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SYPL2 synaptophysin like 2 [ Homo sapiens (human) ]

Gene ID: 284612, updated on 28-Oct-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, Oct 2024]
Expression
Broad expression in kidney (RPKM 4.9), testis (RPKM 4.8) and 20 other tissues See more
Orthologs
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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 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)

Genotypes

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 info@ncbi.nlm.nih.gov for further information.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5VXT5.1 GenPept UniProtKB/Swiss-Prot:Q5VXT5

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