Human Gene SKA2 (uc010dde.1)
  Description: Homo sapiens spindle and kinetochore associated complex subunit 2 (SKA2), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr17:57,187,308-57,232,800 Size: 45,493 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr17:57,189,694-57,232,444 Size: 42,751 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:57,187,308-57,232,800)mRNA (may differ from genome)Protein (75 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
OMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: E9PCB8_HUMAN
DESCRIPTION: SubName: Full=Spindle and kinetochore-associated protein 2;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: SKA2
Diseases sorted by gene-association score: post-traumatic stress disorder (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 31.78 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 432.15 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 -125.50356-0.353 Picture PostScript Text
3' UTR -632.162386-0.265 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
  ModBase Predicted Comparative 3D Structure on E9PCB8
FrontTopSide
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  LF384789 - JP 2014500723-A/192292: Polycomb-Associated Non-Coding RNAs.
BC106003 - Homo sapiens family with sequence similarity 33, member A, mRNA (cDNA clone MGC:110975 IMAGE:6143473), complete cds.
AK056473 - Homo sapiens cDNA FLJ31911 fis, clone NT2RP7004751.
AK022820 - Homo sapiens cDNA FLJ12758 fis, clone NT2RP2001328.
JD561844 - Sequence 542868 from Patent EP1572962.
JD202042 - Sequence 183066 from Patent EP1572962.
JD243017 - Sequence 224041 from Patent EP1572962.
JD304390 - Sequence 285414 from Patent EP1572962.
JD272942 - Sequence 253966 from Patent EP1572962.
JD236498 - Sequence 217522 from Patent EP1572962.
JD449990 - Sequence 431014 from Patent EP1572962.
JD176226 - Sequence 157250 from Patent EP1572962.
JD064499 - Sequence 45523 from Patent EP1572962.
JD242827 - Sequence 223851 from Patent EP1572962.
JD384780 - Sequence 365804 from Patent EP1572962.
JD321718 - Sequence 302742 from Patent EP1572962.
JD454156 - Sequence 435180 from Patent EP1572962.
JD092970 - Sequence 73994 from Patent EP1572962.
JD087502 - Sequence 68526 from Patent EP1572962.
JD350323 - Sequence 331347 from Patent EP1572962.
JD074202 - Sequence 55226 from Patent EP1572962.
JD236652 - Sequence 217676 from Patent EP1572962.
JD454317 - Sequence 435341 from Patent EP1572962.
JD498762 - Sequence 479786 from Patent EP1572962.
JD242557 - Sequence 223581 from Patent EP1572962.
JD300788 - Sequence 281812 from Patent EP1572962.
BC017873 - Homo sapiens family with sequence similarity 33, member A, mRNA (cDNA clone MGC:22673 IMAGE:4685972), complete cds.
JD136317 - Sequence 117341 from Patent EP1572962.
JD474460 - Sequence 455484 from Patent EP1572962.
LF327223 - JP 2014500723-A/134726: Polycomb-Associated Non-Coding RNAs.
JD432045 - Sequence 413069 from Patent EP1572962.
HQ447776 - Synthetic construct Homo sapiens clone IMAGE:100071108; CCSB012915_02 family with sequence similarity 33, member A (FAM33A) gene, encodes complete protein.
KJ896119 - Synthetic construct Homo sapiens clone ccsbBroadEn_05513 SKA2 gene, encodes complete protein.
LF319941 - JP 2014500723-A/127444: Polycomb-Associated Non-Coding RNAs.
LF327222 - JP 2014500723-A/134725: Polycomb-Associated Non-Coding RNAs.
LF327219 - JP 2014500723-A/134722: Polycomb-Associated Non-Coding RNAs.
FJ648812 - Homo sapiens family with sequence similarity 33 member A (FAM33A) mRNA, partial cds.
JD467041 - Sequence 448065 from Patent EP1572962.
MA620366 - JP 2018138019-A/192292: Polycomb-Associated Non-Coding RNAs.
MA562800 - JP 2018138019-A/134726: Polycomb-Associated Non-Coding RNAs.
MA562799 - JP 2018138019-A/134725: Polycomb-Associated Non-Coding RNAs.
MA562796 - JP 2018138019-A/134722: Polycomb-Associated Non-Coding RNAs.
MA555518 - JP 2018138019-A/127444: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: E9PCB8, E9PCB8_HUMAN, NM_001100595, NP_001094065
UCSC ID: uc010dde.1
RefSeq Accession: NM_001100595
Protein: E9PCB8 CCDS: CCDS45748.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001100595.1
exon count: 3CDS single in 3' UTR: no RNA size: 2988
ORF size: 228CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 192.00frame shift in genome: no % Coverage: 99.40
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.