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    SYNPR synaptoporin [ Homo sapiens (human) ]

    Gene ID: 132204, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SYNPRprovided by HGNC
    Official Full Name
    synaptoporinprovided by HGNC
    Primary source
    HGNC:HGNC:16507
    See related
    Ensembl:ENSG00000163630 AllianceGenome:HGNC:16507
    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
    SPO
    Summary
    Predicted to be involved in modulation of chemical synaptic transmission. Predicted to be located in membrane; neuron projection; and synaptic vesicle. Predicted to be active in hippocampal mossy fiber to CA3 synapse and synaptic vesicle membrane. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Restricted expression toward brain (RPKM 14.4) See more
    Orthologs
    mouse all
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    Genomic context

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    See SYNPR in Genome Data Viewer
    Location:
    3p14.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (63200604..63616924)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (63244200..63660530)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (63263984..63602600)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:63082201-63082700 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:63082748-63083248 Neighboring gene long intergenic non-protein coding RNA 698 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:63121623-63122228 Neighboring gene keratin 8 pseudogene 35 Neighboring gene NANOG hESC enhancer GRCh37_chr3:63152724-63153255 Neighboring gene ubiquitin like 5 pseudogene 3 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:63329277-63329919 Neighboring gene NANOG hESC enhancer GRCh37_chr3:63429870-63430414 Neighboring gene SYNPR antisense RNA 1 Neighboring gene RNA, 5S ribosomal pseudogene 134 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:63562463-63562990 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:63631069-63631622 Neighboring gene NANOG hESC enhancer GRCh37_chr3:63637673-63638197 Neighboring gene VISTA enhancer hs1387 Neighboring gene uncharacterized LOC105377119 Neighboring gene sentan, cilia apical structure protein

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Tyrosine nitration of a synaptic protein synaptophysin contributes to amyloid beta-peptide-induced cholinergic dysfunction. Tran MH, et al. Mol Psychiatry, 2003 Apr. PMID 12740598
    2. Expression of the synaptophysin gene family is not restricted to neuronal and neuroendocrine differentiation in rat and human. Leube RE. Differentiation, 1994 May. PMID 8034131
    3. Cloning and sequence analysis of the human cDNA encoding the synaptoporin (delta), a highly conservative synaptic vesicle protein. Dai J, et al. Mol Biol Rep, 2003 Sep. PMID 12974474
    4. Synaptic vesicle protein synaptoporin is differently expressed by subpopulations of mouse hippocampal neurons. Singec I, et al. J Comp Neurol, 2002 Oct 14. PMID 12271488
    5. Genome-wide association study of maternal and inherited effects on left-sided cardiac malformations. Mitchell LE, et al. Hum Mol Genet, 2015 Jan 1. PMID 25138779, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Results from genome-wide association studies identify synaptoporin gene as one of the three susceptibility loci candidate for congenital left-sided lesions.
      Title: Genome-wide association study of maternal and inherited effects on left-sided cardiac malformations.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. cloning and characterization of the human cDNA that encodes the human homologue of synaptoporin
      Title: Cloning and sequence analysis of the human cDNA encoding the synaptoporin (delta), a highly conservative synaptic vesicle protein.
    4. Tyrosine nitration of synaptophysin is related to Amyloid beta induced impairment of acetylcholine release.
      Title: Tyrosine nitration of a synaptic protein synaptophysin contributes to amyloid beta-peptide-induced cholinergic dysfunction.
    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 maternal and inherited effects on left-sided cardiac malformations.
    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

    • MGC26651, DKFZp686G0883

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in neuron projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    synaptoporin

    NCBI Reference Sequences (RefSeq)

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    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_001130003.2 → NP_001123475.1  synaptoporin isoform 1

      See identical proteins and their annotated locations for NP_001123475.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC099056, AC099545, AC104436
      Consensus CDS
      CCDS46859.1
      UniProtKB/TrEMBL
      B3KVD8
      Related
      ENSP00000418994.1, ENST00000478300.6
      Conserved Domains (1) summary
      pfam01284
      Location:16 → 216
      MARVEL; Membrane-associating domain

    2. NM_144642.5 → NP_653243.1  synaptoporin isoform 2 precursor

      See identical proteins and their annotated locations for NP_653243.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate exon in the 5' CDS, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AC104436, AF411860, AL834457, DA505318
      Consensus CDS
      CCDS46860.1
      UniProtKB/Swiss-Prot
      B2R675, G5E9W4, Q8TBG9
      UniProtKB/TrEMBL
      B3KVD8
      Related
      ENSP00000295894.5, ENST00000295894.9
      Conserved Domains (1) summary
      pfam01284
      Location:73 → 196
      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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      63200604..63616924
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017005731.1 → XP_016861220.1  synaptoporin isoform X1

      UniProtKB/TrEMBL
      B3KVD8

    2. XM_017005732.3 → XP_016861221.1  synaptoporin isoform X2

      UniProtKB/TrEMBL
      C9J0A2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      63244200..63660530
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054345290.1 → XP_054201265.1  synaptoporin isoform X1

      UniProtKB/TrEMBL
      B3KVD8

    2. XM_054345291.1 → XP_054201266.1  synaptoporin isoform X2

      UniProtKB/TrEMBL
      C9J0A2
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TBG9.1 GenPept UniProtKB/Swiss-Prot:Q8TBG9

    Gene LinkOut

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

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