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Aliases for SDE2 Gene

Aliases for SDE2 Gene

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

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 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 deubiquinating 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).

Additional gene information for SDE2 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SDE2 Gene

Genomics for SDE2 Gene

GeneHancer (GH) Regulatory Elements for SDE2 Gene

Promoters and enhancers for SDE2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I225995 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 571 -0.9 -933 8.8 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 ZNF548 SP3 SDE2 ACBD3 ACBD3-AS1 H3F3A LINC01703 ENAH LOC105373110 TMEM63A GC01M225948
GH01I226060 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 23.5 -63.9 -63936 5.6 DMAP1 YY1 ZNF213 E2F8 ZNF143 ZNF263 SP3 NFYC ZNF610 GLIS1 H3F3A ENSG00000272562 ACBD3-AS1 SDE2 LOC105373110 LINC01703 ENAH MIXL1 ACBD3 LBR
GH01I226937 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.7 -940.7 -940656 4.4 CLOCK MLX FEZF1 DMAP1 YY1 ZNF213 ZNF143 SP3 NFYC ZFP41 COQ8A CDC42BPA ZNF678 ACBD3 SDE2 LINC01703 ENSG00000228525 GC01P226914 GC01M226920
GH01I225874 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.4 +120.2 120205 10.1 FOXA2 ARID4B NEUROD1 SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF766 ZNF213 TMEM63A LEFTY2 ACBD3 PYCR2 LEFTY1 ENSG00000255835 ENSG00000248322 SDE2 H3F3A ENSG00000242861
GH01I225921 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.9 +75.7 75726 3.7 HDGF PKNOX1 SMAD1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 PYCR2 ENSG00000255835 MIR6741 ACBD3 ENAH SDE2 LINC01703 ACBD3-AS1 LEFTY1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SDE2 on UCSC Golden Path with GeneCards custom track

Genomic Locations for SDE2 Gene

Genomic Locations for SDE2 Gene
chr1:225,982,702-225,999,365
(GRCh38/hg38)
Size:
16,664 bases
Orientation:
Minus strand
chr1:226,170,403-226,187,066
(GRCh37/hg19)

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

    Alternative splice isoforms for SDE2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SDE2 Gene

Post-translational modifications for SDE2 Gene

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

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:
ProtoNet:

Suggested Antigen Peptide Sequences for SDE2 Gene

GenScript: Design optimal peptide antigens:

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 deubiquinating 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 deubiquinating 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 deubiquinating 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 --
genes like me logo Genes that share ontologies with SDE2: view
genes like me logo Genes that share phenotypes with SDE2: view

Animal Model Products

CRISPR Products

miRNA for SDE2 Gene

miRTarBase miRNAs that target SDE2

Inhibitory RNA Products

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 4
cytosol 3
plasma membrane 2
mitochondrion 2
golgi apparatus 2
extracellular 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Golgi apparatus (2)
  • Nuclear speckles (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SDE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
genes like me logo Genes that share ontologies with SDE2: view

Pathways & Interactions for SDE2 Gene

No Data Available

Interacting Proteins for SDE2 Gene

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:0051301 cell division IEA --
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 :
(6) Additional mRNA sequences :
(68) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SDE2 Gene

SDE2 telomere maintenance homolog (S. pombe):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for SDE2 Gene

GeneLoc Exon Structure for
SDE2
ECgene alternative splicing isoforms for
SDE2

Expression for SDE2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for SDE2 Gene



Protein tissue co-expression partners for SDE2 Gene

NURSA nuclear receptor signaling pathways regulating expression of SDE2 Gene:

SDE2

SOURCE GeneReport for Unigene cluster for SDE2 Gene:

Hs.520192

Evidence on tissue expression from TISSUES for SDE2 Gene

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

Primer Products

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 33
  • 99.48 (n)
C1ORF55 34
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SDE2 33 34
  • 84.63 (n)
dog
(Canis familiaris)
Mammalia SDE2 33 34
  • 77.13 (n)
mouse
(Mus musculus)
Mammalia Sde2 33 16 34
  • 76.48 (n)
rat
(Rattus norvegicus)
Mammalia Sde2 33
  • 74.49 (n)
oppossum
(Monodelphis domestica)
Mammalia SDE2 34
  • 60 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SDE2 34
  • 56 (a)
OneToOne
chicken
(Gallus gallus)
Aves C3H1ORF55 33
  • 59.34 (n)
SDE2 34
  • 54 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SDE2 34
  • 56 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sde2 33
  • 56.07 (n)
Str.6740 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.6972 33
zebrafish
(Danio rerio)
Actinopterygii sde2 34
  • 41 (a)
OneToOne
wufi34c02 33
fruit fly
(Drosophila melanogaster)
Insecta CG5986 34
  • 30 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea F53F4.14 34
  • 20 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP9 34
  • 7 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1605 34
  • 33 (a)
OneToOne
Species where no ortholog for SDE2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

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 from dbSNP and Humsavar for SDE2 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000195235 -- 225,994,095(-) T/G intron_variant
rs1000204923 -- 225,993,788(-) G/A intron_variant
rs1000458350 -- 225,999,654(-) A/G upstream_transcript_variant
rs1000514442 -- 225,988,983(-) G/A intron_variant
rs1000519694 -- 225,995,502(-) T/G intron_variant

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

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 58
  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 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. (PMID: 25281560) Lambert JP … Gingras AC (Journal of proteomics 2015) 3 58
  5. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3 58

Products for SDE2 Gene

Sources for SDE2 Gene

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