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SYNPO2 synaptopodin 2 [ Homo sapiens (human) ]

Gene ID: 171024, updated on 11-Jun-2021

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
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Genomic context

See SYNPO2 in Genome Data Viewer
Location:
4q26
Exon count:
7
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (118850681..119061247)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (119771836..119982402)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene methyltransferase 14, N6-adenosine-methyltransferase subunit 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

Associated conditions

Description Tests
A genome-wide association study of total serum and mite-specific IgEs in asthma patients.
GeneReviews: Not available
Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
GeneReviews: Not available

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

General protein information

Preferred Names
synaptopodin-2
Names
genethonin-2
myopodin

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_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_001286755.2NP_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_001389263.1NP_001376192.1  synaptopodin-2 isoform f

    Status: VALIDATED

    Source sequence(s)
    AC096745, AC107048
    Conserved Domains (1) summary
    PHA03247
    Location:198675
    PHA03247; large tegument protein UL36; Provisional
  6. NM_001389264.1NP_001376193.1  synaptopodin-2 isoform g

    Status: VALIDATED

    Source sequence(s)
    AC096745
    Related
    ENSP00000498985.1, ENST00000627783.2
    Conserved Domains (1) summary
    PHA03247
    Location:198675
    PHA03247; large tegument protein UL36; Provisional
  7. 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 109.20210514

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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