Human Gene SDE2 (uc001hpu.4)
  Description: Homo sapiens SDE2 telomere maintenance homolog (S. pombe) (SDE2), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:226,170,403-226,187,066 Size: 16,664 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr1:226,173,003-226,187,013 Size: 14,011 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:226,170,403-226,187,066)mRNA (may differ from genome)Protein (451 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SDE2_HUMAN
DESCRIPTION: RecName: Full=Protein SDE2 homolog;
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the SDE2 family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.46 RPKM in Adipose - Visceral (Omentum)
Total median expression: 279.06 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -17.3053-0.326 Picture PostScript Text
3' UTR -714.522600-0.275 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR024974 - Sde2_N

Pfam Domains:
PF13019 - Telomere stability and silencing
PF13297 - Telomere stability C-terminal

ModBase Predicted Comparative 3D Structure on Q6IQ49
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein Sequence Protein SequenceProtein Sequence 
 Alignment AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding

Biological Process:
GO:0006260 DNA replication
GO:0007049 cell cycle
GO:0051301 cell division

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC016290 - Homo sapiens chromosome 1 open reading frame 55, mRNA (cDNA clone IMAGE:3907648), with apparent retained intron.
BX648319 - Homo sapiens mRNA; cDNA DKFZp686O02131 (from clone DKFZp686O02131).
LF383664 - JP 2014500723-A/191167: Polycomb-Associated Non-Coding RNAs.
BC071563 - Homo sapiens chromosome 1 open reading frame 55, mRNA (cDNA clone MGC:87025 IMAGE:5261192), complete cds.
AK127780 - Homo sapiens cDNA FLJ45881 fis, clone OCBBF3020414.
JD064538 - Sequence 45562 from Patent EP1572962.
JD064537 - Sequence 45561 from Patent EP1572962.
JD242841 - Sequence 223865 from Patent EP1572962.
JD120063 - Sequence 101087 from Patent EP1572962.
AK291008 - Homo sapiens cDNA FLJ76172 complete cds.
AK092701 - Homo sapiens cDNA FLJ35382 fis, clone SKMUS2007915, weakly similar to Splicing factor 3a, subunit 3, 60kD.
AX747679 - Sequence 1204 from Patent EP1308459.
JD504337 - Sequence 485361 from Patent EP1572962.
JD320515 - Sequence 301539 from Patent EP1572962.
LF321188 - JP 2014500723-A/128691: Polycomb-Associated Non-Coding RNAs.
LF321187 - JP 2014500723-A/128690: Polycomb-Associated Non-Coding RNAs.
AK308441 - Homo sapiens cDNA, FLJ98389.
LF321186 - JP 2014500723-A/128689: Polycomb-Associated Non-Coding RNAs.
LF321185 - JP 2014500723-A/128688: Polycomb-Associated Non-Coding RNAs.
LF321184 - JP 2014500723-A/128687: Polycomb-Associated Non-Coding RNAs.
LF321183 - JP 2014500723-A/128686: Polycomb-Associated Non-Coding RNAs.
LF321182 - JP 2014500723-A/128685: Polycomb-Associated Non-Coding RNAs.
MA619241 - JP 2018138019-A/191167: Polycomb-Associated Non-Coding RNAs.
MA556765 - JP 2018138019-A/128691: Polycomb-Associated Non-Coding RNAs.
MA556764 - JP 2018138019-A/128690: Polycomb-Associated Non-Coding RNAs.
MA556763 - JP 2018138019-A/128689: Polycomb-Associated Non-Coding RNAs.
MA556762 - JP 2018138019-A/128688: Polycomb-Associated Non-Coding RNAs.
MA556761 - JP 2018138019-A/128687: Polycomb-Associated Non-Coding RNAs.
MA556760 - JP 2018138019-A/128686: Polycomb-Associated Non-Coding RNAs.
MA556759 - JP 2018138019-A/128685: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K4P3, C1orf55, NM_152608, NP_689821, Q5TD36, Q6IQ49, Q6ZS26, Q8NAG7, SDE2_HUMAN
UCSC ID: uc001hpu.4
RefSeq Accession: NM_152608
Protein: Q6IQ49 (aka SDE2_HUMAN)
CCDS: CCDS41473.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_152608.3
exon count: 7CDS single in 3' UTR: no RNA size: 4029
ORF size: 1356CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2512.00frame shift in genome: no % Coverage: 99.50
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.