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    SYPL1 synaptophysin like 1 [ Homo sapiens (human) ]

    Gene ID: 6856, updated on 5-Mar-2024

    Summary

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    Official Symbol
    SYPL1provided by HGNC
    Official Full Name
    synaptophysin like 1provided by HGNC
    Primary source
    HGNC:HGNC:11507
    See related
    Ensembl:ENSG00000008282 MIM:616665; AllianceGenome:HGNC:11507
    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
    SYPL; H-SP1
    Summary
    Predicted to be involved in chemical synaptic transmission. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 63.3), esophagus (RPKM 56.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    7q22.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (106090505..106112576, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (107405910..107427970, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (105730951..105753022, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ataxin 7 like 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:105470396-105471595 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105477786-105478643 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105478644-105479500 Neighboring gene ribosomal protein L13a pseudogene 16 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105494345-105495094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18524 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:105525198-105525381 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:105528806-105529002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:105596161-105596662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:105596663-105597162 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105602263-105603214 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105603215-105604166 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105631053-105631700 Neighboring gene uncharacterized LOC107986833 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18525 Neighboring gene cadherin related family member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:105671382-105671882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:105683076-105683576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:105698686-105699237 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26482 Neighboring gene Sharpr-MPRA regulatory region 14293 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105720431-105720970 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105720971-105721508 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:105751988-105752820 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18529 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26483 Neighboring gene DDB1 and CUL4 associated factor 13 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18531 Neighboring gene NANOG hESC enhancer GRCh37_chr7:105821183-105821690 Neighboring gene RNA, U6 small nuclear 392, pseudogene

    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. Evaluation of fecal SYPL1 as a diagnostic biomarker in colorectal cancer. Shu T, et al. Clin Biochem, 2022 May. PMID 35218739
    2. Serum SYPL1 is a promising diagnostic biomarker for colorectal cancer. Liu L, et al. Clin Chim Acta, 2020 Oct. PMID 32502495
    3. SYPL1 overexpression predicts poor prognosis of hepatocellular carcinoma and associates with epithelial-mesenchymal transition. Chen DH, et al. Oncol Rep, 2017 Sep. PMID 28731154
    4. Elevated synaptophysin I in the prefrontal cortex of human chronic alcoholics. Henriksson R, et al. Synapse, 2008 Nov. PMID 18720419, Free PMC Article
    5. Pantophysin is a phosphoprotein component of adipocyte transport vesicles and associates with GLUT4-containing vesicles. Brooks CC, et al. J Biol Chem, 2000 Jan 21. PMID 10636906

    See all (42) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Evaluation of fecal SYPL1 as a diagnostic biomarker in colorectal cancer.
      Title: Evaluation of fecal SYPL1 as a diagnostic biomarker in colorectal cancer.
    2. Serum SYPL1 is a promising diagnostic biomarker for colorectal cancer.
      Title: Serum SYPL1 is a promising diagnostic biomarker for colorectal cancer.
    3. SYPL1 overexpression predicts poor prognosis of HCC.
      Title: SYPL1 overexpression predicts poor prognosis of hepatocellular carcinoma and associates with epithelial-mesenchymal transition.
    4. A role is found for synaptophysin I in the enduring neuroplasticity in the prefrontal cortical glutamate circuitry that is associated with ethanol dependence.
      Title: Elevated synaptophysin I in the prefrontal cortex of human chronic alcoholics.
    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ46439

    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 chemical synaptic transmission TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in melanosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in secretory granule 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
    synaptophysin-like protein 1
    Names
    pantophysin

    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_001381910.1 → NP_001368839.1  synaptophysin-like protein 1 isoform c

      Status: VALIDATED

      Source sequence(s)
      AC005095
      Consensus CDS
      CCDS94175.1
      UniProtKB/TrEMBL
      A0A994J846, A8K865
      Related
      ENSP00000516340.1, ENST00000706299.1
      Conserved Domains (1) summary
      pfam01284
      Location:135 → 257
      MARVEL; Membrane-associating domain

    2. NM_001381911.1 → NP_001368840.1  synaptophysin-like protein 1 isoform d

      Status: VALIDATED

      Source sequence(s)
      AC005095
      UniProtKB/TrEMBL
      A8K865
      Conserved Domains (1) summary
      pfam01284
      Location:117 → 239
      MARVEL; Membrane-associating domain

    3. NM_001381912.1 → NP_001368841.1  synaptophysin-like protein 1 isoform e precursor

      Status: VALIDATED

      Source sequence(s)
      AC005095
      UniProtKB/TrEMBL
      A8K865
      Conserved Domains (1) summary
      pfam01284
      Location:87 → 209
      MARVEL; Membrane-associating domain

