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SYNPO synaptopodin [ Homo sapiens (human) ]

Gene ID: 11346, updated on 2-Oct-2018

Summary

Official Symbol
SYNPOprovided by HGNC
Official Full Name
synaptopodinprovided by HGNC
Primary source
HGNC:HGNC:30672
See related
Ensembl:ENSG00000171992 MIM:608155; Vega:OTTHUMG00000130078
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Synaptopodin is an actin-associated protein that may play a role in actin-based cell shape and motility. The name synaptopodin derives from the protein's associations with postsynaptic densities and dendritic spines and with renal podocytes (Mundel et al., 1997 [PubMed 9314539]).[supplied by OMIM, Mar 2008]
Expression
Broad expression in heart (RPKM 65.2), fat (RPKM 35.1) and 20 other tissues See more
Orthologs

Genomic context

See SYNPO in Genome Data Viewer
Location:
5q33.1
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (150586026..150659230)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149980642..150038792)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein S14 Neighboring gene NDST1 antisense RNA 1 Neighboring gene N-deacetylase and N-sulfotransferase 1 Neighboring gene myozenin 3 Neighboring gene RNA binding motif protein 22

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef HIV-1 Nef downregulates expression of synaptopodin, a marker for differentiation in podocytes PubMed
Tat tat The gene expression of synaptopodin is significantly upregulated in both clade B and clade C Tat treated SK-N-MC neuroblastoma cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Primary Focal Segmental Glomerulosclerosis FSGS, organism-specific biosystem (from WikiPathways)
    Primary Focal Segmental Glomerulosclerosis FSGS, organism-specific biosystemPrimary or idiopathic focal segmental glomerulosclerosis (FSGS) a cause of nephrotic syndrome in children and adolescents, as well as an important cause of end stage renal disease in adults. FSGS is ...
  • Tight junction, organism-specific biosystem (from KEGG)
    Tight junction, organism-specific biosystemTight junctions (TJs) are essential for establishing a selectively permeable barrier to diffusion through the paracellular space between neighboring cells. TJs are composed of at least three types of...
  • Tight junction, conserved biosystem (from KEGG)
    Tight junction, conserved biosystemTight junctions (TJs) are essential for establishing a selectively permeable barrier to diffusion through the paracellular space between neighboring cells. TJs are composed of at least three types of...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1029

Gene Ontology Provided by GOA

Function Evidence Code Pubs
actin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
actin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
modification of dendritic spine IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
modification of dendritic spine IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of actin filament bundle assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of postsynaptic cytosolic calcium concentration IEA
Inferred from Electronic Annotation
more info
 
postsynaptic modulation of chemical synaptic transmission IEA
Inferred from Electronic Annotation
more info
 
regulation of long-term neuronal synaptic plasticity IEA
Inferred from Electronic Annotation
more info
 
spine apparatus assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
visual learning IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Schaffer collateral - CA1 synapse IEA
Inferred from Electronic Annotation
more info
 
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
 
actin cytoskeleton ISS
Inferred from Sequence or Structural Similarity
more info
 
bicellular tight junction IEA
Inferred from Electronic Annotation
more info
 
dendritic spine TAS
Traceable Author Statement
more info
PubMed 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
perikaryon IEA
Inferred from Electronic Annotation
more info
 
postsynaptic density 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 
stress fiber IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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_001109974.2NP_001103444.1  synaptopodin isoform B

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (B), also referred to as 'Synpo-short', has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AL831818, BC146665, DA333058, F30246
    Consensus CDS
    CCDS54938.1
    UniProtKB/Swiss-Prot
    Q8N3V7
    Related
    ENSP00000429268.1, OTTHUMP00000227739, ENST00000519664.1, OTTHUMT00000380640
    Conserved Domains (2) summary
    PHA03247
    Location:269668
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:15142
    PRK13914; invasion associated secreted endopeptidase; Provisional
  2. NM_001166208.1NP_001159680.1  synaptopodin isoform C

