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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SKA3 Gene

protein-coding   GIFtS: 47
GCID: GC13M021728

spindle and kinetochore associated complex subunit 3

(Previous name: chromosome 13 open reading frame 3 )
(Previous symbol: C13orf3)
 Explore 3 diseases affiliated with
SKA3 via our new
 Human Malady Compendium 
Biological research products
for SKA3
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Spindle And Kinetochore Associated Complex Subunit 31 2
C13orf31 2 3
RAMA11 2 3
MGC48321
Chromosome 13 Open Reading Frame 31
Spindle And Kinetochore-Associated Protein 32

External Ids:    HGNC: 202621   Entrez Gene: 2211502   Ensembl: ENSG000001654807   UniProtKB: Q8IX903   

Export aliases for SKA3 gene to outside databases

Previous GC identifers: GC13M020626 GC13M002529


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for SKA3:
This gene encodes a component of the spindle and kinetochore-associated protein complex that regulates microtubule
attachment to the kinetochores during mitosis. The encoded protein localizes to the outer kinetechore and may be
required for normal chromosome segregation and cell division. Alternative splicing results in multiple transcript
variants. (provided by RefSeq, Oct 2009)

UniProtKB/Swiss-Prot: SKA3_HUMAN, Q8IX90
Function: Component of the SKA1 complex, a microtubule-binding subcomplex of the outer kinetochore that is essential
for proper chromosome segregation. The SKA1 complex is a direct component of the kinetochore-microtubule interface and
directly associates with microtubules as oligomeric assemblies. The complex facilitates the processive movement of
microspheres along a microtubule in a depolymerization-coupled manner. In the complex, it mediates the
microtubule-stimulated oligomerization




(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000013.10  NC_018924.1  NT_024524.14  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for SKA3
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SKA3


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

Entrez Gene cytogenetic band: 13q12.11   Ensembl cytogenetic band:  13q12.11   HGNC cytogenetic band: 13q11

SKA3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SKA3 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13M021728:  view genomic region     (about GC identifiers)

Start:
21,727,734 bp from pter      End:
21,750,741 bp from pter
Size:
23,008 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: SKA3_HUMAN, Q8IX90 (See protein sequence)
Recommended Name: Spindle and kinetochore-associated protein 3  
Size: 412 amino acids; 46359 Da
Subunit: Component of the SKA1 complex, composed of SKA1, SKA2 and SKA3. The core SKA1 complex is composed of 2
SKA1-SKA2 heterodimers, each heterodimer interacting with a molecule of the SKA3 homodimer. The core SKA1 complex
associates with microtubules and forms oligomeric assemblies. Interacts directly with SKA1
Subcellular location: Cytoplasm, cytoskeleton, spindle. Chromosome, centromere, kinetochore. Note=Localizes to the
outer kinetochore and spindle microtubules during mitosis in a NDC80 complex-dependent manner
Sequence caution: Sequence=AAH13418.1; Type=Erroneous translation; Note=Wrong choice of frame; Sequence=BAG37379.1;
Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAG37379.1; Type=Frameshift; Positions=29;
Sequence=CAH69950.1; Type=Erroneous gene model prediction; Sequence=EAX08294.1; Type=Erroneous gene model prediction;
1 PDB 3D structure from and Proteopedia for SKA3:
4AJ5 (3D)    
Secondary accessions: A2A330 A2A331 B2RBY2 Q5VZV5 Q86WR2 Q8NBG1 Q96D22
Alternative splicing: 3 isoforms:  Q8IX90-1   Q8IX90-2   Q8IX90-3   (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for SKA3: NX_Q8IX90

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8IX90

  • SKA3 Protein expression data from MOPED and PaxDb:    About this image 
    SKA3 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001159489.1  NP_659498.4  

    ENSEMBL proteins: 
     ENSP00000382896   ENSP00000298260   ENSP00000319417   ENSP00000443543   ENSP00000441632  

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    Uscn Proteins for SKA3

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000940condensed chromosome outer kinetochore IDA19289083
    GO:0005737cytoplasm IEA--
    GO:0005876spindle microtubule IDA19289083

    SKA3 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    ProtoNet protein and cluster: Q8IX90

    UniProtKB/Swiss-Prot: SKA3_HUMAN, Q8IX90
    Similarity: Belongs to the SKA3 family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SKA3_HUMAN, Q8IX90
    Function: Component of the SKA1 complex, a microtubule-binding subcomplex of the outer kinetochore that is essential
    for proper chromosome segregation. The SKA1 complex is a direct component of the kinetochore-microtubule interface and
    directly associates with microtubules as oligomeric assemblies. The complex facilitates the processive movement of
    microspheres along a microtubule in a depolymerization-coupled manner. In the complex, it mediates the
    microtubule-stimulated oligomerization

