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    SYPL2 synaptophysin like 2 [ Homo sapiens (human) ]

    Gene ID: 284612, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SYPL2provided by HGNC
    Official Full Name
    synaptophysin like 2provided by HGNC
    Primary source
    HGNC:HGNC:27638
    See related
    Ensembl:ENSG00000143028 AllianceGenome:HGNC:27638
    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
    MG29
    Summary
    Involved in substantia nigra development. Predicted to be located in membrane and synaptic vesicle. Predicted to be active in synaptic vesicle membrane. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in kidney (RPKM 4.9), testis (RPKM 4.8) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SYPL2 in Genome Data Viewer
    Location:
    1p13.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (109466546..109482134)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (109499325..109514907)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (110009168..110024756)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak354 silencer Neighboring gene sortilin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1147 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1148 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1149 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:109940693-109941674 Neighboring gene proteasome 20S subunit alpha 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:109969133-109970064 Neighboring gene MPRA-validated peak355 silencer Neighboring gene MPRA-validated peak356 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110008599-110009100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110009101-110009600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110020155-110020674 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110025999-110026616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110026617-110027236 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1151 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1441 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110036856-110037356 Neighboring gene Sharpr-MPRA regulatory region 8825 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110042111-110042610 Neighboring gene ataxin 7 like 2 Neighboring gene cytochrome b561 family member D1

    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
    • 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. Exome sequencing followed by genotyping suggests SYPL2 as a susceptibility gene for morbid obesity. Jiao H, et al. Eur J Hum Genet, 2015 Sep. PMID 25406998, Free PMC Article
    2. Mitsugumin 29 is transcriptionally induced in senile plaque-associated astrocytes. Satoh K, et al. Brain Res, 2012 Mar 2. PMID 22290180
    3. Genome-wide association study of recurrent early-onset major depressive disorder. Shi J, et al. Mol Psychiatry, 2011 Feb. PMID 20125088, Free PMC Article
    4. New loci associated with kidney function and chronic kidney disease. Köttgen A, et al. Nat Genet, 2010 May. PMID 20383146, Free PMC Article
    5. Quantitative proteomic analysis of human substantia nigra in Alzheimer's disease, Huntington's disease and Multiple sclerosis. Chen S, et al. Neurochem Res, 2012 Dec. PMID 22926577

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SYPL2 is a susceptibility gene for morbid obesity.
      Title: Exome sequencing followed by genotyping suggests SYPL2 as a susceptibility gene for morbid obesity.
    2. Mitsugumin (MG)29 is expressed in astrocytes of Alzheimer disease brains associated with senile plaques, but is is not expressed in neurons around lesions.
      Title: Mitsugumin 29 is transcriptionally induced in senile plaque-associated astrocytes.
    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
    Genome-wide association study of recurrent early-onset major depressive disorder.
    EBI GWAS Catalog
    New loci associated with kidney function and chronic kidney disease.
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in T-tubule organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in heart development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intracellular calcium ion homeostasis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in substantia nigra development HEP PubMed 
    Component Evidence Code Pubs
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    synaptophysin-like protein 2
    Names
    mitsugumin 29

    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_001040709.2 → NP_001035799.1  synaptophysin-like protein 2

      See identical proteins and their annotated locations for NP_001035799.1

      Status: VALIDATED

      Source sequence(s)
      AI983207, AL355145, DA097637, DB071160, DB291596, DN831287
      Consensus CDS
      CCDS41365.1
      UniProtKB/Swiss-Prot
      A8K0E8, A8KAL7, I0IT67, Q5VXT5, Q6ZMX1
      Related
      ENSP00000358888.3, ENST00000369872.4
      Conserved Domains (1) summary
      pfam01284
      Location:30 → 232
      MARVEL; Membrane-associating domain

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      109466546..109482134
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011541283.3 → XP_011539585.1  synaptophysin-like protein 2 isoform X1

      Conserved Domains (1) summary
      pfam01284
      Location:30 → 232
      MARVEL; Membrane-associating domain

    2. XM_011541285.2 → XP_011539587.1  synaptophysin-like protein 2 isoform X3

      See identical proteins and their annotated locations for XP_011539587.1

      UniProtKB/TrEMBL
      B4DYR7
      Conserved Domains (1) summary
      pfam01284
      Location:30 → 162
      MARVEL; Membrane-associating domain

    3. XM_011541284.3 → XP_011539586.1  synaptophysin-like protein 2 isoform X2

      Conserved Domains (1) summary
      pfam01284
      Location:30 → 162
      MARVEL; Membrane-associating domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      109499325..109514907
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336131.1 → XP_054192106.1  synaptophysin-like protein 2 isoform X1

    2. XM_054336132.1 → XP_054192107.1  synaptophysin-like protein 2 isoform X2

    3. XM_054336133.1 → XP_054192108.1  synaptophysin-like protein 2 isoform X3

      UniProtKB/TrEMBL
      B4DYR7

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001006603.1: Suppressed sequence

      Description
      NM_001006603.1: This RefSeq was permanently suppressed because it is primarily UTR sequence.

    2. NM_198280.1: Suppressed sequence

      Description
      NM_198280.1: This RefSeq record was removed by NCBI staff. Contact [email protected] for further information.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VXT5.1 GenPept UniProtKB/Swiss-Prot:Q5VXT5

    Gene LinkOut

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

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