Aliases for SIDT2 Gene

Aliases for SIDT2 Gene

  • SID1 Transmembrane Family Member 2 2 3 4 5
  • CGI-40 2 3
  • SID1 Transmembrane Family, Member 2 2
  • SIDT2 5

External Ids for SIDT2 Gene

Previous GeneCards Identifiers for SIDT2 Gene

  • GC11P116554
  • GC11P117049
  • GC11P112982

Summaries for SIDT2 Gene

GeneCards Summary for SIDT2 Gene

SIDT2 (SID1 Transmembrane Family Member 2) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include RNA transmembrane transporter activity. An important paralog of this gene is SIDT1.

UniProtKB/Swiss-Prot Summary for SIDT2 Gene

  • Mediates the translocation of RNA and DNA across the lysosomal membrane during RNA and DNA autophagy (RDA), a process in which RNA or DNA is directly imported into lysosomes in an ATP-dependent manner, and degraded (PubMed:27046251, PubMed:27846365). Involved in the uptake of single-stranded oligonucleotides by living cells, a process called gymnosis (PubMed:28277980). In vitro, mediates the uptake of linear DNA more efficiently than that of circular DNA, but exhibits similar uptake efficacy toward RNA and DNA. Binds long double-stranded RNA (dsRNA) (500 - 700 base pairs), but not dsRNA shorter than 100 bp (By similarity).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SIDT2 Gene

Genomics for SIDT2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SIDT2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SIDT2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SIDT2

Top Transcription factor binding sites by QIAGEN in the SIDT2 gene promoter:
  • AML1a
  • AP-1
  • CUTL1
  • HFH-1
  • Sp1
  • STAT5B
  • TBP

Genomic Locations for SIDT2 Gene

Latest Assembly
chr11:117,178,736-117,197,445
(GRCh38/hg38)
Size:
18,710 bases
Orientation:
Plus strand

Previous Assembly
chr11:117,049,459-117,068,158
(GRCh37/hg19 by Entrez Gene)
Size:
18,700 bases
Orientation:
Plus strand

chr11:117,049,449-117,068,160
(GRCh37/hg19 by Ensembl)
Size:
18,712 bases
Orientation:
Plus strand

Genomic View for SIDT2 Gene

Genes around SIDT2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SIDT2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SIDT2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SIDT2 Gene

Proteins for SIDT2 Gene

  • Protein details for SIDT2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NBJ9-SIDT2_HUMAN
    Recommended name:
    SID1 transmembrane family member 2
    Protein Accession:
    Q8NBJ9
    Secondary Accessions:
    • Q8NBY7
    • Q9Y357

    Protein attributes for SIDT2 Gene

    Size:
    832 amino acids
    Molecular mass:
    94454 Da
    Quaternary structure:
    • Interacts with adapter protein complex 1 (AP-1) and AP-2, but not AP-3 and AP-4 (By similarity). Interacts with LAMP2 (PubMed:27046251).
    SequenceCaution:
    • Sequence=BAC11427.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAC11641.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for SIDT2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SIDT2 Gene

Post-translational modifications for SIDT2 Gene

  • Glycosylated.
  • Glycosylation at Asn27, Asn54, Asn60, Asn123, Asn141, Asn165, Asn476, Asn496, Asn572, and Asn603
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SIDT2 Gene

Domains & Families for SIDT2 Gene

Gene Families for SIDT2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for SIDT2 Gene

InterPro:

Suggested Antigen Peptide Sequences for SIDT2 Gene

GenScript: Design optimal peptide antigens:
  • SIDT2 protein (Q24JR2_HUMAN)
  • SID1 transmembrane family member 2 (SIDT2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8NBJ9

UniProtKB/Swiss-Prot:

SIDT2_HUMAN :
  • Belongs to the SID1 family.
Family:
  • Belongs to the SID1 family.
genes like me logo Genes that share domains with SIDT2: view

Function for SIDT2 Gene

Molecular function for SIDT2 Gene

UniProtKB/Swiss-Prot Function:
Mediates the translocation of RNA and DNA across the lysosomal membrane during RNA and DNA autophagy (RDA), a process in which RNA or DNA is directly imported into lysosomes in an ATP-dependent manner, and degraded (PubMed:27046251, PubMed:27846365). Involved in the uptake of single-stranded oligonucleotides by living cells, a process called gymnosis (PubMed:28277980). In vitro, mediates the uptake of linear DNA more efficiently than that of circular DNA, but exhibits similar uptake efficacy toward RNA and DNA. Binds long double-stranded RNA (dsRNA) (500 - 700 base pairs), but not dsRNA shorter than 100 bp (By similarity).

