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SYNPO2L synaptopodin 2 like [ Homo sapiens (human) ]

Gene ID: 79933, updated on 2-Nov-2024

Summary

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Official Symbol
SYNPO2Lprovided by HGNC
Official Full Name
synaptopodin 2 likeprovided by HGNC
Primary source
HGNC:HGNC:23532
See related
Ensembl:ENSG00000166317 AllianceGenome:HGNC:23532
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
Predicted to enable actin binding activity. Predicted to be involved in several processes, including positive regulation of Rho protein signal transduction; positive regulation of stress fiber assembly; and sarcomere organization. Predicted to be located in cytoplasm and cytoskeleton. Predicted to be active in Z disc; actin cytoskeleton; and nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Restricted expression toward heart (RPKM 82.2) See more
Orthologs
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Genomic context

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See SYNPO2L in Genome Data Viewer
Location:
10q22.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (73644886..73656029, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (74516308..74527453, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (75404644..75415787, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ubiquitin specific peptidase 54 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:75303318-75303526 Neighboring gene MPRA-validated peak1012 silencer Neighboring gene ribosomal protein S26 pseudogene 41 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:75351383-75352133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:75407469-75408172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3567 Neighboring gene myozenin 1 Neighboring gene Sharpr-MPRA regulatory region 4994 Neighboring gene SYNPO2L antisense RNA 1 Neighboring gene BMS1P4-AGAP5 readthrough Neighboring gene ArfGAP with GTPase domain, ankyrin repeat and PH domain 5 Neighboring gene RNA, 5S ribosomal pseudogene 320 Neighboring gene BMS1 pseudogene 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Whole Exome Sequencing in Atrial Fibrillation. Lubitz SA, et al. PLoS Genet, 2016 Sep. PMID 27589061, Free PMC Article
  2. METTL16 Promotes Stability of SYNPO2L mRNA and leading to Cancer Cell Lung Metastasis by Secretion of COL10A1 and attract the Cancer-Associated Fibroblasts. Wu J, et al. Int J Biol Sci, 2024. PMID 39247832, Free PMC Article
  3. Z-disc protein CHAPb induces cardiomyopathy and contractile dysfunction in the postnatal heart. van Eldik W, et al. PLoS One, 2017. PMID 29206857, Free PMC Article
  4. Meta-analysis identifies six new susceptibility loci for atrial fibrillation. Ellinor PT, et al. Nat Genet, 2012 Apr 29. PMID 22544366, Free PMC Article
  5. Host PDZ-containing proteins targeted by SARS-CoV-2. Caillet-Saguy C, et al. FEBS J, 2021 Sep. PMID 33864728, Free PMC Article

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. METTL16 Promotes Stability of SYNPO2L mRNA and leading to Cancer Cell Lung Metastasis by Secretion of COL10A1 and attract the Cancer-Associated Fibroblasts.
    Title: METTL16 Promotes Stability of SYNPO2L mRNA and leading to Cancer Cell Lung Metastasis by Secretion of COL10A1 and attract the Cancer-Associated Fibroblasts.
  2. we did not observe associations between coding genetic variants and Atrial fibrillation (AF), suggesting that large-effect coding variation is not the predominant mechanism underlying AF. A coding variant in SYNPO2L requires further evaluation to determine whether it is causally related to AF
    Title: Whole Exome Sequencing in Atrial Fibrillation.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
Submit: New GeneRIF Correction

Phenotypes

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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
Meta-analysis identifies six new susceptibility loci for atrial fibrillation.
EBI GWAS Catalog

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

Homology

Clone Names

  • FLJ12921

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables actin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in heart morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in positive regulation of Rho protein signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in positive regulation of actin filament bundle assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of stress fiber assembly ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in sarcomere organization ISS
Inferred from Sequence or Structural Similarity
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 ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
is_active_in actin cytoskeleton IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
synaptopodin 2-like protein

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_001114133.3 → NP_001107605.1  synaptopodin 2-like protein isoform a

    See identical proteins and their annotated locations for NP_001107605.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AB188489, AK022983
    Consensus CDS
    CCDS44438.1
    UniProtKB/Swiss-Prot
    A5PKV9, Q68A20, Q9H987
    UniProtKB/TrEMBL
    B4DJ09
    Related
    ENSP00000378289.2, ENST00000394810.3
    Conserved Domains (1) summary
    cd00992
    Location:6 → 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_024875.5 → NP_079151.2  synaptopodin 2-like protein isoform b

    See identical proteins and their annotated locations for NP_079151.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon resulting in different 5' UTR and 5' coding regions, compared to variant 1. It encodes isoform b, which is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AB188489, AC073389, AK022983, BC142635, DA685385
    Consensus CDS
    CCDS7331.1
    Related
    ENSP00000361964.4, ENST00000372873.8
    Conserved Domains (1) summary
    cl26247
    Location:191 → 326
    DNA_pol3_delta2; DNA polymerase III, delta subunit

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    73644886..73656029 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    74516308..74527453 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H987.3 GenPept UniProtKB/Swiss-Prot:Q9H987

Gene LinkOut

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

Other Literature Sources
Chemical Information
Molecular Biology Databases
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