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SYNPO2 synaptopodin 2 [ Homo sapiens (human) ]

Gene ID: 171024, updated on 21-Dec-2019

Summary

Official Symbol
SYNPO2provided by HGNC
Official Full Name
synaptopodin 2provided by HGNC
Primary source
HGNC:HGNC:17732
See related
Ensembl:ENSG00000172403
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
Expression
Broad expression in esophagus (RPKM 79.5), prostate (RPKM 71.0) and 14 other tissues See more
Orthologs

Genomic context

See SYNPO2 in Genome Data Viewer
Location:
4q26
Exon count:
7
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (118850681..119061247)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (119809996..119982402)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene methyltransferase like 14 Neighboring gene SEC24 homolog D, COPII coat complex component Neighboring gene uncharacterized LOC105377393 Neighboring gene uncharacterized LOC105377394 Neighboring gene uncharacterized LOC102723967 Neighboring gene uncharacterized LOC105377395 Neighboring gene uncharacterized LOC105379404 Neighboring gene myozenin 2

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study of total serum and mite-specific IgEs in asthma patients.
NHGRI GWA Catalog
Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp686G051

Gene Ontology Provided by GOA

Function Evidence Code Pubs
14-3-3 protein binding ISS
Inferred from Sequence or Structural Similarity
more info
 
actin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
alpha-actinin binding IDA
Inferred from Direct Assay
more info
PubMed 
filamin binding IDA
Inferred from Direct Assay
more info
PubMed 
muscle alpha-actinin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding, bridging IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
autophagosome assembly IEA
Inferred from Electronic Annotation
more info
 
chaperone-mediated autophagy IEA
Inferred from Electronic Annotation
more info
 
positive regulation of actin filament bundle assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
Z disc IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Z disc IDA
Inferred from Direct Assay
more info
PubMed 
Z disc ISS
Inferred from Sequence or Structural Similarity
more info
 
actin cytoskeleton IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
actin cytoskeleton IDA
Inferred from Direct Assay
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
focal adhesion HDA PubMed 
focal adhesion IDA
Inferred from Direct Assay
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
stress fiber IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
stress fiber IDA
Inferred from Direct Assay
more info
PubMed 
tethering complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
synaptopodin-2
Names
genethonin-2
myopodin

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_001128933.3NP_001122405.1  synaptopodin-2 isoform b

    See identical proteins and their annotated locations for NP_001122405.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks part of the 3' coding region, and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (b) has a shorter and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AC096745, AL833294, AL833547
    Consensus CDS
    CCDS47129.1
    UniProtKB/Swiss-Prot
    Q9UMS6
    Related
    ENSP00000395143.2, ENST00000429713.7
    Conserved Domains (1) summary
    cd00992
    Location:785
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
  2. NM_001128934.3NP_001122406.1  synaptopodin-2 isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate 3'-terminal exon, compared to variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (c) has a shorter and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AK000774, AL833294, AL833547, EU481975
    Consensus CDS
    CCDS47128.1
    UniProtKB/Swiss-Prot
    Q9UMS6
    Related
    ENSP00000390965.2, ENST00000434046.6
    Conserved Domains (1) summary
    cd00992
    Location:785
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
  3. NM_001286754.2NP_001273683.1  synaptopodin-2 isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains an alternate 5'-terminal exon, compared to variant 1. The encoded isoform (d) has a shorter and distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AC108030, AL833294, AV734727, CB998857, CR936673, EU481975, KF147165
    Consensus CDS
    CCDS75185.1
    UniProtKB/Swiss-Prot
    Q9UMS6
    Related
    ENSP00000484885.1, ENST00000610556.4
    Conserved Domains (1) summary
    cd00992
    Location:254
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
  4. NM_001286755.1NP_001273684.1  synaptopodin-2 isoform e

    See identical proteins and their annotated locations for NP_001273684.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks two consecutive exons in the central coding region, which results in a frameshift, compared to variant 1. The encoded isoform (e) has a shorter and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AL833547, AV734727, CB998857, CR936673
    Consensus CDS
    CCDS75186.1
    UniProtKB/TrEMBL
    B4E258
    Related
    ENSP00000412623.2, ENST00000448416.6
    Conserved Domains (1) summary
    cd00992
    Location:785
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
  5. NM_133477.3NP_597734.2  synaptopodin-2 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AC107048, AL833294, AL833547, BC150629
    Consensus CDS
    CCDS34054.1
    UniProtKB/Swiss-Prot
    Q9UMS6
    Related
    ENSP00000306015.4, ENST00000307142.9
    Conserved Domains (1) summary
    cd00992
    Location:785
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    118850681..119061247
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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