U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SYNPO2 synaptopodin 2 [ Homo sapiens (human) ]

Gene ID: 171024, updated on 10-Dec-2024

Summary

Go to the top of the page Help
Official Symbol
SYNPO2provided by HGNC
Official Full Name
synaptopodin 2provided by HGNC
Primary source
HGNC:HGNC:17732
See related
Ensembl:ENSG00000172403 MIM:620941; AllianceGenome:HGNC:17732
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
Also known as
SYISL
Summary
Enables alpha-actinin binding activity and filamin binding activity. Involved in positive regulation of actin filament bundle assembly; positive regulation of cell migration; and regulation of Rho-dependent protein serine/threonine kinase activity. Located in several cellular components, including Z disc; focal adhesion; and stress fiber. [provided by Alliance of Genome Resources, Dec 2024]
Expression
Broad expression in esophagus (RPKM 79.5), prostate (RPKM 71.0) and 14 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See SYNPO2 in Genome Data Viewer
Location:
4q26
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (118850681..119061247)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (122156026..122366575)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (119771836..119982402)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21848 Neighboring gene methyltransferase 14, N6-adenosine-methyltransferase non-catalytic subunit Neighboring gene SEC24 homolog D, COPII coat complex component Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:119756637-119757528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15653 Neighboring gene uncharacterized LOC105377393 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:119838359-119838859 Neighboring gene uncharacterized LOC105377394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21851 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:119952827-119953326 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:119989169-119989985 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:119994879-119995380 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:119995381-119995880 Neighboring gene uncharacterized LOC102723967 Neighboring gene Sharpr-MPRA regulatory region 3409 Neighboring gene uncharacterized LOC105377395 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:120042725-120043224 Neighboring gene uncharacterized LOC105379404 Neighboring gene myozenin 2

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Diagnostic and prognostic utility of methylation and protein expression patterns of myopodin in colon cancer. Esteban S, et al. Tumour Biol, 2012 Apr. PMID 22252522
  2. The Genexpress Index: a resource for gene discovery and the genic map of the human genome. Houlgatte R, et al. Genome Res, 1995 Oct. PMID 8593614
  3. Tumor suppressor role for myopodin in bladder cancer: loss of nuclear expression of myopodin is cell-cycle dependent and predicts clinical outcome. Sanchez-Carbayo M, et al. Oncogene, 2003 Aug 14. PMID 12917631
  4. Expression of myopodin induces suppression of tumor growth and metastasis. Jing L, et al. Am J Pathol, 2004 May. PMID 15111326, Free PMC Article
  5. Multiple isoforms of the tumor suppressor myopodin are simultaneously transcribed in cancer cells. De Ganck A, et al. Biochem Biophys Res Commun, 2008 May 30. PMID 18371299

