Aliases for SDE2 Gene

Aliases for SDE2 Gene

  • SDE2 Telomere Maintenance Homolog 2 3 5
  • Replication Stress Response Regulator SDE2 3 4
  • C1orf55 3 4
  • SDE2 Telomere Maintenance Homolog (S. Pombe) 2
  • Chromosome 1 Open Reading Frame 55 2
  • UPF0667 Protein C1orf55 3
  • Protein SDE2 Homolog 3
  • DJ671D7.1 3
  • FLJ35382 2
  • SDE2 5

External Ids for SDE2 Gene

Previous HGNC Symbols for SDE2 Gene

  • C1orf55

Previous GeneCards Identifiers for SDE2 Gene

  • GC01M226171

Summaries for SDE2 Gene

GeneCards Summary for SDE2 Gene

SDE2 (SDE2 Telomere Maintenance Homolog) is a Protein Coding gene. An important paralog of this gene is SF3A3.

UniProtKB/Swiss-Prot Summary for SDE2 Gene

  • Involved in both DNA replication and cell cycle control (PubMed:27906959). Unprocessed SDE2 interacts with PCNA via its PIP-box. The interaction with PCNA prevents monoubiquitination of the latter thereby inhibiting translesion DNA synthesis. The binding of SDE2 to PCNA also leads to processing of SDE2 by an unidentified deubiquitinating enzyme, cleaving off the N-terminal ubiquitin-like domain. The resulting mature SDE2 is degraded by the DCX(DTL) complex in a cell cycle- and DNA damage dependent manner (PubMed:27906959). Binding of SDE2 to PCNA is necessary to counteract damage due to ultraviolet light induced replication stress. The complete degradation of SDE2 is necessary to allow S-phase progression (PubMed:27906959).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SDE2 Gene

Genomics for SDE2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SDE2 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 SDE2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SDE2

Genomic Locations for SDE2 Gene

Latest Assembly
chr1:225,982,702-225,999,343
(GRCh38/hg38)
Size:
16,642 bases
Orientation:
Minus strand

Previous Assembly
chr1:226,170,403-226,187,044
(GRCh37/hg19 by Entrez Gene)
Size:
16,642 bases
Orientation:
Minus strand

chr1:226,170,403-226,187,032
(GRCh37/hg19 by Ensembl)
Size:
16,630 bases
Orientation:
Minus strand

Genomic View for SDE2 Gene

Genes around SDE2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SDE2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SDE2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SDE2 Gene

Proteins for SDE2 Gene

  • Protein details for SDE2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6IQ49-SDE2_HUMAN
    Recommended name:
    Replication stress response regulator SDE2
    Protein Accession:
    Q6IQ49
    Secondary Accessions:
    • A8K4P3
    • Q5TD36
    • Q6ZS26
    • Q8NAG7

    Protein attributes for SDE2 Gene

    Size:
    451 amino acids
    Molecular mass:
    49742 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for SDE2 Gene

    Alternative splice isoforms for SDE2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SDE2 Gene

Post-translational modifications for SDE2 Gene

  • The protein is cleaved at Gly-77 by a deubiquitinating enzyme to form the active SDE2.
  • Both SDE2-UBL and the mature SDE2 are polyubiquitinated.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SDE2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SDE2 Gene

Domains & Families for SDE2 Gene

Gene Families for SDE2 Gene

Protein Domains for SDE2 Gene

InterPro:

Suggested Antigen Peptide Sequences for SDE2 Gene

GenScript: Design optimal peptide antigens:
  • UPF0667 protein C1orf55 (CA055_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6IQ49

UniProtKB/Swiss-Prot:

SDE2_HUMAN :
  • The PIP-box (PCNA interacting peptide) motif mediates both the interaction with PCNA and cleavage of the SDE2 precursor by a deubiquitinating enzyme.
  • Belongs to the SDE2 family.
Domain:
  • The PIP-box (PCNA interacting peptide) motif mediates both the interaction with PCNA and cleavage of the SDE2 precursor by a deubiquitinating enzyme.
  • The SAP domain is necessary for specific binding to DNA.
  • The propeptide displays a ubiquitin-like fold.
Family:
  • Belongs to the SDE2 family.
genes like me logo Genes that share domains with SDE2: view

Function for SDE2 Gene

Molecular function for SDE2 Gene

UniProtKB/Swiss-Prot Function:
Involved in both DNA replication and cell cycle control (PubMed:27906959). Unprocessed SDE2 interacts with PCNA via its PIP-box. The interaction with PCNA prevents monoubiquitination of the latter thereby inhibiting translesion DNA synthesis. The binding of SDE2 to PCNA also leads to processing of SDE2 by an unidentified deubiquitinating enzyme, cleaving off the N-terminal ubiquitin-like domain. The resulting mature SDE2 is degraded by the DCX(DTL) complex in a cell cycle- and DNA damage dependent manner (PubMed:27906959). Binding of SDE2 to PCNA is necessary to counteract damage due to ultraviolet light induced replication stress. The complete degradation of SDE2 is necessary to allow S-phase progression (PubMed:27906959).