    4. NM_001381913.1 → NP_001368842.1  synaptophysin-like protein 1 isoform f

      Status: VALIDATED

      Source sequence(s)
      AC005095
      Conserved Domains (2) summary
      pfam01284
      Location:109 → 186
      MARVEL; Membrane-associating domain
      pfam03896
      Location:67 → 148
      TRAP_alpha; Translocon-associated protein (TRAP), alpha subunit

    5. NM_001381915.1 → NP_001368844.1  synaptophysin-like protein 1 isoform g

      Status: VALIDATED

      Source sequence(s)
      AC005095
      Conserved Domains (1) summary
      pfam01284
      Location:24 → 102
      MARVEL; Membrane-associating domain

    6. NM_001381916.1 → NP_001368845.1  synaptophysin-like protein 1 isoform h

      Status: VALIDATED

      Source sequence(s)
      AC005095

    7. NM_001381917.1 → NP_001368846.1  synaptophysin-like protein 1 isoform i precursor

      Status: VALIDATED

      Source sequence(s)
      AC005095
      Conserved Domains (1) summary
      pfam01284
      Location:1 → 81
      MARVEL; Membrane-associating domain

    8. NM_001381918.1 → NP_001368847.1  synaptophysin-like protein 1 isoform j

      Status: VALIDATED

      Description
      Transcript Variant: This variant (10), as well as variant 11, encodes isoform j.
      Source sequence(s)
      AC005095
      Consensus CDS
      CCDS94174.1
      UniProtKB/TrEMBL
      A0A994J5J4, A8K865

    9. NM_001381919.1 → NP_001368848.1  synaptophysin-like protein 1 isoform j

      Status: VALIDATED

      Description
      Transcript Variant: This variant (11), as well as variant 10, encodes isoform j.
      Source sequence(s)
      AC005095
      Consensus CDS
      CCDS94174.1
      UniProtKB/TrEMBL
      A0A994J5J4, A8K865
      Related
      ENSP00000516339.1, ENST00000706298.1

    10. NM_001381920.1 → NP_001368849.1  synaptophysin-like protein 1 isoform k

      Status: VALIDATED

      Description
      Transcript Variant: This variant (12), as well as variant 13, encodes isoform k.
      Source sequence(s)
      AC005095
      Consensus CDS
      CCDS94173.1
      UniProtKB/TrEMBL
      C9JYN0
      Conserved Domains (1) summary
      pfam01284
      Location:91 → 185
      MARVEL; Membrane-associating domain

    11. NM_001381921.1 → NP_001368850.1  synaptophysin-like protein 1 isoform k

      Status: VALIDATED

      Description
      Transcript Variant: This variant (13), as well as variant 12, encodes isoform k.
      Source sequence(s)
      AC005095
      Consensus CDS
      CCDS94173.1
      UniProtKB/TrEMBL
      C9JYN0
      Related
      ENSP00000419070.1, ENST00000470347.1
      Conserved Domains (1) summary
      pfam01284
      Location:91 → 185
      MARVEL; Membrane-associating domain

    12. NM_006754.5 → NP_006745.1  synaptophysin-like protein 1 isoform a

      See identical proteins and their annotated locations for NP_006745.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform a.
      Source sequence(s)
      AC005095
      Consensus CDS
      CCDS5736.1
      UniProtKB/Swiss-Prot
      A4D0R2, Q16563, Q96AR8
      UniProtKB/TrEMBL
      A4D0R1, A8K865
      Related
      ENSP00000011473.2, ENST00000011473.6
      Conserved Domains (1) summary
      pfam01284
      Location:109 → 231
      MARVEL; Membrane-associating domain

    13. NM_182715.4 → NP_874384.1  synaptophysin-like protein 1 isoform b

      See identical proteins and their annotated locations for NP_874384.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus, compared to isoform a.
      Source sequence(s)
      AC005095
      Consensus CDS
      CCDS47685.1
      UniProtKB/TrEMBL
      A8K865
      Related
      ENSP00000388336.2, ENST00000455385.7
      Conserved Domains (1) summary
      pfam01284
      Location:86 → 213
      MARVEL; Membrane-associating domain

    RNA

    1. NR_167729.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC005095
      Related
      ENST00000706297.1

    2. NR_167730.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC005095

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      106090505..106112576 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      107405910..107427970 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q16563.1 GenPept UniProtKB/Swiss-Prot:Q16563

    Gene LinkOut

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

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