See all (46) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Synaptopodin-2 Isoforms Have Specific Binding Partners and Display Distinct, Muscle Cell Type-Specific Expression Patterns.
    Title: Synaptopodin-2 Isoforms Have Specific Binding Partners and Display Distinct, Muscle Cell Type-Specific Expression Patterns.
  2. SYNPO2 promotes the development of BLCA by upregulating the infiltration of resting mast cells and increasing the resistance to immunotherapy.
    Title: SYNPO2 promotes the development of BLCA by upregulating the infiltration of resting mast cells and increasing the resistance to immunotherapy.
  3. SYNPO2 suppresses hypoxia-induced proliferation and migration of colorectal cancer cells by regulating YAP-KLF5 axis.
    Title: SYNPO2 suppresses hypoxia-induced proliferation and migration of colorectal cancer cells by regulating YAP-KLF5 axis.
  4. Synaptopodin-2 promotes hepatocellular carcinoma metastasis via calcineurin-induced nuclear-cytoplasmic translocation.
    Title: Synaptopodin-2 promotes hepatocellular carcinoma metastasis via calcineurin-induced nuclear-cytoplasmic translocation.
  5. These findings uncover a suppressive role of SYNPO2 in triple-negative breast cancer (TNBC) metastasis via inhibition of YAP/TAZ, and suggest that SYNPO2 might provide a potential prognosis marker and novel therapeutic strategy.
    Title: Synaptopodin-2 suppresses metastasis of triple-negative breast cancer via inhibition of YAP/TAZ activity.
  6. LMOD1, SYNPO2, PDLIM7, PLN, and SYNM down-regulation reflect the altered phenotype of smooth muscle cells in vascular disease and could be early sensitive markers of SMC dedifferentiation.
    Title: Phenotypic Modulation of Smooth Muscle Cells in Atherosclerosis Is Associated With Downregulation of LMOD1, SYNPO2, PDLIM7, PLN, and SYNM.
  7. Results show that SYNPO2 gene plays an important role in the etiology of epithelial ovarian cancer, suggesting that this gene may be a potential genetic modifier for developing epithelial ovarian cancer.
    Title: Association of a common variant of SYNPO2 gene with increased risk of serous epithelial ovarian cancer.
  8. High Myopodin methylation is associated with metastasis in kidney cancer.
    Title: Myopodin methylation is a prognostic biomarker and predicts antiangiogenic response in advanced kidney cancer.
  9. High Synaptopodin-2 induces assembly of peripheral actin bundles and immature focal adhesions to promote lamellipodia formation and prostate cancer cell migration.
    Title: Synaptopodin-2 induces assembly of peripheral actin bundles and immature focal adhesions to promote lamellipodia formation and prostate cancer cell migration.
  10. Promoter hypermethylation and down regulation of SYNPO2 has significance in the prognosis of melanoma patients.
    Title: Prognostic Significance of Promoter Hypermethylation and Diminished Gene Expression of SYNPO2 in Melanoma.
Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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
  
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 
Process Evidence Code Pubs
involved_in positive regulation of actin filament bundle assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of actin filament bundle assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cell migration IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of Rho-dependent protein serine/threonine kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in Z disc IBA
Inferred from Biological aspect of Ancestor
more info
  
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
  
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
  
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
  
located_in stress fiber IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
synaptopodin-2
Names
SYNPO2 intron sense-overlapping lncRNA
genethonin-2
myopodin

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001128933.3 → NP_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
    B2RWP6, B2Y8J9, C6H0M7, Q9UK89, Q9UMS6, S5XAM4
    UniProtKB/TrEMBL
    B9EG60
    Related
    ENSP00000395143.2, ENST00000429713.7
    Conserved Domains (1) summary
    cd00992
    Location:7 → 85
    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_001128934.3 → NP_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/TrEMBL
    B9EG60
    Related
    ENSP00000390965.2, ENST00000434046.6
    Conserved Domains (1) summary
    cd00992
    Location:7 → 85
    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_001286754.2 → NP_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/TrEMBL
    B9EG60
    Related
    ENSP00000484885.1, ENST00000610556.4
    Conserved Domains (1) summary
    cd00992
    Location:2 → 54
    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_001286755.2 → NP_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:7 → 85
    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_001389263.1 → NP_001376192.1  synaptopodin-2 isoform f

    Status: VALIDATED

    Source sequence(s)
    AC096745, AC107048
    Conserved Domains (1) summary
    PHA03247
    Location:198 → 675
    PHA03247; large tegument protein UL36; Provisional

  6. NM_001389264.1 → NP_001376193.1  synaptopodin-2 isoform g

    Status: VALIDATED

    Source sequence(s)
    AC096745
    Consensus CDS
    CCDS93613.1
    UniProtKB/TrEMBL
    B4DLE4
    Related
    ENSP00000498985.1, ENST00000627783.2
    Conserved Domains (1) summary
    PHA03247
    Location:198 → 675
    PHA03247; large tegument protein UL36; Provisional

  7. NM_133477.3 → NP_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/TrEMBL
    B9EG60
    Related
    ENSP00000306015.4, ENST00000307142.9
    Conserved Domains (1) summary
    cd00992
    Location:7 → 85
    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: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    122156026..122366575
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054349143.1 → XP_054205118.1  synaptopodin-2 isoform X1

    UniProtKB/TrEMBL
    B9EG60
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UMS6.2 GenPept UniProtKB/Swiss-Prot:Q9UMS6

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools