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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
    mouse all
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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.

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