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SDE2 Gene

protein-coding   GIFtS: 36
GCID: GC01M226171

SDE2 Telomere Maintenance Homolog (S. Pombe)

(Previous name: chromosome 1 open reading frame 55)
(Previous symbol: C1orf55)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
SDE2 Telomere Maintenance Homolog (S. Pombe)1 2
C1orf551 2 3
Chromosome 1 Open Reading Frame 551
dJ671D7.12
Protein SDE2 Homolog2
UPF0667 Protein C1orf552

External Ids:    HGNC: 266431   Entrez Gene: 1638592   Ensembl: ENSG000001437517   UniProtKB: Q6IQ493   

Export aliases for SDE2 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SDE2 Gene:
SDE2 (SDE2 telomere maintenance homolog (S. pombe)) is a protein-coding gene. An important paralog of this gene is SF3A3.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000001.10  NT_167186.2  NC_018912.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SDE2
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SDE2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SDE2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1q42.12   Ensembl cytogenetic band:  1q42.12   HGNC cytogenetic band: 1q42.12

SDE2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SDE2 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M226171:  view genomic region     (about GC identifiers)

Start:
226,170,403 bp from pter      End:
226,187,066 bp from pter
Size:
16,664 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: SDE2_HUMAN, Q6IQ49 (See protein sequence)
Recommended Name: Protein SDE2 homolog  
Size: 451 amino acids; 49742 Da
Secondary accessions: A8K4P3 Q5TD36 Q6ZS26 Q8NAG7
Alternative splicing: 3 isoforms:  Q6IQ49-1   Q6IQ49-2   Q6IQ49-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SDE2: NX_Q6IQ49

Explore proteomics data for SDE2 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SDE2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_689821.3  
    ENSEMBL proteins: 
     ENSP00000272091  

    SDE2 Human Recombinant Protein Products:

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    antibodies-online proteins for SDE2 (3 products) 

     
    antibodies-online peptides for SDE2

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    antibodies-online antibodies for SDE2 (20 products) 

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    antibodies-online kits for SDE2 (2 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR024974 Sde2_N

    Graphical View of Domain Structure for InterPro Entry Q6IQ49

    ProtoNet protein and cluster: Q6IQ49

    UniProtKB/Swiss-Prot: SDE2_HUMAN, Q6IQ49
    Similarity: Belongs to the SDE2 family


    Find genes that share domains with SDE2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for SDE2

    miRNA
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    miRTarBase miRNAs that target SDE2:
    hsa-mir-615-3p (MIRT039854), hsa-mir-30c-5p (MIRT047992)

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SDE2


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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      --

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SDE2
    Interactions:

        Search GeneGlobe Interaction Network for SDE2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 8)

    Selected Interacting proteins for SDE2 (Q6IQ493 ENSP000002720914) via UniProtKB, MINT, STRING, and/or I2D (see all 10)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MEPCEQ7L2J03, ENSP000003085464I2D: score=1 STRING: ENSP00000308546
    SLX4Q8IY923, ENSP000002940084I2D: score=1 STRING: ENSP00000294008
    GRB2P629933I2D: score=2 
    PRKAA2P546463I2D: score=1 
    CDC40ENSP000003043704STRING: ENSP00000304370
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SDE2



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SDE2 gene: 
    NM_152608.3  

    Unigene Cluster for SDE2:

    SDE2 telomere maintenance homolog (S. pombe)
    Hs.520192  [show with all ESTs]
    Unigene Representative Sequence: BC016290
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000272091(uc001hpu.4)
    miRNA
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat SDE2
      QuantiFast Probe-based Assays in human, mouse, rat SDE2

    Additional mRNA sequence: 

    AK092701.1 AK127780.1 AK291008.1 AK308441.1 BC016290.1 BX648319.1 

    8 DOTS entries:

    DT.102822741  DT.203198  DT.101981451  DT.40300955  DT.100781130  DT.121356720  DT.91946303  DT.91690018 

    Selected AceView cDNA sequences (see all 68):

    BC016290 CR599350 AX747679 AK092701 NM_152608 BX498290 AI830502 AW069644 
    BG615109 BI520048 BU150244 AW963092 BG502215 BX281956 AK127780 BX490143 
    AA449121 CD639397 BC071563 BG494106 AA449552 BG570780 BE883773 BM467243 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SDE2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SDE2 Expression
    About this image

    SDE2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SDE2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.520192
        Custom PCR Arrays for SDE2
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SDE2

