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SYNJ1 synaptojanin 1 [ Homo sapiens (human) ]

Gene ID: 8867, updated on 8-Jul-2021

Summary

Official Symbol
SYNJ1provided by HGNC
Official Full Name
synaptojanin 1provided by HGNC
Primary source
HGNC:HGNC:11503
See related
Ensembl:ENSG00000159082 MIM:604297
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
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Genomic context

See SYNJ1 in Genome Data Viewer
Location:
21q22.11
Exon count:
34
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 21 NC_000021.9 (32628759..32731247, complement)
105.20201022 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 cilia and flagella associated protein 298 Neighboring gene olfactory receptor family 7 subfamily E member 23 pseudogene Neighboring gene PAXBP1 antisense RNA 1 Neighboring gene PAX3 and PAX7 binding protein 1 Neighboring gene C21orf62 antisense RNA 1 Neighboring gene chromosome 21 open reading frame 62

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables EH domain binding IEA
Inferred from Electronic Annotation
more info
 
enables RNA binding IEA
Inferred from Electronic Annotation
more info
 
enables SH3 domain binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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-phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables phosphatidylinositol-3-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
PubMed 
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 C-terminus binding IEA
Inferred from Electronic Annotation
more info
 
enables protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in brain development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in inositol phosphate dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in inositol phosphate dephosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
 
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
PubMed 
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 positive regulation of gliogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of receptor-mediated endocytosis IEA
Inferred from Electronic Annotation
more info
 
involved_in response to cytokine IEA
Inferred from Electronic Annotation
more info
 
involved_in response to retinoic acid IEA
Inferred from Electronic Annotation
more info
 
involved_in synaptic vesicle endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
located_in parallel fiber to Purkinje cell synapse IEA
Inferred from Electronic Annotation
more info
 
is_active_in perinuclear region of cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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_016883983.1
XP_016883984.1
XP_016883985.1
XP_016883986.1
XP_016883987.1
XP_016883988.1
XP_016883989.1
XP_016883990.1
XP_016883991.1
XP_016883992.1
XP_016883993.1
XP_016883994.1

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_030017.1 RefSeqGene

    Range
    5001..104283
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001160302.1NP_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)
    AB020717, AP000275, BP350252, CA944966
    Consensus CDS
    CCDS54483.1
    UniProtKB/Swiss-Prot
    O43426
    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
    O43426
    UniProtKB/TrEMBL
    A0A0D9SGJ6, B9EGN3
    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_003895.3NP_003886.3  synaptojanin-1 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AB020717, AF009040, AP000279, BC019630, CA944966, DB071394
    Consensus CDS
    CCDS33539.2
    UniProtKB/Swiss-Prot
    O43426
    UniProtKB/TrEMBL
    J3KQV8, Q05CZ1
    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
    CCDS33540.2
    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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p13 Primary Assembly

    Range
    32628759..32731247 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028497.2XP_016883986.1  synaptojanin-1 isoform X4

  2. XM_017028499.2XP_016883988.1  synaptojanin-1 isoform X6

  3. XM_017028505.2XP_016883994.1  synaptojanin-1 isoform X12

    Related
    ENSP00000371931.4, ENST00000382491.7
  4. XM_017028495.2XP_016883984.1  synaptojanin-1 isoform X2

  5. XM_017028498.1XP_016883987.1  synaptojanin-1 isoform X5

  6. XM_017028504.1XP_016883993.1  synaptojanin-1 isoform X11

  7. XM_017028496.1XP_016883985.1  synaptojanin-1 isoform X3

  8. XM_017028503.1XP_016883992.1  synaptojanin-1 isoform X10

  9. XM_017028494.1XP_016883983.1  synaptojanin-1 isoform X1

  10. XM_017028502.1XP_016883991.1  synaptojanin-1 isoform X9

  11. XM_017028501.1XP_016883990.1  synaptojanin-1 isoform X8

  12. XM_017028500.1XP_016883989.1  synaptojanin-1 isoform X7

    UniProtKB/Swiss-Prot
    O43426
    Related
    ENSP00000501504.1, ENST00000674204.1
    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)
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