Synj2 synaptojanin 2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Synj2provided by MGI
Official Full Name: synaptojanin 2provided by MGI
Primary source: MGI:MGI:1201671
See related: Ensembl:ENSMUSG00000023805 AllianceGenome:MGI:1201671
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: SJ2; mKIAA0348
Summary: Enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity. Predicted to be involved in several processes, including dephosphorylation; intracellular distribution of mitochondria; and synaptic vesicle endocytosis. Predicted to be located in axon terminus; cytoplasmic microtubule; and ruffle membrane. Predicted to be extrinsic component of mitochondrial outer membrane. Predicted to be active in perinuclear region of cytoplasm and presynapse. Is expressed in several structures, including alimentary system; genitourinary system; liver; nose; and spleen. Orthologous to human SYNJ2 (synaptojanin 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in testis adult (RPKM 5.1), cortex adult (RPKM 4.6) and 27 other tissues See more
Orthologs: human all
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Genomic context

Location:: 17 A1; 17 3.59 cM

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	17	NC_000083.7 (5991555..6106041)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	17	NC_000083.6 (5941280..6055766)

Chromosome 17 - NC_000083.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

report showing expression, location and isoforms of Synj1 and Synj2 in the small and large intestine and that they might participate in intestinal pathology.
Title: The Synaptojanins in the murine small and large intestine.
Clustering all known mouse Synj2 transcripts led to uncover a novel subset of transcripts that appears to derive from a region located within intron 7.
Title: Analysis of an intronic promoter within Synj2.
These results reveal Synj2 as a critical regulator of hair cell survival that is essential for hair cell maintenance and hearing function.
Title: A mutation in synaptojanin 2 causes progressive hearing loss in the ENU-mutagenised mouse strain Mozart.
role in proximal t-haplotype mediated mouse sterility
Title: Mutations in Serac1 or Synj2 cause proximal t haplotype-mediated male mouse sterility but not transmission ratio distortion.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1)
Targeted (2) 1 citation
Chemically induced (ENU) (1) 1 citation
Endonuclease-mediated (4)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Synj2 (e-PCR), detects polymorphism
- UniSTS:479288

AI481647 (e-PCR)
- UniSTS:166027

RH126060 (e-PCR)
- UniSTS:162772

Synj2 (e-PCR), detects polymorphism
- UniSTS:256493

NoName (e-PCR)
- UniSTS:237562

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
NOT enables PDZ domain binding	IBA Inferred from Biological aspect of Ancestor 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
enables SH3 domain binding	ISO Inferred from Sequence Orthology more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity	ISO Inferred from Sequence Orthology more info
enables inositol-1,4,5-trisphosphate 5-phosphatase activity	ISO Inferred from Sequence Orthology more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables phosphatase activity	IEA Inferred from Electronic Annotation more info
enables phosphatidylinositol monophosphate phosphatase activity	ISO Inferred from Sequence Orthology more info
enables phosphatidylinositol-3-phosphate phosphatase activity	IEA Inferred from Electronic Annotation 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

Process	Evidence Code	Pubs
involved_in inositol phosphate catabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lipid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in phosphatidylinositol dephosphorylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in phosphatidylinositol dephosphorylation	ISO Inferred from Sequence Orthology more info
involved_in synaptic vesicle endocytosis	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in axon terminus	ISO Inferred from Sequence Orthology more info
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic microtubule	ISO Inferred from Sequence Orthology more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in perinuclear region of cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
is_active_in presynapse	IBA Inferred from Biological aspect of Ancestor more info
is_active_in presynapse	ISO Inferred from Sequence Orthology more info
located_in ruffle membrane	ISO Inferred from Sequence Orthology more info
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: synaptojanin-2