Phenotypes From GWAS Catalog for SDE2 Gene

Gene Ontology (GO) - Molecular Function for SDE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003684 damaged DNA binding IDA 27906959
GO:0005515 protein binding IPI 24981860
genes like me logo Genes that share ontologies with SDE2: view
genes like me logo Genes that share phenotypes with SDE2: view

miRNA for SDE2 Gene

miRTarBase miRNAs that target SDE2

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SDE2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SDE2 Gene

Localization for SDE2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SDE2 Gene

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 SDE2 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 4
golgi apparatus 4
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
extracellular 0
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (4)
  • Cytosol (3)
  • Plasma membrane (3)
  • Golgi apparatus (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SDE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 27906959
GO:0005654 nucleoplasm IDA --
GO:0005794 Golgi apparatus IDA --
GO:0005829 cytosol IDA --
GO:0005886 plasma membrane IDA --
genes like me logo Genes that share ontologies with SDE2: view

Pathways & Interactions for SDE2 Gene

PathCards logo

SuperPathways for SDE2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SDE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006260 DNA replication IEA --
GO:0007049 cell cycle IEA --
GO:0016485 protein processing IDA 27906959
GO:0016567 protein ubiquitination IDA 27906959
GO:0034644 cellular response to UV IDA 27906959
genes like me logo Genes that share ontologies with SDE2: view

No data available for Pathways by source and SIGNOR curated interactions for SDE2 Gene

Drugs & Compounds for SDE2 Gene

No Compound Related Data Available

Transcripts for SDE2 Gene

mRNA/cDNA for SDE2 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
1 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 SDE2

Alternative Splicing Database (ASD) splice patterns (SP) for SDE2 Gene

No ASD Table

Relevant External Links for SDE2 Gene

GeneLoc Exon Structure for
SDE2

Expression for SDE2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SDE2 Gene

Protein differential expression in normal tissues from HIPED for SDE2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (20.0), Lymph node (11.8), and Heart (9.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SDE2 Gene



Protein tissue co-expression partners for SDE2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SDE2

SOURCE GeneReport for Unigene cluster for SDE2 Gene:

Hs.520192

Evidence on tissue expression from TISSUES for SDE2 Gene

  • Nervous system(4.3)
  • Muscle(4.3)
  • Liver(4.3)
genes like me logo Genes that share expression patterns with SDE2: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SDE2 Gene

Orthologs for SDE2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SDE2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SDE2 29
  • 99.48 (n)
C1ORF55 30
  • 99 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia SDE2 29 30
  • 84.63 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SDE2 29 30
  • 77.13 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Sde2 29 16 30
  • 76.48 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sde2 29
  • 74.49 (n)
Oppossum
(Monodelphis domestica)
Mammalia SDE2 30
  • 60 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SDE2 30
  • 56 (a)
OneToOne
Chicken
(Gallus gallus)
Aves C3H1ORF55 29
  • 59.34 (n)
SDE2 30
  • 54 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SDE2 30
  • 56 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sde2 29
  • 56.07 (n)
Str.6740 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.6972 29
Zebrafish
(Danio rerio)
Actinopterygii sde2 30
  • 41 (a)
OneToOne
wufi34c02 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG5986 30
  • 30 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea F53F4.14 30
  • 20 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP9 30
  • 7 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.1605 30
  • 33 (a)
OneToOne
Species where no ortholog for SDE2 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)
  • 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)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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 SDE2 Gene

ENSEMBL:
Gene Tree for SDE2 (if available)
TreeFam:
Gene Tree for SDE2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SDE2: view image
Alliance of Genome Resources:
Additional Orthologs for SDE2

Paralogs for SDE2 Gene

Paralogs for SDE2 Gene

genes like me logo Genes that share paralogs with SDE2: view

Variants for SDE2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SDE2 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs34348128 -- p.Met312Ile

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SDE2 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 SDE2 Gene

Variant ID Type Subtype PubMed ID
esv2762223 CNV gain 21179565
esv3589004 CNV loss 21293372
nsv524126 CNV gain 19592680

Variation tolerance for SDE2 Gene

Residual Variation Intolerance Score: 44.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.57; 30.40% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SDE2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SDE2
Leiden Open Variation Database (LOVD)
SDE2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SDE2 Gene

Disorders for SDE2 Gene

Additional Disease Information for SDE2

No disorders were found for SDE2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SDE2 Gene

Publications for SDE2 Gene

  1. PCNA-Dependent Cleavage and Degradation of SDE2 Regulates Response to Replication Stress. (PMID: 27906959) Jo U … Kim H (PLoS genetics 2016) 3 4
  2. Sde2: a novel nuclear protein essential for telomeric silencing and genomic stability in Schizosaccharomyces pombe. (PMID: 21333630) Sugioka-Sugiyama R … Sugiyama T (Biochemical and biophysical research communications 2011) 2 3
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. SDE2 integrates into the TIMELESS-TIPIN complex to protect stalled replication forks. (PMID: 33127907) Rageul J … Kim H (Nature communications 2020) 3
  5. Synthetic Lethal and Resistance Interactions with BET Bromodomain Inhibitors in Triple-Negative Breast Cancer. (PMID: 32416067) Shu S … Polyak K (Molecular cell 2020) 3

Products for SDE2 Gene

Sources for SDE2 Gene