Synpo synaptopodin [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Synpoprovided by MGI
Official Full Name: synaptopodinprovided by MGI
Primary source: MGI:MGI:1099446
See related: Ensembl:ENSMUSG00000043079 AllianceGenome:MGI:1099446
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: 9130229N11; 9030217H17Rik; 9330140I15Rik
Summary: Enables actin binding activity. Involved in several processes, including modulation of chemical synaptic transmission; regulation of actin filament bundle assembly; and regulation of postsynaptic cytosolic calcium ion concentration. Located in cell periphery and stress fiber. Is active in Schaffer collateral - CA1 synapse and glutamatergic synapse. Is expressed in several structures, including genitourinary system; respiratory system; sensory organ; skeleton; and tooth. Orthologous to human SYNPO (synaptopodin). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Broad expression in ovary adult (RPKM 55.3), duodenum adult (RPKM 31.8) and 19 other tissues See more
Orthologs: human all
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Genomic context

Location:: 18 D3- E1; 18 34.36 cM

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	18	NC_000084.7 (60727053..60793241, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	18	NC_000084.6 (60593981..60660173, complement)

Chromosome 18 - NC_000084.7 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?

Synaptopodin is required for long-term depression at Schaffer collateral-CA1 synapses.
Title: Synaptopodin is required for long-term depression at Schaffer collateral-CA1 synapses.
Synaptopodin Regulates Denervation-Induced Plasticity at Hippocampal Mossy Fiber Synapses.
Title: Synaptopodin Regulates Denervation-Induced Plasticity at Hippocampal Mossy Fiber Synapses.
Autism-related KLHL17 and SYNPO act in concert to control activity-dependent dendritic spine enlargement and the spine apparatus.
Title: Autism-related KLHL17 and SYNPO act in concert to control activity-dependent dendritic spine enlargement and the spine apparatus.
All-trans retinoic acid induces synaptopodin-dependent metaplasticity in mouse dentate granule cells.
Title: All-trans retinoic acid induces synaptopodin-dependent metaplasticity in mouse dentate granule cells.
Granule Cell Ensembles in Mouse Dentate Gyrus Rapidly Upregulate the Plasticity-Related Protein Synaptopodin after Exploration Behavior.
Title: Granule Cell Ensembles in Mouse Dentate Gyrus Rapidly Upregulate the Plasticity-Related Protein Synaptopodin after Exploration Behavior.
Myosin V regulates synaptopodin clustering and localization in the dendrites of hippocampal neurons.
Title: Myosin V regulates synaptopodin clustering and localization in the dendrites of hippocampal neurons.
Study indicates that a reduction in the expression of synaptopodin ameliorates Alzheimer's Disease-associated phenotype in 3xTg mice.
Title: Synaptopodin Deficiency Ameliorates Symptoms in the 3xTg Mouse Model of Alzheimer's Disease.
These findings indicate that NEFH is expressed in podocytes during the disease course and that it prevents the reduction in synaptopodin expression and detachment of podocytes.
Title: Neurofilament heavy polypeptide protects against reduction in synaptopodin expression and prevents podocyte detachment.
synaptopodin-deficient mice lacking the cisternal organelle showed AIS shortening in the dark
Title: Structural Plasticity of Synaptopodin in the Axon Initial Segment during Visual Cortex Development.
Results link synaptopodin (SP) with ryanodine receptors, in that ryanodine is able to convert short-term potentiation to long-term potentiation under our testing conditions only in ventral hippocampus, and only in the presence of SP in this region of the hippocampus.
Title: Ryanodine-mediated conversion of STP to LTP is lacking in synaptopodin-deficient mice.

Submit: New GeneRIF Correction See all GeneRIFs (28)

Variation

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Alleles

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

Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC343810P5 (e-PCR)
- UniSTS:273196

AW046661 (e-PCR)
- UniSTS:166099

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables actin binding	IBA Inferred from Biological aspect of Ancestor more info
enables actin binding	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 cortical cytoskeleton organization	NAS Non-traceable Author Statement more info	PubMed
involved_in modification of dendritic spine	IBA Inferred from Biological aspect of Ancestor more info
involved_in modification of dendritic spine	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of actin filament bundle assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of actin filament bundle assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in postsynaptic modulation of chemical synaptic transmission	IDA Inferred from Direct Assay more info	PubMed
involved_in postsynaptic modulation of chemical synaptic transmission	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of long-term neuronal synaptic plasticity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of postsynaptic cytosolic calcium ion concentration	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of postsynaptic cytosolic calcium ion concentration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of stress fiber assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in spine apparatus assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in spine apparatus assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in visual learning	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in Schaffer collateral - CA1 synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in Schaffer collateral - CA1 synapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in Z disc	IBA Inferred from Biological aspect of Ancestor more info
is_active_in actin cytoskeleton	IBA Inferred from Biological aspect of Ancestor more info
located_in actin cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
located_in actin cytoskeleton	ISO Inferred from Sequence Orthology more info
NOT located_in axon	ISO Inferred from Sequence Orthology more info	PubMed
located_in bicellular tight junction	IEA Inferred from Electronic Annotation more info
located_in cell periphery	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
located_in dendrite	ISO Inferred from Sequence Orthology more info	PubMed
located_in dendritic spine	NAS Non-traceable Author Statement more info	PubMed
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in perikaryon	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info
is_active_in spine apparatus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in spine apparatus	ISO Inferred from Sequence Orthology more info
is_active_in stress fiber	IBA Inferred from Biological aspect of Ancestor more info
located_in stress fiber	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: synaptopodin

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_001109975.1 → NP_001103445.1 synaptopodin isoform B

See identical proteins and their annotated locations for NP_001103445.1

Status: VALIDATED

Description

Transcript Variant: This variant (B) uses an alternate splice site in the coding region which results in an early stop codon, compared to variant A. The resulting protein (isoform B) has a shorter, distinct C-terminus when compared to isoform A.