Phenotypes From GWAS Catalog for SIDT2 Gene

Gene Ontology (GO) - Molecular Function for SIDT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IEA --
GO:0003725 double-stranded RNA binding IEA,IBA 21873635
GO:0035612 AP-2 adaptor complex binding IEA,ISS --
GO:0035650 AP-1 adaptor complex binding IEA,ISS --
genes like me logo Genes that share ontologies with SIDT2: view
genes like me logo Genes that share phenotypes with SIDT2: view

Animal Models for SIDT2 Gene

MGI Knock Outs for SIDT2:

Animal Models for research

  • Taconic Biosciences Mouse Models for SIDT2

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SIDT2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SIDT2 Gene

Localization for SIDT2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SIDT2 Gene

Lysosome membrane. Multi-pass membrane protein. Cell membrane. Note=Mainly localizes to lysosomes and only partly to the plasma membrane (PubMed:28277980). Lysosomal localization is required for SIDT2-mediated intracellular degradation of endogenous RNA (By similarity). {ECO:0000250 UniProtKB:Q8CIF6, ECO:0000269 PubMed:28277980}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SIDT2 gene
Compartment Confidence
plasma membrane 5
lysosome 5
extracellular 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SIDT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IEA,IDA 28277980
GO:0005765 lysosomal membrane IEA,IDA 17897319
GO:0005886 plasma membrane IEA,IDA 28277980
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SIDT2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SIDT2 Gene

Pathways & Interactions for SIDT2 Gene

PathCards logo

SuperPathways for SIDT2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SIDT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000902 cell morphogenesis IEA --
GO:0003323 type B pancreatic cell development IEA --
GO:0006401 RNA catabolic process IEA,ISS --
GO:0009749 response to glucose IEA --
GO:0042593 glucose homeostasis IEA --
genes like me logo Genes that share ontologies with SIDT2: view

No data available for Pathways by source and SIGNOR curated interactions for SIDT2 Gene

Drugs & Compounds for SIDT2 Gene

No Compound Related Data Available

Transcripts for SIDT2 Gene

mRNA/cDNA for SIDT2 Gene

2 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
20 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SIDT2

Alternative Splicing Database (ASD) splice patterns (SP) for SIDT2 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b · 16c · 16d ^ 17a ·
SP1: - - - - -
SP2: - - - - - -
SP3: - -
SP4: - - - -
SP5:
SP6: - -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12: - -
SP13:

ExUns: 17b ^ 18a · 18b ^ 19a · 19b ^ 20a · 20b ^ 21a · 21b · 21c ^ 22 ^ 23 ^ 24a · 24b ^ 25 ^ 26a · 26b ^ 27 ^ 28a · 28b · 28c
SP1: - - - -
SP2: - - - -
SP3:
SP4:
SP5: -
SP6:
SP7: - - -
SP8:
SP9: - -
SP10:
SP11:
SP12:
SP13:

Relevant External Links for SIDT2 Gene

GeneLoc Exon Structure for
SIDT2

Expression for SIDT2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SIDT2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SIDT2 Gene

This gene is overexpressed in Pancreas (24.7), Placenta (15.2), Testis (15.0), and Ovary (9.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SIDT2 Gene



Protein tissue co-expression partners for SIDT2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SIDT2

SOURCE GeneReport for Unigene cluster for SIDT2 Gene:

Hs.712144

Evidence on tissue expression from TISSUES for SIDT2 Gene

  • Nervous system(4.1)
  • Stomach(2.4)
  • Liver(2.2)
  • Muscle(2.2)
  • Pancreas(2)
genes like me logo Genes that share expression patterns with SIDT2: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SIDT2 Gene

Orthologs for SIDT2 Gene

This gene was present in the common ancestor of animals.

