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Synpo synaptopodin [ Rattus norvegicus (Norway rat) ]

Gene ID: 60324, updated on 25-Nov-2021

Summary

Official Symbol
Synpoprovided by RGD
Official Full Name
synaptopodinprovided by RGD
Primary source
RGD:620668
See related
EnsemblRapid:ENSRNOG00000019181
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
may associate with actin to regulate cell shape; may play a role in synaptic plasticity [RGD, Feb 2006]
Expression
Biased expression in Heart (RPKM 151.3), Muscle (RPKM 128.6) and 9 other tissues See more
Orthologs
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Genomic context

See Synpo in Genome Data Viewer
Location:
18q12.1
Exon count:
12
Annotation release Status Assembly Chr Location
108 current mRatBN7.2 (GCF_015227675.2) 18 NC_051353.1 (54048299..54106388, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 18 NC_005117.4 (55863081..55921412, complement)

Chromosome 18 - NC_051353.1Genomic Context describing neighboring genes Neighboring gene RNA binding motif protein 22 Neighboring gene myozenin 3 Neighboring gene uncharacterized LOC120098275 Neighboring gene N-deacetylase and N-sulfotransferase 1

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables actin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables actin binding IEA
Inferred from Electronic Annotation
more info
 
enables actin binding ISO
Inferred from Sequence Orthology
more info
 
enables actin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
is_active_in Schaffer collateral - CA1 synapse ISO
Inferred from Sequence Orthology
more info
 
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 IEA
Inferred from Electronic Annotation
more info
 
located_in actin cytoskeleton ISO
Inferred from Sequence Orthology
more info
 
located_in actin cytoskeleton ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in bicellular tight junction IEA
Inferred from Electronic Annotation
more info
 
located_in cell periphery ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol ISS
Inferred from Sequence or Structural Similarity
more info
 
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
located_in glutamatergic synapse IDA
Inferred from Direct Assay
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
PubMed 
located_in perikaryon IEA
Inferred from Electronic Annotation
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
PubMed 
is_active_in spine apparatus IDA
Inferred from Direct Assay
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 ISO
Inferred from Sequence Orthology
more info
 

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_021695.2NP_067727.2  synaptopodin

    See identical proteins and their annotated locations for NP_067727.2

    Status: VALIDATED

    Source sequence(s)
    AB013130, CB769636, CB794090, DY313339, EV779156
    UniProtKB/Swiss-Prot
    Q9Z327
    Related
    ENSRNOP00000061109.1, ENSRNOT00000064686.2
    Conserved Domains (3) summary
    PHA03247
    Location:50361
    PHA03247; large tegument protein UL36; Provisional
    PRK12323
    Location:496689
    PRK12323; DNA polymerase III subunits gamma and tau; Provisional
    PRK13914
    Location:15125
    PRK13914; invasion associated secreted endopeptidase; Provisional

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051353.1 Reference mRatBN7.2 Primary Assembly

    Range
    54048299..54106388 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017601017.2XP_017456506.1  synaptopodin isoform X1

    Conserved Domains (2) summary
    PHA03247
    Location:7551102
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:254364
    PRK13914; invasion associated endopeptidase
  2. XM_017601015.2XP_017456504.1  synaptopodin isoform X1

    Conserved Domains (2) summary
    PHA03247
    Location:7551102
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:254364
    PRK13914; invasion associated endopeptidase
  3. XM_039097053.1XP_038952981.1  synaptopodin isoform X1

    Conserved Domains (2) summary
    PHA03247
    Location:7551102
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:254364
    PRK13914; invasion associated endopeptidase
  4. XM_017601016.2XP_017456505.1  synaptopodin isoform X1

    Related
    ENSRNOP00000025934.6, ENSRNOT00000025934.6
    Conserved Domains (2) summary
    PHA03247
    Location:7551102
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:254364
    PRK13914; invasion associated endopeptidase
  5. XM_017601021.2XP_017456510.1  synaptopodin isoform X4

    UniProtKB/TrEMBL
    B1VKB4
    Conserved Domains (2) summary
    PHA03247
    Location:516863
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:15125
    PRK13914; invasion associated endopeptidase
  6. XM_017601020.1XP_017456509.1  synaptopodin isoform X4

    UniProtKB/TrEMBL
    B1VKB4
    Conserved Domains (2) summary
    PHA03247
    Location:516863
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:15125
    PRK13914; invasion associated endopeptidase
  7. XM_017601024.2XP_017456513.1  synaptopodin isoform X4

    UniProtKB/TrEMBL
    B1VKB4
    Conserved Domains (2) summary
    PHA03247
    Location:516863
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:15125
    PRK13914; invasion associated endopeptidase
  8. XM_039097054.1XP_038952982.1  synaptopodin isoform X2

    Related
    ENSRNOP00000094210.1, ENSRNOT00000093773.1
    Conserved Domains (2) summary
    PHA03247
    Location:640987
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:139249
    PRK13914; invasion associated endopeptidase
  9. XM_017601022.2XP_017456511.1  synaptopodin isoform X4

    UniProtKB/TrEMBL
    B1VKB4
    Conserved Domains (2) summary
    PHA03247
    Location:516863
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:15125
    PRK13914; invasion associated endopeptidase
  10. XM_039097056.1XP_038952984.1  synaptopodin isoform X4

    Conserved Domains (2) summary
    PHA03247
    Location:516863
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:15125
    PRK13914; invasion associated endopeptidase
  11. XM_039097055.1XP_038952983.1  synaptopodin isoform X3

    Related
    ENSRNOP00000077576.1, ENSRNOT00000102376.1
    Conserved Domains (2) summary
    PHA03247
    Location:289600
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:254364
    PRK13914; invasion associated endopeptidase
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