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SYNJ1 synaptojanin 1 [ Homo sapiens (human) ]

Gene ID: 8867, updated on 9-Dec-2018

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
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

Genomic context

See SYNJ1 in Genome Data Viewer
Location:
21q22.11
Exon count:
34
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 21 NC_000021.9 (32628759..32731247, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (33997269..34100351, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene C21orf59-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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding IEA
Inferred from Electronic Annotation
more info
 
SH3 domain binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity TAS
Traceable Author Statement
more info
 
inositol-1,4,5-trisphosphate 5-phosphatase activity TAS
Traceable Author Statement
more info
 
phosphatidylinositol phosphate 4-phosphatase activity TAS
Traceable Author Statement
more info
 
phosphatidylinositol phosphate 5-phosphatase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity TAS
Traceable Author Statement
more info
 
phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity TAS
Traceable Author Statement
more info
 
phosphatidylinositol-3-phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol-3-phosphatase activity TAS
Traceable Author Statement
more info
 
phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity TAS
Traceable Author Statement
more info
 
phosphatidylinositol-4-phosphate phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
brain development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
inositol phosphate dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
inositol phosphate dephosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
 
inositol phosphate metabolic process TAS
Traceable Author Statement
more info
 
learning IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
learning IMP
Inferred from Mutant Phenotype
more info
PubMed 
membrane organization TAS
Traceable Author Statement
more info
 
neurotransmitter transport ISS
Inferred from Sequence or Structural Similarity
more info
 
phosphatidylinositol biosynthetic process TAS
Traceable Author Statement
more info
 
phosphatidylinositol dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylinositol dephosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol dephosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
phosphatidylinositol dephosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
 
phosphatidylinositol metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
phosphatidylinositol-3-phosphate biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of endosome organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
synaptic vesicle endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synaptic vesicle endocytosis IGI
Inferred from Genetic Interaction
more info
PubMed 
synaptic vesicle endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
synaptic vesicle priming ISS
Inferred from Sequence or Structural Similarity
more info
 
synaptic vesicle transport ISS
Inferred from Sequence or Structural Similarity
more info
 
synaptic vesicle uncoating ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
clathrin coat of coated pit ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
membrane coat ISS
Inferred from Sequence or Structural Similarity
more info
 
colocalizes_with microtubule ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
perinuclear region of cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
perinuclear region of cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
postsynapse IEA
Inferred from Electronic Annotation
more info
 
presynapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
presynapse IDA
Inferred from Direct Assay
more info
PubMed 
synaptic membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
terminal bouton ISS
Inferred from Sequence or Structural Similarity
more info
 
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_982271.2
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)

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_001160306.1NP_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, ENST00000630077.2
    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, ENST00000433931.6
    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_203446.2NP_982271.2  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, AP000279, BC019630, CA944966, DB071394
    Consensus CDS
    CCDS33540.2
    UniProtKB/Swiss-Prot
    O43426
    UniProtKB/TrEMBL
    C9JFZ1, Q05CZ1
    Related
    ENSP00000371939.2, ENST00000382499.6
    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)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p12 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
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