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for SDE2 gene from Selected species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sde21 , 5 cDNA sequence BC0317815
    SDE2 telomere maintenance homolog (S. pombe)1
    76.48(n)1
    69.41(a)1
      1 (84.46 cM)5
    2087681  NM_145943.11  NP_666055.11 
     1808511515 
    chicken
    (Gallus gallus)
    Aves C3H1ORF551 chromosome 3 open reading frame, human C1orf55 59.34(n)
    56.81(a)
      421318  XM_419383.4  XP_419383.2 
    lizard
    (Anolis carolinensis)
    Reptilia SDE26
    SDE2 telomere maintenance homolog (S. pombe)
    56(a)
    1 ↔ 1
    1(251609377-251618482)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.69722 Xenopus laevis transcribed sequence with weak similarity more 76.27(n)    BX843396.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufi34c022 Danio rerio cDNA clone IMAGE6799173, partial cds 78.68(n)    BC054640.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG59866
    --
    30(a)
    1 ↔ 1
    3R(19873512-19874890)
    worm
    (Caenorhabditis elegans)
    Secernentea F53F4.146
    Protein F53F4.14 (F53F4.14) mRNA, complete cds
    20(a)
    1 ↔ 1
    V(13627573-13629837) WBGene00009996
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes PRP96
    Subunit of the SF3a splicing factor complex, requi...
    7(a)
    1 → many
    IV(397537-399129) YDL030W


    ENSEMBL Gene Tree for SDE2 (if available)
    TreeFam Gene Tree for SDE2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SDE2 gene
    SF3A32  

    Find genes that share paralogs with SDE2           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SDE2 (see all 412)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs28163261,2
    C,F,H--226169966(-) AGAATT/CTCTTC 1 -- int122Minor allele frequency- C:0.22NS EA NA WA CSA 2049
    rs27551001,2
    C--226170076(+) ccaacG/Atggag 1 -- int16Minor allele frequency- A:0.09NA WA CSA 11
    rs1511651511,2
    C--226170381(+) GAAATG/TAAGAA 1 -- int10--------
    rs1810603201,2
    --226170497(+) CAGGAC/TTTACA 1 -- ut310--------
    rs1871803201,2
    --226170511(+) TTTAAA/GTATGT 1 -- ut310--------
    rs1910584391,2
    --226170581(+) ACTTAC/TAAGAT 1 -- ut310--------
    rs1402371871,2
    --226170674(+) AACTTA/TAAAAA 1 -- ut310--------
    rs1828963601,2
    --226170781(+) ATAATC/TACATT 1 -- ut310--------
    rs1502963791,2
    --226170785(+) TTACAC/TTTAAT 1 -- ut310--------
    rs1378591801,2
    --226171011(+) TTTCAC/TAATGA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for SDE2 (226170403 - 226187066 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SDE2: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SDE2
    DNA2.0 Custom Variant and Variant Library Synthesis for SDE2

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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      --

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SDE2 gene, integrated from 10 sources (see all 16):
    (articles sorted by number of sources associating them with SDE2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Sde2: a novel nuclear protein essential for telomeric silencing and genomic stability in Schizosaccharomyces pombe. (PubMed id 21333630)1, 3 Sugioka-Sugiyama R. and Sugiyama T. (Biochem. Biophys. Res. Commun. 2011)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    4. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    5. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    6. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (Sci. Signal. 2010)
    7. Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. (PubMed id 19690332)2 Mayya V.... Han D.K. (Sci. Signal. 2009)
    8. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (EMBO J. 2009)
    9. Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis. (PubMed id 18220336)2 Cantin G.T....Yates J.R. III (J. Proteome Res. 2008)
    10. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (Proc. Natl. Acad. Sci. U.S.A. 2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 163859 HGNC: 26643 AceView: FLJ35382 Ensembl:ENSG00000143751 euGenes: HUgn163859
    ECgene: SDE2 H-InvDB: SDE2

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SDE2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SDE2 gene:
    Search GeneIP for patents involving SDE2

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from genOway)
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     Custom PCR Arrays for SDE2 Search Chromatin IP Primers for SDE2
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     GenScript Custom Purified and Recombinant Proteins Services for SDE2 GenScript Custom cDNA clones with any tag delivered in your preferred vector Services for SDE2
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     Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

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     Browse ESI BIO Cell Lines and PureStem Progenitors for SDE2
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     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SDE2
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     Search Addgene for plasmids for SDE2
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     genOway: Develop your customized and physiologically relevant rodent model for SDE2
     antibodies-online antibodies for SDE2 (20 products)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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