SYNPO2 synaptopodin 2 [Homo sapiens (human)] - Gene

Summary

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, Nov 2024]
Expression: Broad expression in esophagus (RPKM 79.5), prostate (RPKM 71.0) and 14 other tissues See more
Orthologs: mouse all
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Genomic context

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_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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

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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 EBI GWAS CatalogPubMed
Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-11067 (e-PCR)
- UniSTS:68096

RH91250 (e-PCR)
- UniSTS:88065

STS-H16233 (e-PCR)
- UniSTS:62216

SHGC-50261 (e-PCR)
- UniSTS:41491

RH93997 (e-PCR)
- UniSTS:88089

D4S2499E (e-PCR)
- UniSTS:34076

D4S2802 (e-PCR)
- UniSTS:63523

SHGC-24713 (e-PCR)
- UniSTS:63524

NoName (e-PCR)
- UniSTS:483123

D4S1271 (e-PCR)
- UniSTS:13129

L18426 (e-PCR)
- UniSTS:34648

SHGC-31993 (e-PCR)
- UniSTS:46169

G33852 (e-PCR)
- UniSTS:6493

SHGC-24076 (e-PCR)
- UniSTS:6494

SHGC-77833 (e-PCR)
- UniSTS:101990

D10S16 (e-PCR)
- UniSTS:155756

G35510 (e-PCR)
- UniSTS:44150

RH119821 (e-PCR)
- UniSTS:133511

D4S2494E (e-PCR)
- UniSTS:11429

SHGC-8563 (e-PCR)
- UniSTS:26287

G20686 (e-PCR)
- UniSTS:76211

A006B40 (e-PCR)
- UniSTS:76212

SHGC-67749 (e-PCR)
- UniSTS:10423

SHGC-24709 (e-PCR)
- UniSTS:61879

SHGC-67759 (e-PCR)
- UniSTS:68029

SHGC-50263 (e-PCR)
- UniSTS:70333

SHGC-67326 (e-PCR)
- UniSTS:86461

SHGC-24073 (e-PCR)
- UniSTS:70334

D4S1172 (e-PCR)
- UniSTS:80321

RH41926 (e-PCR)
- UniSTS:70604

SHGC-51065 (e-PCR)
- UniSTS:38618

D4S2524E (e-PCR)
- UniSTS:38111

ksks245 (e-PCR)
- UniSTS:514281

SHGC-79982 (e-PCR)
- UniSTS:101611

D11S3316 (e-PCR)
- UniSTS:152558

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 more info	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

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Preferred Names: synaptopodin-2

Names: SYNPO2 intron sense-overlapping lncRNA; 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)

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) ...
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) ...
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) ...
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) ...
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
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
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) ...