Names: synaptic inositol-1,4,5-trisphosphate 5-phosphatase 2

NP_001106822.1

EC 3.1.3.36

NP_001106823.1

EC 3.1.3.36

NP_001106824.1

EC 3.1.3.36

NP_001277627.1

EC 3.1.3.36

NP_001344594.1

EC 3.1.3.36

NP_001344596.1

EC 3.1.3.36

NP_035653.2

EC 3.1.3.36

XP_006523265.1

EC 3.1.3.36

XP_006523266.1

EC 3.1.3.36

XP_006523267.1

EC 3.1.3.36

XP_006523268.1

EC 3.1.3.36

XP_006523269.1

EC 3.1.3.36

XP_006523271.1

EC 3.1.3.36

XP_017172861.1

EC 3.1.3.36

NCBI Reference Sequences (RefSeq)

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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)

NM_001113351.1 → NP_001106822.1 synaptojanin-2 isoform d

Status: VALIDATED

Description

Transcript Variant: This variant (4) has multiple differences in the coding region but maintains the reading frame compared to variant 1. This variant encodes isoform d which is shorter than isoform a.

Source sequence(s)

AF041862, AK163512, BC060214

UniProtKB/Swiss-Prot

Q9D2G5

Related

ENSMUST00000115788.8

Conserved Domains (3) summary

pfam02383
Location:3 → 257

Syja_N; SacI homology domain

pfam08952
Location:787 → 923

DUF1866; Domain of unknown function (DUF1866)

cl00490
Location:445 → 776

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
NM_001113352.2 → NP_001106823.1 synaptojanin-2 isoform b

See identical proteins and their annotated locations for NP_001106823.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1 that results in a shorter protein (isoform b).

Source sequence(s)

AF041857, AK142919, BC060214

Consensus CDS

CCDS49932.1

UniProtKB/Swiss-Prot

O35404, O88399, O88400, O88401, O88402, O88403, O88404, Q9D2G5

Related

ENSMUSP00000079164.7, ENSMUST00000080283.13

Conserved Domains (4) summary

pfam02383
Location:61 → 342

Syja_N; SacI homology domain

pfam08952
Location:872 → 1008

DUF1866; Domain of unknown function (DUF1866)

pfam15677
Location:1245 → 1360

CEND1; Cell cycle exit and neuronal differentiation protein 1

cl00490
Location:530 → 861

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
NM_001113353.2 → NP_001106824.1 synaptojanin-2 isoform a

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AF041857, AF041859, AK142919, AK148053, BC058749

Consensus CDS

CCDS49931.1

UniProtKB/TrEMBL

F8WHD8

Related

ENSMUSP00000111457.3, ENSMUST00000115791.10

Conserved Domains (4) summary

pfam02383
Location:61 → 342

Syja_N; SacI homology domain

pfam08952
Location:872 → 1008

DUF1866; Domain of unknown function (DUF1866)

pfam15677
Location:1290 → 1405

CEND1; Cell cycle exit and neuronal differentiation protein 1

cl00490
Location:530 → 861

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
NM_001290698.1 → NP_001277627.1 synaptojanin-2 isoform e

Status: VALIDATED

Description

Transcript Variant: This variant (5) has multiple differences compared to variant 1 and initiates translation at an alternate start codon. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform a.

Source sequence(s)

AK019694, AK142919, AK161467

Consensus CDS

CCDS70757.1

UniProtKB/TrEMBL

E9Q4P5, Q3TTB3

Related

ENSMUSP00000111451.2, ENSMUST00000115785.8

Conserved Domains (3) summary

pfam08952
Location:556 → 692

DUF1866; Domain of unknown function (DUF1866)

pfam15677
Location:929 → 1044

CEND1; Cell cycle exit and neuronal differentiation protein 1

cl00490
Location:214 → 545

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
NM_001357665.1 → NP_001344594.1 synaptojanin-2 isoform f

Status: VALIDATED

Source sequence(s)

AC154650, BU701096

UniProtKB/TrEMBL

F7BI35

Conserved Domains (3) summary

pfam08952
Location:497 → 633

DUF1866; Domain of unknown function (DUF1866)

cl00490
Location:155 → 486

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

cl27434
Location:2 → 110

Syja_N; SacI homology domain
NM_001357667.1 → NP_001344596.1 synaptojanin-2 isoform g

Status: VALIDATED

Source sequence(s)

AC154650, AK142919, BC060214, BU610521, BU701096, CJ113008

UniProtKB/TrEMBL

Q3TTB3

Conserved Domains (3) summary

pfam08952
Location:787 → 923

DUF1866; Domain of unknown function (DUF1866)

cl00490
Location:445 → 776

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

cl27434
Location:2 → 400

Syja_N; SacI homology domain
NM_011523.2 → NP_035653.2 synaptojanin-2 isoform c

See identical proteins and their annotated locations for NP_035653.2

Status: VALIDATED

Description

Transcript Variant: This variant (3) has multiple differences in the coding region but maintains the reading frame compared to variant 1. This variant encodes isoform c which is shorter than isoform a.

Source sequence(s)

AF041859, AF041862, AK163512, BC058749

Consensus CDS

CCDS28365.1

UniProtKB/Swiss-Prot

Q9D2G5

Related

ENSMUSP00000060382.8, ENSMUST00000061091.14

Conserved Domains (3) summary

pfam02383
Location:3 → 257

Syja_N; SacI homology domain

pfam08952
Location:787 → 923

DUF1866; Domain of unknown function (DUF1866)

cl00490
Location:445 → 776

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

RNA

NR_151772.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC154650, AF041857, AK142919, BU610521, BU701096

Related

ENSMUST00000134767.8

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000083.7 Reference GRCm39 C57BL/6J

Range

5991555..6106041

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006523203.2 → XP_006523266.1 synaptojanin-2 isoform X2

Conserved Domains (3) summary

COG5329
Location:30 → 485

COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]

pfam08952
Location:872 → 1008

DUF1866; Domain of unknown function (DUF1866)

cl00490
Location:530 → 861

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
XM_006523204.2 → XP_006523267.1 synaptojanin-2 isoform X3

Conserved Domains (3) summary

COG5329
Location:30 → 485

COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]

pfam08952
Location:872 → 1008

DUF1866; Domain of unknown function (DUF1866)

cl00490
Location:530 → 861

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
XM_006523205.4 → XP_006523268.1 synaptojanin-2 isoform X4

UniProtKB/Swiss-Prot

Q9D2G5

Conserved Domains (3) summary

COG5329
Location:30 → 485

COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]

pfam08952
Location:872 → 1008

DUF1866; Domain of unknown function (DUF1866)

cl00490
Location:530 → 861

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
XM_006523208.3 → XP_006523271.1 synaptojanin-2 isoform X6

Conserved Domains (3) summary

COG5329
Location:30 → 485

COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]

pfam08952
Location:872 → 1008

DUF1866; Domain of unknown function (DUF1866)

cl00490
Location:530 → 861

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
XM_006523206.3 → XP_006523269.1 synaptojanin-2 isoform X5

UniProtKB/TrEMBL

Q3TTB3

Conserved Domains (4) summary

COG5329
Location:7 → 245

COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]

pfam08952
Location:632 → 768

DUF1866; Domain of unknown function (DUF1866)

pfam15677
Location:1050 → 1165

CEND1; Cell cycle exit and neuronal differentiation protein 1

cl00490
Location:290 → 621

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
XM_006523202.5 → XP_006523265.1 synaptojanin-2 isoform X1

UniProtKB/TrEMBL

D3YZB2, Q3TTB3

Related

ENSMUSP00000111456.2, ENSMUST00000115790.8

Conserved Domains (4) summary

COG5329
Location:2 → 400

COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]

pfam08952
Location:787 → 923

DUF1866; Domain of unknown function (DUF1866)

pfam15677
Location:1205 → 1320

CEND1; Cell cycle exit and neuronal differentiation protein 1

cl00490
Location:445 → 776

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
XM_017317372.2 → XP_017172861.1 synaptojanin-2 isoform X7

UniProtKB/TrEMBL

Q3TTB3

Conserved Domains (4) summary

COG5329
Location:2 → 110

COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]

pfam08952
Location:497 → 633

DUF1866; Domain of unknown function (DUF1866)

pfam15677
Location:915 → 1030

CEND1; Cell cycle exit and neuronal differentiation protein 1

cl00490
Location:155 → 486

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily