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    SYS1 SYS1 golgi trafficking protein [ Homo sapiens (human) ]

    Gene ID: 90196, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SYS1provided by HGNC
    Official Full Name
    SYS1 golgi trafficking proteinprovided by HGNC
    Primary source
    HGNC:HGNC:16162
    See related
    Ensembl:ENSG00000204070 MIM:612979; AllianceGenome:HGNC:16162
    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
    C20orf169; dJ453C12.4; dJ453C12.4.1
    Summary
    SYS1 forms a complex with ADP-ribosylation factor-related protein ARFRP1 (MIM 604699) and targets ARFRP1 to the Golgi apparatus (Behnia et al., 2004 [PubMed 15077113]).[supplied by OMIM, Aug 2009]
    Expression
    Ubiquitous expression in thyroid (RPKM 8.9), ovary (RPKM 6.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SYS1 in Genome Data Viewer
    Location:
    20q13.12
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (45361949..45376798)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (47097832..47112667)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (43990589..44005438)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene tRNA-Val (anticodon CAC) 14-1 Neighboring gene syndecan 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:43971073-43971967 Neighboring gene uncharacterized LOC124904914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17947 Neighboring gene SYS1-DBNDD2 readthrough (NMD candidate) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12957 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17950 Neighboring gene TP53 target 5 Neighboring gene NADH:ubiquinone oxidoreductase subunit B4 pseudogene 10 Neighboring gene uncharacterized LOC107985404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44035517-44036066 Neighboring gene dysbindin domain containing 2

    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. Targeting of the Arf-like GTPase Arl3p to the Golgi requires N-terminal acetylation and the membrane protein Sys1p. Behnia R, et al. Nat Cell Biol, 2004 May. PMID 15077113
    2. A Novel Interacting Protein SERP1 Regulates the N-Linked Glycosylation and Function of GLP-1 Receptor in the Liver. Xiao Y, et al. J Cell Biochem, 2017 Nov. PMID 28597972
    3. Comparative Host Interactomes of the SARS-CoV-2 Nonstructural Protein 3 and Human Coronavirus Homologs. Almasy KM, et al. Mol Cell Proteomics, 2021. PMID 34186245, Free PMC Article
    4. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Otsuki T, et al. DNA Res, 2005. PMID 16303743
    5. Receptor-mediated clustering of FIP200 bypasses the role of LC3 lipidation in autophagy. Ohnstad AE, et al. EMBO J, 2020 Dec 15. PMID 33226137, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough SYS1-DBNDD2

    Readthrough gene: SYS1-DBNDD2, Included gene: DBNDD2

    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 Golgi to endosome transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in Golgi to plasma membrane protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein localization to Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in Golgi membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in trans-Golgi network membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    protein SYS1 homolog
    Names
    SYS1 Golgi-localized integral membrane protein homolog

    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_001099791.3 → NP_001093261.1  protein SYS1 homolog isoform b

      See identical proteins and their annotated locations for NP_001093261.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate 3' exon and thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (b) has a distinct and shorter C-terminus, compared to isoform a.
      Source sequence(s)
      AK172738, AL021578, H09823
      Consensus CDS
      CCDS56192.1
      UniProtKB/Swiss-Prot
      Q8N2H4
      Related
      ENSP00000416506.1, ENST00000426004.5
      Conserved Domains (1) summary
      pfam09801
      Location:5 → 76
      SYS1; Integral membrane protein S linking to the trans Golgi network

    2. NM_001197129.2 → NP_001184058.1  protein SYS1 homolog isoform a

      See identical proteins and their annotated locations for NP_001184058.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode the same isoform (a).
      Source sequence(s)
      AL591714, BI820996
      Consensus CDS
      CCDS13351.1
      UniProtKB/Swiss-Prot
      C9JFB3, E1P620, Q5QPU7, Q8N2H4, Q96SD8, Q9BQZ2, Q9BQZ4, Q9H1F7
      Related
      ENSP00000361812.1, ENST00000372727.5
      Conserved Domains (1) summary
      pfam09801
      Location:5 → 148
      SYS1; Integral membrane protein S linking to the trans Golgi network

    3. NM_033542.4 → NP_291020.1  protein SYS1 homolog isoform a

      See identical proteins and their annotated locations for NP_291020.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant encodes the longer isoform (a). Both variants 1 and 3 encode the same isoform.
      Source sequence(s)
      AL591714, DA526637
      Consensus CDS
      CCDS13351.1
      UniProtKB/Swiss-Prot
      C9JFB3, E1P620, Q5QPU7, Q8N2H4, Q96SD8, Q9BQZ2, Q9BQZ4, Q9H1F7
      Related
      ENSP00000243918.5, ENST00000243918.10
      Conserved Domains (1) summary
      pfam09801
      Location:5 → 148
      SYS1; Integral membrane protein S linking to the trans Golgi network

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      45361949..45376798
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      47097832..47112667
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N2H4.1 GenPept UniProtKB/Swiss-Prot:Q8N2H4

    Gene LinkOut

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

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