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Synpo synaptopodin [ Mus musculus (house mouse) ]

Gene ID: 104027, updated on 31-Jan-2019

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

Genomic context

See Synpo in Genome Data Viewer
Location:
18; 18 D3
Exon count:
10
Annotation release Status Assembly Chr Location
106 current GRCm38.p4 (GCF_000001635.24) 18 NC_000084.6 (60593981..60660174, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 18 NC_000084.5 (60753644..60783959, complement)

Chromosome 18 - NC_000084.6Genomic Context describing neighboring genes Neighboring gene RNA binding motif protein 22 Neighboring gene myozenin 3 Neighboring gene RIKEN cDNA G630071F17 gene 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 FunctionsWhat's a GeneRIF?

Variation

Alleles

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

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

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

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.

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
    ENSMUSP00000110973.3, ENSMUST00000115318.3
    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
    ENSMUSP00000095174.3, ENSMUST00000097566.9
    Conserved Domains (2) summary
    PHA03247
    Location:576848
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:15132
    PRK13914; invasion associated secreted endopeptidase; Provisional

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

Reference GRCm38.p4 C57BL/6J

Genomic

  1. NC_000084.6 Reference GRCm38.p4 C57BL/6J

    Range
    60593981..60660174 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006525471.1XP_006525534.1  synaptopodin isoform X1

    See identical proteins and their annotated locations for XP_006525534.1

    Conserved Domains (2) summary
    PHA03247
    Location:8151087
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:254371
    PRK13914; invasion associated secreted endopeptidase; Provisional
  2. XM_006525472.3XP_006525535.1  synaptopodin isoform X2

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

    See identical proteins and their annotated locations for XP_006525531.1

    Conserved Domains (2) summary
    PHA03247
    Location:8151087
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:254371
    PRK13914; invasion associated secreted endopeptidase; Provisional
  4. XM_006525470.2XP_006525533.1  synaptopodin isoform X1

    See identical proteins and their annotated locations for XP_006525533.1

    Conserved Domains (2) summary
    PHA03247
    Location:8151087
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:254371
    PRK13914; invasion associated secreted endopeptidase; Provisional
  5. XM_006525476.1XP_006525539.1  synaptopodin isoform X4

    See identical proteins and their annotated locations for XP_006525539.1

    UniProtKB/TrEMBL
    Q3U336
    Related
    ENSMUSP00000121756.1, ENSMUST00000130044.1
    Conserved Domains (2) summary
    PHA03247
    Location:576848
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:15132
    PRK13914; invasion associated secreted endopeptidase; Provisional
  6. XM_006525475.2XP_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 secreted endopeptidase; Provisional
  7. XM_006525474.3XP_006525537.1  synaptopodin isoform X3

    Conserved Domains (3) summary
    PHA03247
    Location:700972
    PHA03247; large tegument protein UL36; Provisional
    PRK12323
    Location:555759
    PRK12323; DNA polymerase III subunits gamma and tau; Provisional
    PRK13914
    Location:139256
    PRK13914; invasion associated secreted endopeptidase; Provisional
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