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Synpo synaptopodin [ Mus musculus (house mouse) ]

Gene ID: 104027, updated on 7-Apr-2025

Summary

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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, Apr 2025]
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

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See Synpo in Genome Data Viewer
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_000084.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E9978 Neighboring gene RNA binding motif protein 22 Neighboring gene myozenin 3 Neighboring gene STARR-seq mESC enhancer starr_44719 Neighboring gene RIKEN cDNA G630071F17 gene Neighboring gene VISTA enhancer mm1623 Neighboring gene STARR-positive B cell enhancer ABC_E7590 Neighboring gene N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1 Neighboring gene STARR-seq mESC enhancer starr_44724 Neighboring gene STARR-positive B cell enhancer mm9_chr18:60904284-60904585

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Synaptopodin is required for long-term depression at Schaffer collateral-CA1 synapses. Inglebert Y, et al. Mol Brain, 2024 Apr 2. PMID 38566234, Free PMC Article
  2. The spine apparatus, synaptopodin, and dendritic spine plasticity. Segal M, et al. Neuroscientist, 2010 Apr. PMID 20400711
  3. Granule Cell Ensembles in Mouse Dentate Gyrus Rapidly Upregulate the Plasticity-Related Protein Synaptopodin after Exploration Behavior. Paul MH, et al. Cereb Cortex, 2020 Apr 14. PMID 31812981, Free PMC Article
  4. Structural Plasticity of Synaptopodin in the Axon Initial Segment during Visual Cortex Development. Schlüter A, et al. Cereb Cortex, 2017 Sep 1. PMID 28922860
  5. Loss of the cisternal organelle in the axon initial segment of cortical neurons in synaptopodin-deficient mice. Bas Orth C, et al. J Comp Neurol, 2007 Oct 10. PMID 17701995

See all (109) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. Synaptopodin Regulates Denervation-Induced Plasticity at Hippocampal Mossy Fiber Synapses.
    Title: Synaptopodin Regulates Denervation-Induced Plasticity at Hippocampal Mossy Fiber Synapses.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 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)

  1. 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

  2. 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

  1. NC_000084.7 Reference GRCm39 C57BL/6J

    Range
    60727053..60793241 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8CC35.2 GenPept UniProtKB/Swiss-Prot:Q8CC35

Gene LinkOut

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