Orthologs for SIDT2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SIDT2 29 30
  • 99.44 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SIDT2 29 30
  • 91.34 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SIDT2 29 30
  • 91.12 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Sidt2 29 16 30
  • 89.82 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sidt2 29
  • 89.22 (n)
Oppossum
(Monodelphis domestica)
Mammalia SIDT2 30
  • 89 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SIDT2 29 30
  • 80.02 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SIDT2 30
  • 84 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sidt2 29
  • 67.96 (n)
Str.18477 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.14690 29
Zebrafish
(Danio rerio)
Actinopterygii sidt2 30
  • 69 (a)
OneToOne
wufc73a07 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6494 29
Worm
(Caenorhabditis elegans)
Secernentea tag-130 29
  • 46.57 (n)
chup-1 30
  • 35 (a)
ManyToMany
sid-1 30
  • 21 (a)
ManyToMany
Species where no ortholog for SIDT2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SIDT2 Gene

ENSEMBL:
Gene Tree for SIDT2 (if available)
TreeFam:
Gene Tree for SIDT2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SIDT2: view image
Alliance of Genome Resources:
Additional Orthologs for SIDT2

Paralogs for SIDT2 Gene

Paralogs for SIDT2 Gene

(1) SIMAP similar genes for SIDT2 Gene using alignment to 11 proteins:

  • SIDT2_HUMAN
  • C9JBG5_HUMAN
  • E9PMC3_HUMAN
  • E9PME7_HUMAN
  • E9PPN9_HUMAN
  • F5H8L4_HUMAN
  • G3V172_HUMAN
  • H0YEI3_HUMAN
  • L7X6U2_HUMAN
  • Q1RMF0_HUMAN
  • Q24JR2_HUMAN
genes like me logo Genes that share paralogs with SIDT2: view

Variants for SIDT2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SIDT2 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
rs12285035 Benign: not provided 117,192,273(+) C/Tp.Thr631Met
NM_001040455.2(SIDT2):c.1892C>T (p.Thr631Met)
MISSENSE
rs12285062 Benign: not provided 117,192,304(+) C/T
NM_001040455.2(SIDT2):c.1923C>T (p.His641=)
SYNONYMOUS
rs143730905 Benign: not provided 117,186,578(+) A/G
NM_001040455.2(SIDT2):c.963-6A>G
INTRON
rs17120425 -- p.Val636Ile

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SIDT2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SIDT2 Gene

Variant ID Type Subtype PubMed ID
dgv2186n54 CNV loss 21841781
dgv730n106 OTHER inversion 24896259
nsv1078301 OTHER inversion 25765185
nsv518908 CNV loss 19592680
nsv524270 CNV loss 19592680
nsv7223 OTHER inversion 18451855

Variation tolerance for SIDT2 Gene

Residual Variation Intolerance Score: 41.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.09; 60.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SIDT2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SIDT2
Leiden Open Variation Database (LOVD)
SIDT2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SIDT2 Gene

Disorders for SIDT2 Gene

Additional Disease Information for SIDT2

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for SIDT2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SIDT2 Gene

Publications for SIDT2 Gene

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4
  2. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai CH … Lin W (Genome research 2000) 2 3 4
  3. Lysosomal membrane protein SIDT2 mediates the direct uptake of DNA by lysosomes. (PMID: 27846365) Aizawa S … Kabuta T (Autophagy 2017) 3 4
  4. SIDT2 mediates gymnosis, the uptake of naked single-stranded oligonucleotides into living cells. (PMID: 28277980) Takahashi M … Kabuta T (RNA biology 2017) 3 4
  5. Lysosomal putative RNA transporter SIDT2 mediates direct uptake of RNA by lysosomes. (PMID: 27046251) Aizawa S … Kabuta T (Autophagy 2016) 3 4

Products for SIDT2 Gene

Sources for SIDT2 Gene