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    SIDT2 SID1 transmembrane family member 2 [ Homo sapiens (human) ]

    Gene ID: 51092, updated on 5-Mar-2024

    Summary

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    Official Symbol
    SIDT2provided by HGNC
    Official Full Name
    SID1 transmembrane family member 2provided by HGNC
    Primary source
    HGNC:HGNC:24272
    See related
    Ensembl:ENSG00000149577 MIM:617551; AllianceGenome:HGNC:24272
    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
    CGI-40
    Summary
    Predicted to enable several functions, including AP-1 adaptor complex binding activity; AP-2 adaptor complex binding activity; and RNA transmembrane transporter activity. Involved in RNA transport. Located in lysosomal membrane and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in stomach (RPKM 22.3), prostate (RPKM 21.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SIDT2 in Genome Data Viewer
    Location:
    11q23.3
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (117178743..117197442)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (117194038..117212742)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (117049459..117068158)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:117008445-117009330 Neighboring gene proprotein convertase subtilisin/kexin type 7 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5565 Neighboring gene platelet activating factor acetylhydrolase 1b catalytic subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5567 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:117052141-117052936 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117058437-117058937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5568 Neighboring gene uncharacterized LOC100652768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117066811-117067310 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:117068643-117069306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117072631-117073294 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:117076473-117077103 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:117077104-117077734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:117077735-117078365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117079206-117079706 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117079707-117080207 Neighboring gene transgelin Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:117088224-117089423 Neighboring gene proprotein convertase subtilisin/kexin type 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117089878-117090378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5570 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3935 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117106511-117107012 Neighboring gene Sharpr-MPRA regulatory region 1788 Neighboring gene ring finger protein 214 Neighboring gene small Cajal body-specific RNA 11

    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. Structural insight into the human SID1 transmembrane family member 2 reveals its lipid hydrolytic activity. Qian D, et al. Nat Commun, 2023 Jun 15. PMID 37322007, Free PMC Article
    2. [Lysosomal membrane protein Sidt2 knockout induces apoptosis of human hepatocytes in vitro independent of the autophagy-lysosomal pathway]. Xu J, et al. Nan Fang Yi Ke Da Xue Xue Bao, 2023 Apr 20. PMID 37202201, Free PMC Article
    3. Pathology-associated change in levels and localization of SIDT2 in postmortem brains of Parkinson's disease and dementia with Lewy bodies patients. Fujiwara Y, et al. Neurochem Int, 2022 Jan. PMID 34800582
    4. [Lysosomal membrane protein Sidt2 deletion impairs autophagy in human hepatocytes]. Geng M, et al. Nan Fang Yi Ke Da Xue Xue Bao, 2021 Aug 20. PMID 34549712, Free PMC Article
    5. Genome-Wide Association Study Identifies a Functional SIDT2 Variant Associated With HDL-C (High-Density Lipoprotein Cholesterol) Levels and Premature Coronary Artery Disease. León-Mimila P, et al. Arterioscler Thromb Vasc Biol, 2021 Sep. PMID 34233476, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SIDT2 Associates with Apolipoprotein A1 (ApoA1) and Facilitates ApoA1 Secretion in Hepatocytes.
      Title: SIDT2 Associates with Apolipoprotein A1 (ApoA1) and Facilitates ApoA1 Secretion in Hepatocytes.
    2. Structural insight into the human SID1 transmembrane family member 2 reveals its lipid hydrolytic activity.
      Title: Structural insight into the human SID1 transmembrane family member 2 reveals its lipid hydrolytic activity.
    3. [Lysosomal membrane protein Sidt2 knockout induces apoptosis of human hepatocytes in vitro independent of the autophagy-lysosomal pathway].
      Title: [Lysosomal membrane protein Sidt2 knockout induces apoptosis of human hepatocytes in vitro independent of the autophagy-lysosomal pathway].
    4. Interaction between SIDT2 and ABCA1 Variants with Nutrients on HDL-c Levels in Mexican Adults.
      Title: Interaction between SIDT2 and ABCA1 Variants with Nutrients on HDL-c Levels in Mexican Adults.
    5. Long non-coding RNA LIFR-AS1 suppressed the proliferation, angiogenesis, migration and invasion of papillary thyroid cancer cells via the miR-31-5p/SIDT2 axis.
      Title: Long non-coding RNA LIFR-AS1 suppressed the proliferation, angiogenesis, migration and invasion of papillary thyroid cancer cells via the miR-31-5p/SIDT2 axis.
    6. Pathology-associated change in levels and localization of SIDT2 in postmortem brains of Parkinson's disease and dementia with Lewy bodies patients.
      Title: Pathology-associated change in levels and localization of SIDT2 in postmortem brains of Parkinson's disease and dementia with Lewy bodies patients.
    7. [Lysosomal membrane protein Sidt2 deletion impairs autophagy in human hepatocytes].
      Title: [Lysosomal membrane protein Sidt2 deletion impairs autophagy in human hepatocytes].
    8. Genome-Wide Association Study Identifies a Functional SIDT2 Variant Associated With HDL-C (High-Density Lipoprotein Cholesterol) Levels and Premature Coronary Artery Disease.
      Title: Genome-Wide Association Study Identifies a Functional SIDT2 Variant Associated With HDL-C (High-Density Lipoprotein Cholesterol) Levels and Premature Coronary Artery Disease.
    9. The Variant rs1784042 of the SIDT2 Gene is Associated with Metabolic Syndrome through Low HDL-c Levels in a Mexican Population.
      Title: The Variant rs1784042 of the SIDT2 Gene is Associated with Metabolic Syndrome through Low HDL-c Levels in a Mexican Population.
    10. this study found an association between metabolic syndrome and an intronic SNP pair, rs7107152 and rs1242229, in SIDT2 gene at 11q23.3.
      Title: Multiple genotype-phenotype association study reveals intronic variant pair on SIDT2 associated with metabolic syndrome in a Korean population.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    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

    Potential readthrough

    Included gene: TAGLN

    Homology

    Clone Names

    • FLJ90656, DKFZp686L17253

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables AP-1 adaptor complex binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables AP-2 adaptor complex binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables double-stranded RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleic acid transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in RNA transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in RNA transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cell morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glucose homeostasis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of insulin secretion involved in cellular response to glucose stimulus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to glucose IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in type B pancreatic cell development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in type B pancreatic cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SID1 transmembrane family member 2

    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_001040455.2 → NP_001035545.1  SID1 transmembrane family member 2 precursor

      See identical proteins and their annotated locations for NP_001035545.1

      Status: VALIDATED

      Source sequence(s)
      AP005018, AY358442
      Consensus CDS
      CCDS31682.1
      UniProtKB/Swiss-Prot
      Q8NBJ9, Q8NBY7, Q9Y357
      UniProtKB/TrEMBL
      L7X6U2
      Related
      ENSP00000314023.4, ENST00000324225.9
      Conserved Domains (1) summary
      pfam13965
      Location:172 → 832
      SID-1_RNA_chan; dsRNA-gated channel SID-1

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      117178743..117197442
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      117194038..117212742
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_015996.1: Suppressed sequence

      Description
      NM_015996.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NBJ9.2 GenPept UniProtKB/Swiss-Prot:Q8NBJ9

    Gene LinkOut

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

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