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate start codon, compared to variant 1. The encoded protein (isoform C) is longer than isoform 1 and contains unique N- and C-termini. Both variants 3 and 4 encode the same isoform (C).
    Source sequence(s)
    AK127049, AL831818, F30246
    Consensus CDS
    CCDS54937.1
    UniProtKB/Swiss-Prot
    Q8N3V7
    Related
    ENSP00000377789.1, OTTHUMP00000160557, ENST00000394243.5, OTTHUMT00000252371
    Conserved Domains (1) summary
    PHA03247
    Location:513912
    PHA03247; large tegument protein UL36; Provisional
  3. NM_001166209.1NP_001159681.1  synaptopodin isoform C

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate start codon, compared to variant 1. The encoded protein (isoform C) is longer than isoform 1 and contains unique N- and C-termini. Both variants 3 and 4 encode the same isoform (C).
    Source sequence(s)
    AK127049, AL831818, F30246
    Consensus CDS
    CCDS54937.1
    UniProtKB/Swiss-Prot
    Q8N3V7
    Related
    ENSP00000428378.1, OTTHUMP00000227738, ENST00000522122.1, OTTHUMT00000380638
    Conserved Domains (1) summary
    PHA03247
    Location:513912
    PHA03247; large tegument protein UL36; Provisional
  4. NM_007286.5NP_009217.3  synaptopodin isoform A

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform A, also referred to as 'Synpo-long'.
    Source sequence(s)
    AA303936, AB028952, DA333058
    Consensus CDS
    CCDS4308.1
    UniProtKB/Swiss-Prot
    Q8N3V7
    Related
    ENSP00000302139.4, OTTHUMP00000160556, ENST00000307662.4, OTTHUMT00000252370
    Conserved Domains (2) summary
    cl26464
    Location:499900
    Atrophin-1; Atrophin-1 family
    cl28464
    Location:15142
    Spr; Cell wall-associated hydrolase, NlpC family [Cell wall/membrane/envelope biogenesis]

RefSeqs of Annotated Genomes: Homo sapiens 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 GRCh38.p12 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

    Range
    150586026..150659230
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006714755.3XP_006714818.1  synaptopodin isoform X1

    Conserved Domains (2) summary
    PHA03247
    Location:7431144
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:259386
    PRK13914; invasion associated secreted endopeptidase; Provisional
  2. XM_011537552.2XP_011535854.1  synaptopodin isoform X2

    UniProtKB/Swiss-Prot
    Q8N3V7
    Conserved Domains (1) summary
    PHA03247
    Location:513912
    PHA03247; large tegument protein UL36; Provisional
  3. XM_017009008.1XP_016864497.1  synaptopodin isoform X1

    Conserved Domains (2) summary
    PHA03247
    Location:7431144
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:259386
    PRK13914; invasion associated secreted endopeptidase; Provisional
  4. XM_017009007.1XP_016864496.1  synaptopodin isoform X1

    Conserved Domains (2) summary
    PHA03247
    Location:7431144
    PHA03247; large tegument protein UL36; Provisional
    PRK13914
    Location:259386
    PRK13914; invasion associated secreted endopeptidase; Provisional
  5. XM_024454351.1XP_024310119.1  synaptopodin isoform X3

    Conserved Domains (2) summary
    cl26464
    Location:499900
    Atrophin-1; Atrophin-1 family
    cl28464
    Location:15142
    Spr; Cell wall-associated hydrolase, NlpC family [Cell wall/membrane/envelope biogenesis]
  6. XM_005268370.1XP_005268427.1  synaptopodin isoform X3

    UniProtKB/Swiss-Prot
    Q8N3V7
    Conserved Domains (2) summary
    cl26464
    Location:499900
    Atrophin-1; Atrophin-1 family
    cl28464
    Location:15142
    Spr; Cell wall-associated hydrolase, NlpC family [Cell wall/membrane/envelope biogenesis]
  7. XM_005268371.1XP_005268428.1  synaptopodin isoform X3

    UniProtKB/Swiss-Prot
    Q8N3V7
    Conserved Domains (2) summary
    cl26464
    Location:499900
    Atrophin-1; Atrophin-1 family
    cl28464
    Location:15142
    Spr; Cell wall-associated hydrolase, NlpC family [Cell wall/membrane/envelope biogenesis]
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