Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Synpo synaptopodin [ Mus musculus (house mouse) ]

    Gene ID: 104027, updated on 11-May-2021

    Summary

    Official Symbol
    Synpoprovided by MGI
    Official Full Name
    synaptopodinprovided by MGI
    Primary source
    MGI:MGI:1099446
    See related
    Ensembl:ENSMUSG00000043079
    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
    AW046661; 9130229N11; 9030217H17Rik; 9330140I15Rik
    Expression
    Broad expression in ovary adult (RPKM 55.3), duodenum adult (RPKM 31.8) and 19 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Synpo in Genome Data Viewer
    Location:
    18; 18 D3- E1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    109 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)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 18 NC_000084.5 (60753644..60783959, complement)

    Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene RNA binding motif protein 22 Neighboring gene myozenin 3 Neighboring gene RIKEN cDNA G630071F17 gene Neighboring gene VISTA enhancer mm1623 Neighboring gene N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables actin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables actin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_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
    PubMed 
    is_active_in actin cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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 junction IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cell periphery IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    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 
    located_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in glutamatergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    is_active_in spine apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in spine apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in spine apparatus ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in stress fiber IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in stress fiber IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
     

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001109975.1NP_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
      Q3URF1
      Related
      ENSMUSP00000110973.4, ENSMUST00000115318.4
      Conserved Domains (2) summary
      PHA03247
      Location:52356
      PHA03247; large tegument protein UL36; Provisional
      PRK13914
      Location:15132
      PRK13914; invasion associated secreted endopeptidase; Provisional
    2. NM_177340.2NP_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
      Q3TY32, Q3U336
      Related
      ENSMUSP00000095174.4, ENSMUST00000097566.10
      Conserved Domains (2) summary
      PHA03247
      Location:576848
      PHA03247; large tegument protein UL36; Provisional
      PRK13914
      Location:15132
      PRK13914; invasion associated endopeptidase

    RefSeqs of Annotated Genomes: Mus musculus 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 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_006525471.3XP_006525534.1  synaptopodin isoform X1

      See identical proteins and their annotated locations for XP_006525534.1

      Conserved Domains (3) summary
      PTZ00449
      Location:51367
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PHA03247
      Location:8151087
      PHA03247; large tegument protein UL36; Provisional
      PRK13914
      Location:254371
      PRK13914; invasion associated endopeptidase
    2. XM_006525472.5XP_006525535.1  synaptopodin isoform X2

      UniProtKB/TrEMBL
      E9Q3E2
      Related
      ENSMUSP00000115355.2, ENSMUST00000130360.2
      Conserved Domains (3) summary
      PTZ00449
      Location:51367
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PHA03247
      Location:7391059
      PHA03247; large tegument protein UL36; Provisional
      PRK13914
      Location:254371
      PRK13914; invasion associated endopeptidase
    3. XM_006525468.4XP_006525531.1  synaptopodin isoform X1

      See identical proteins and their annotated locations for XP_006525531.1

      Conserved Domains (3) summary
      PTZ00449
      Location:51367
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PHA03247
      Location:8151087
      PHA03247; large tegument protein UL36; Provisional
      PRK13914
      Location:254371
      PRK13914; invasion associated endopeptidase
    4. XM_006525470.3XP_006525533.1  synaptopodin isoform X1

      See identical proteins and their annotated locations for XP_006525533.1

      Conserved Domains (3) summary
      PTZ00449
      Location:51367
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PHA03247
      Location:8151087
      PHA03247; large tegument protein UL36; Provisional
      PRK13914
      Location:254371
      PRK13914; invasion associated endopeptidase
    5. XM_036160910.1XP_036016803.1  synaptopodin isoform X4

      Conserved Domains (2) summary
      PHA03247
      Location:576848
      PHA03247; large tegument protein UL36; Provisional
      PRK13914
      Location:15132
      PRK13914; invasion associated endopeptidase
    6. XM_006525475.4XP_006525538.1  synaptopodin isoform X4

      See identical proteins and their annotated locations for XP_006525538.1

      UniProtKB/TrEMBL
      Q3U336
      Conserved Domains (2) summary
      PHA03247
      Location:576848
      PHA03247; large tegument protein UL36; Provisional
      PRK13914
      Location:15132
      PRK13914; invasion associated endopeptidase
    7. XM_036160914.1XP_036016807.1  synaptopodin isoform X4

      Conserved Domains (2) summary
      PHA03247
      Location:576848
      PHA03247; large tegument protein UL36; Provisional
      PRK13914
      Location:15132
      PRK13914; invasion associated endopeptidase
    8. XM_036160913.1XP_036016806.1  synaptopodin isoform X4

      Related
      ENSMUSP00000121756.2, ENSMUST00000130044.2
      Conserved Domains (2) summary
      PHA03247
      Location:576848
      PHA03247; large tegument protein UL36; Provisional
      PRK13914
      Location:15132
      PRK13914; invasion associated endopeptidase
    9. XM_006525474.3XP_006525537.1  synaptopodin isoform X3

      Conserved Domains (2) summary
      PHA03247
      Location:700972
      PHA03247; large tegument protein UL36; Provisional
      PRK13914
      Location:139256
      PRK13914; invasion associated endopeptidase
    10. XM_030250252.2XP_030106112.1  synaptopodin isoform X4

      Conserved Domains (2) summary
      PHA03247
      Location:576848
      PHA03247; large tegument protein UL36; Provisional
      PRK13914
      Location:15132
      PRK13914; invasion associated endopeptidase
    11. XM_036160911.1XP_036016804.1  synaptopodin isoform X4

      Conserved Domains (2) summary
      PHA03247
      Location:576848
      PHA03247; large tegument protein UL36; Provisional
      PRK13914
      Location:15132
      PRK13914; invasion associated endopeptidase
    Support Center