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

Gene ID: 51092, updated on 2-Nov-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, Nov 2024]
Expression
Ubiquitous expression in stomach (RPKM 22.3), prostate (RPKM 21.9) and 25 other tissues See more
Orthologs
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (117178743..117197442)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (117194038..117212742)
RS_2024_09 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 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 (32) 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 Variation Viewer (GRCh37.p13)

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_2024_08

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.

Chemical Information
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