Source sequence(s)

AK141564, AW050323

Consensus CDS

CCDS50298.1

UniProtKB/TrEMBL

Q3TY32, Q3URF1

Related

ENSMUSP00000110973.4, ENSMUST00000115318.4

Conserved Domains (2) summary

PHA03247
Location:52 → 356

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:15 → 132

PRK13914; invasion associated secreted endopeptidase; Provisional
NM_177340.2 → NP_796314.2 synaptopodin isoform A

See identical proteins and their annotated locations for NP_796314.2

Status: VALIDATED

Description

Transcript Variant: This variant (A) represents the longer transcript and encodes the longer isoform (A).

Source sequence(s)

AK158933, BC065127, BY128958

Consensus CDS

CCDS37833.1

UniProtKB/TrEMBL

Q3TA13, Q3U336

Related

ENSMUSP00000095174.4, ENSMUST00000097566.10

Conserved Domains (2) summary

PHA03247
Location:576 → 848

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:15 → 132

PRK13914; invasion associated endopeptidase

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_000084.7 Reference GRCm39 C57BL/6J

Range

60727053..60793241 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006525471.3 → XP_006525534.1 synaptopodin isoform X1

See identical proteins and their annotated locations for XP_006525534.1

UniProtKB/Swiss-Prot

Q8CC35, Q99JI0

Conserved Domains (3) summary

PTZ00449
Location:51 → 367

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PHA03247
Location:815 → 1087

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:254 → 371

PRK13914; invasion associated endopeptidase
XM_006525472.5 → XP_006525535.1 synaptopodin isoform X2

UniProtKB/Swiss-Prot

Q8CC35, Q99JI0

UniProtKB/TrEMBL

E9Q3E2

Related

ENSMUSP00000115355.2, ENSMUST00000130360.2

Conserved Domains (3) summary

PTZ00449
Location:51 → 367

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PHA03247
Location:739 → 1059

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:254 → 371

PRK13914; invasion associated endopeptidase
XM_006525468.4 → XP_006525531.1 synaptopodin isoform X1

See identical proteins and their annotated locations for XP_006525531.1

UniProtKB/Swiss-Prot

Q8CC35, Q99JI0

Conserved Domains (3) summary

PTZ00449
Location:51 → 367

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PHA03247
Location:815 → 1087

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:254 → 371

PRK13914; invasion associated endopeptidase
XM_006525470.3 → XP_006525533.1 synaptopodin isoform X1

See identical proteins and their annotated locations for XP_006525533.1

UniProtKB/Swiss-Prot

Q8CC35, Q99JI0

Conserved Domains (3) summary

PTZ00449
Location:51 → 367

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PHA03247
Location:815 → 1087

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:254 → 371

PRK13914; invasion associated endopeptidase
XM_036160910.1 → XP_036016803.1 synaptopodin isoform X4

UniProtKB/TrEMBL

Q3TA13, Q3U336

Conserved Domains (2) summary

PHA03247
Location:576 → 848

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:15 → 132

PRK13914; invasion associated endopeptidase
XM_006525475.4 → XP_006525538.1 synaptopodin isoform X4

See identical proteins and their annotated locations for XP_006525538.1

UniProtKB/TrEMBL

Q3TA13, Q3U336

Conserved Domains (2) summary

PHA03247
Location:576 → 848

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:15 → 132

PRK13914; invasion associated endopeptidase
XM_036160914.1 → XP_036016807.1 synaptopodin isoform X4

UniProtKB/TrEMBL

Q3TA13, Q3U336

Conserved Domains (2) summary

PHA03247
Location:576 → 848

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:15 → 132

PRK13914; invasion associated endopeptidase
XM_036160913.1 → XP_036016806.1 synaptopodin isoform X4

UniProtKB/TrEMBL

Q3TA13, Q3U336

Related

ENSMUSP00000121756.2, ENSMUST00000130044.2

Conserved Domains (2) summary

PHA03247
Location:576 → 848

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:15 → 132

PRK13914; invasion associated endopeptidase
XM_006525474.3 → XP_006525537.1 synaptopodin isoform X3

UniProtKB/TrEMBL

Q3TA13

Conserved Domains (2) summary

PHA03247
Location:700 → 972

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:139 → 256

PRK13914; invasion associated endopeptidase
XM_030250252.2 → XP_030106112.1 synaptopodin isoform X4

UniProtKB/TrEMBL

Q3TA13, Q3U336

Conserved Domains (2) summary

PHA03247
Location:576 → 848

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:15 → 132

PRK13914; invasion associated endopeptidase
XM_036160911.1 → XP_036016804.1 synaptopodin isoform X4

UniProtKB/TrEMBL

Q3TA13, Q3U336

Conserved Domains (2) summary

PHA03247
Location:576 → 848

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:15 → 132

PRK13914; invasion associated endopeptidase