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SYNJ2 synaptojanin 2 [ Homo sapiens (human) ]

Gene ID: 8871, updated on 21-Dec-2019

Summary

Official Symbol
SYNJ2provided by HGNC
Official Full Name
synaptojanin 2provided by HGNC
Primary source
HGNC:HGNC:11504
See related
Ensembl:ENSG00000078269 MIM:609410
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
INPP5H
Summary
The gene is a member of the inositol-polyphosphate 5-phosphatase family. The encoded protein interacts with the ras-related C3 botulinum toxin substrate 1, which causes translocation of the encoded protein to the plasma membrane where it inhibits clathrin-mediated endocytosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
Expression
Ubiquitous expression in brain (RPKM 8.6), colon (RPKM 3.7) and 25 other tissues See more
Orthologs

Genomic context

See SYNJ2 in Genome Data Viewer
Location:
6q25.3
Exon count:
31
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (157981856..158099176)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (158402888..158520208)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene sorting nexin 9 Neighboring gene RNA, U6 small nuclear 786, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr6.5510 Neighboring gene SYNJ2 intronic transcript 1 Neighboring gene serine active site containing 1 Neighboring gene general transcription factor IIH subunit 5

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?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide search for gene-gene interactions in colorectal cancer.
NHGRI GWA Catalog
The genetic aetiology of cannabis use initiation: a meta-analysis of genome-wide association studies and a SNP-based heritability estimation.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0348, MGC44422

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NOT PDZ domain binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA binding IEA
Inferred from Electronic Annotation
more info
 
SH3 domain binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
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 
membrane organization TAS
Traceable Author Statement
more info
 
phosphatidylinositol biosynthetic process TAS
Traceable Author Statement
more info
 
phosphatidylinositol dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
axon IEA
Inferred from Electronic Annotation
more info
 
cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
cytosol TAS
Traceable Author Statement
more info
 
membrane raft IEA
Inferred from Electronic Annotation
more info
 
perinuclear region of cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
presynapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
synaptojanin-2
Names
inositol phosphate 5'-phosphatase 2
inositol polyphosphate-5-phosphatase H
phosphoinositide 5-phosphatase
synaptic inositol 1,4,5-trisphosphate 5-phosphatase 2
NP_001171559.1
NP_003889.1
XP_005267255.1
XP_005267256.1
XP_005267257.1
XP_006715655.1
XP_011534526.1
XP_011534527.1
XP_011534528.1
XP_011534529.1
XP_011534530.1
XP_011534532.1
XP_016866895.1

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_029907.1 RefSeqGene

    Range
    5008..122321
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001178088.2NP_001171559.1  synaptojanin-2 isoform 2

    See identical proteins and their annotated locations for NP_001171559.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The resulting protein (isoform 2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AF086449, AL139330, BX648749, DA327619
    Consensus CDS
    CCDS87462.1
    UniProtKB/Swiss-Prot
    O15056
    UniProtKB/TrEMBL
    A0A1W2PR85
    Related
    ENSP00000492369.1, ENST00000638626.1
    Conserved Domains (3) summary
    pfam02383
    Location:8105
    Syja_N; SacI homology domain
    pfam08952
    Location:635771
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:293624
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
  2. NM_003898.4NP_003889.1  synaptojanin-2 isoform 1

    See identical proteins and their annotated locations for NP_003889.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1). This variant (1) is also known as synaptojanin 2B or 2B2 (SJ2B2).
    Source sequence(s)
    AF086449, AF318616, AK294480, AL139330
    Consensus CDS
    CCDS5254.1
    UniProtKB/Swiss-Prot
    O15056
    UniProtKB/TrEMBL
    B4DG94
    Related
    ENSP00000347792.4, ENST00000355585.9
    Conserved Domains (3) summary
    pfam02383
    Location:61342
    Syja_N; SacI homology domain
    pfam08952
    Location:8721008
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:530861
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    157981856..158099176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006715592.3XP_006715655.1  synaptojanin-2 isoform X2

    See identical proteins and their annotated locations for XP_006715655.1

    UniProtKB/Swiss-Prot
    O15056
    Related
    ENSP00000492532.1, ENST00000640338.1
    Conserved Domains (3) summary
    pfam02383
    Location:61342
    Syja_N; SacI homology domain
    pfam08952
    Location:8721008
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:530861
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
  2. XM_011536230.2XP_011534532.1  synaptojanin-2 isoform X8

    Conserved Domains (3) summary
    pfam02383
    Location:61342
    Syja_N; SacI homology domain
    pfam08952
    Location:8721008
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:530861
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
  3. XM_011536224.1XP_011534526.1  synaptojanin-2 isoform X1

    Conserved Domains (3) summary
    pfam02383
    Location:61342
    Syja_N; SacI homology domain
    pfam08952
    Location:8721008
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:530861
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
  4. XM_011536227.2XP_011534529.1  synaptojanin-2 isoform X5

    Conserved Domains (3) summary
    pfam02383
    Location:61342
    Syja_N; SacI homology domain
    pfam08952
    Location:8721008
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:530861
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
  5. XM_011536225.1XP_011534527.1  synaptojanin-2 isoform X3

    See identical proteins and their annotated locations for XP_011534527.1

    UniProtKB/Swiss-Prot
    O15056
    UniProtKB/TrEMBL
    A0A1W2PR85
    Conserved Domains (3) summary
    pfam02383
    Location:8105
    Syja_N; SacI homology domain
    pfam08952
    Location:635771
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:293624
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
  6. XM_017011406.1XP_016866895.1  synaptojanin-2 isoform X6

    Conserved Domains (2) summary
    pfam08952
    Location:489625
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:147478
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
  7. XM_005267198.4XP_005267255.1  synaptojanin-2 isoform X4

    See identical proteins and their annotated locations for XP_005267255.1

    Conserved Domains (2) summary
    pfam08952
    Location:541677
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:199530
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
  8. XM_005267199.2XP_005267256.1  synaptojanin-2 isoform X6

    See identical proteins and their annotated locations for XP_005267256.1

    Conserved Domains (2) summary
    pfam08952
    Location:489625
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:147478
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
  9. XM_011536228.3XP_011534530.1  synaptojanin-2 isoform X6

    See identical proteins and their annotated locations for XP_011534530.1

    Conserved Domains (2) summary
    pfam08952
    Location:489625
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:147478
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
  10. XM_011536226.3XP_011534528.1  synaptojanin-2 isoform X4

    See identical proteins and their annotated locations for XP_011534528.1

    Conserved Domains (2) summary
    pfam08952
    Location:541677
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:199530
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
  11. XM_005267200.1XP_005267257.1  synaptojanin-2 isoform X7

    Related
    ENSP00000356089.3, ENST00000367122.6
    Conserved Domains (2) summary
    pfam08952
    Location:285421
    DUF1866; Domain of unknown function (DUF1866)
    cl00490
    Location:1274
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

RNA

  1. XR_245556.1 RNA Sequence

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