781262
      Med25_SD1; Mediator complex subunit 25 synapsin 1
    2. NM_001160306.2NP_001153778.1  synaptojanin-1 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, uses a downstream translational start codon, and has multiple differences in the coding region, compared to variant 1. The encoded isoform (d) has a shorter N-terminus, a distinct C-terminus, and is shorter than isoform a.
      Source sequence(s)
      AB020717, BC098395, BC136603, BP350252, CA944966
      Consensus CDS
      CCDS54484.1
      UniProtKB/Swiss-Prot
      O43425, O43426, O94984, Q4KMR1
      UniProtKB/TrEMBL
      A0A0D9SGJ6
      Related
      ENSP00000487560.1, ENST00000630077.3
      Conserved Domains (4) summary
      cd09098
      Location:528863
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      pfam02383
      Location:60340
      Syja_N; SacI homology domain
      pfam08952
      Location:8621003
      DUF1866; Domain of unknown function (DUF1866)
      pfam11235
      Location:10541231
      Med25_SD1; Mediator complex subunit 25 synapsin 1
    3. NM_003895.4NP_003886.3  synaptojanin-1 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AP000275, AP000276, AP000277, AP000278, AP000279
      Consensus CDS
      CCDS33539.2
      UniProtKB/Swiss-Prot
      O43425, O43426, O94984, Q4KMR1
      UniProtKB/TrEMBL
      J3KQV8
      Related
      ENSP00000409667.2, ENST00000433931.7
      Conserved Domains (3) summary
      cd09098
      Location:572907
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      pfam02383
      Location:99379
      Syja_N; SacI homology domain
      pfam08952
      Location:9061047
      DUF1866; Domain of unknown function (DUF1866)
    4. NM_203446.3NP_982271.3  synaptojanin-1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) includes an alternate exon in the 3' coding region that causes a frameshift, compared to variant 1. The encoded isoform (b) has a distinct and shorter C-terminus, compared to isoform a.
      Source sequence(s)
      AB020717, AF009039, AF009040, AP000275, AP000279, BC019630
      Consensus CDS
      CCDS33540.3
      UniProtKB/TrEMBL
      J3KPK1
      Related
      ENSP00000501530.1, ENST00000674351.1
      Conserved Domains (4) summary
      cd09098
      Location:533868
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      PHA03247
      Location:10541278
      PHA03247; large tegument protein UL36; Provisional
      COG5329
      Location:34480
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam08952
      Location:8671008
      DUF1866; Domain of unknown function (DUF1866)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      32628759..32728394 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441038.1XP_047296994.1  synaptojanin-1 isoform X8

    2. XM_017028497.3XP_016883986.1  synaptojanin-1 isoform X3

      UniProtKB/Swiss-Prot
      O43425, O43426, O94984, Q4KMR1
      Conserved Domains (4) summary
      cd09098
      Location:572907
      INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
      PHA03247
      Location:10981491
      PHA03247; large tegument protein UL36; Provisional
      COG5329
      Location:73519
      COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
      pfam08952
      Location:9061047
      DUF1866; Domain of unknown function (DUF1866)
    3. XM_017028499.3XP_016883988.1  synaptojanin-1 isoform X7

      UniProtKB/Swiss-Prot
      O43425, O43426, O94984, Q4KMR1
    4. XM_047441036.1XP_047296992.1  synaptojanin-1 isoform X5

    5. XM_017028495.3XP_016883984.1  synaptojanin-1 isoform X1

      UniProtKB/Swiss-Prot
      O43425, O43426, O94984, Q4KMR1
    6. XM_047441037.1XP_047296993.1  synaptojanin-1 isoform X6

    7. XM_047441035.1XP_047296991.1  synaptojanin-1 isoform X4

    8. XM_047441034.1XP_047296990.1  synaptojanin-1 isoform X2

    9. XM_047441039.1XP_047296995.1  synaptojanin-1 isoform X9

    10. XM_047441040.1XP_047296996.1  synaptojanin-1 isoform X10

    11. XM_047441041.1XP_047296997.1  synaptojanin-1 isoform X11

    12. XM_047441047.1XP_047297003.1  synaptojanin-1 isoform X17

      Related
      ENSP00000371931.4, ENST00000382491.7
    13. XM_047441046.1XP_047297002.1  synaptojanin-1 isoform X16

    14. XM_047441050.1XP_047297006.1  synaptojanin-1 isoform X20

    15. XM_047441045.1XP_047297001.1  synaptojanin-1 isoform X15

    16. XM_047441043.1XP_047296999.1  synaptojanin-1 isoform X13

      UniProtKB/TrEMBL
      C9JFZ1
      Related
      ENSP00000371939.2, ENST00000382499.7
    17. XM_047441048.1XP_047297004.1  synaptojanin-1 isoform X18

    18. XM_047441044.1XP_047297000.1  synaptojanin-1 isoform X14

    19. XM_047441042.1XP_047296998.1  synaptojanin-1 isoform X12

    20. XM_047441049.1XP_047297005.1  synaptojanin-1 isoform X19

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      30994760..31094413 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324938.1XP_054180913.1  synaptojanin-1 isoform X8

    2. XM_054324933.1XP_054180908.1  synaptojanin-1 isoform X3

    3. XM_054324937.1XP_054180912.1  synaptojanin-1 isoform X7

    4. XM_054324935.1XP_054180910.1  synaptojanin-1 isoform X5

    5. XM_054324931.1XP_054180906.1  synaptojanin-1 isoform X1

    6. XM_054324936.1XP_054180911.1  synaptojanin-1 isoform X6

    7. XM_054324934.1XP_054180909.1  synaptojanin-1 isoform X4

    8. XM_054324932.1XP_054180907.1  synaptojanin-1 isoform X2

    9. XM_054324939.1XP_054180914.1  synaptojanin-1 isoform X9

    10. XM_054324940.1XP_054180915.1  synaptojanin-1 isoform X10

    11. XM_054324941.1XP_054180916.1  synaptojanin-1 isoform X11

    12. XM_054324947.1XP_054180922.1  synaptojanin-1 isoform X17

    13. XM_054324946.1XP_054180921.1  synaptojanin-1 isoform X16

    14. XM_054324950.1XP_054180925.1  synaptojanin-1 isoform X20

    15. XM_054324945.1XP_054180920.1  synaptojanin-1 isoform X15

    16. XM_054324943.1XP_054180918.1  synaptojanin-1 isoform X13

      UniProtKB/TrEMBL
      C9JFZ1
    17. XM_054324948.1XP_054180923.1  synaptojanin-1 isoform X18

    18. XM_054324944.1XP_054180919.1  synaptojanin-1 isoform X14

    19. XM_054324942.1XP_054180917.1  synaptojanin-1 isoform X12

    20. XM_054324949.1XP_054180924.1  synaptojanin-1 isoform X19