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI19289083
         
    SKA3 for ontologies           About GeneDecksing


    Phenotypes:
         5 GenomeRNAi human phenotypes for SKA3:
     Abundance of large cells with   Cell cycle / mitosis defect  Decreased Hepatitis C virus re  Increased gamma-H2AX phosphory 
     Increased number of cells in m 

    Animal Models:
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SKA3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/52 Interacting proteins for SKA3 (Q8IX902, 3 ENSP000003194174) via UniProtKB, MINT, STRING, and/or I2D (see all 52)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SKA1Q96BD82, 3, ENSP000002851164MINT-7277243 MINT-7277267 MINT-7277189 MINT-7277201 MINT-7277219 I2D: score=1 STRING: ENSP00000285116
    SKA2Q8WVK72, ENSP000003334334MINT-7277243 MINT-7277189 MINT-7277201 MINT-7277219 STRING: ENSP00000333433
    PPP2R2BQ000053, ENSP000003365914I2D: score=1 STRING: ENSP00000336591
    PPP2R2DQ66LE63I2D: score=1 
    BIRC5ENSP000003016334STRING: ENSP00000301633
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007059chromosome segregation IMP19289083
    GO:0007067mitosis IMP19289083
    GO:0031110regulation of microtubule polymerization or depolymerization IDA19289083
    GO:0051301cell division IEA--

    SKA3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SKA3
    Search CenterWatch for drugs/clinical trials and news about SKA3 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SKA3 gene (2 alternative transcripts): 
    NM_001166017.1  NM_145061.5  

    Unigene Cluster for SKA3:

    Spindle and kinetochore associated complex subunit 3
    Hs.88523  [show with all ESTs]
    Unigene Representative Sequence: NM_145061
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000400018 ENST00000298260 ENST00000314759(uc001unt.3 uc001unu.3 uc001unv.3)
    ENST00000462482 ENST00000465471 ENST00000536239 ENST00000475251

    miRNA
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    Additional cDNA sequence: 

    AF361358.1 AK090584.1 AK307976.1 AK314864.1 BC048988.1 

    6 DOTS entries:

    DT.441004  DT.95163667  DT.40228666  DT.100784802  DT.120784170  DT.116749 

    24/90 AceView cDNA sequences (see all 90):

    AA587984 AW238816 AI292347 CR625062 CR603666 AI291972 AI371153 BQ961423 
    BU165957 BQ691614 BX383352 NM_145061 BP870584 BX370568 BX394655 CB143796 
    BU506973 AI362963 AI037931 BI460315 BF430974 AF361358 BG105671 BC013418 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for SKA3    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c
    SP1:                    -                                                               
    SP2:                    -                                         -                     
    SP3:                    -     -     -     -     -     -     -                           
    SP4:                                                                                    


    ECgene alternative splicing isoforms for SKA3

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SKA3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ATAGTGCTTT
    SKA3 Expression
    About this image

    SKA3 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table

    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    Neural TubeTelencephalonNeural Tube
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See SKA3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SKA3

    SOURCE GeneReport for Unigene cluster: Hs.88523
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SKA3

    (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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for SKA3 gene from 3/9 species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ska31 , 5 RIKEN cDNA F630043A04 gene5
    spindle and kinetochore associated complex subunit more1
    76.1(n)1
    64.02(a)1
      14 (30.51 cM)5
    2191141  NM_198605.31  NP_941007.11 
     578065615 
    chicken
    (Gallus gallus)
    Aves SKA31 spindle and kinetochore associated complex subunit more 55.31(n)
    42.82(a)
      418948  XM_417142.3  XP_417142.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ska31 spindle and kinetochore associated complex subunit more 42.61(n)
    33.33(a)
      570479  NM_001202437.1  NP_001189366.1 


    ENSEMBL Gene Tree for SKA3 (if available)
    TreeFam Gene Tree for SKA3 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/394 NCBI SNPs in SKA3 are shown (see all 394    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs20163191,2
    C,F,A--21727250(-) GATTCG/AGTTAC 2 -- ds50016Minor allele frequency- A:0.41NA WA EA 364
    rs1132404081,2
    --21727286(+) TTCTCT/ATAATA 2 -- ds50011Minor allele frequency- A:0.50CSA 2
    rs1464405581,2
    C--21727370(+) TGTAA-/GACGT 
            
    GACGT
    2 -- ds50010--------
    rs1387718971,2
    --21727448(+) CATTAA/GACCTC 2 -- ds50010--------
    rs1413783561,2
    --21727502(+) AGCGTA/GAGAAC 2 -- ds50010--------
    rs9132061,2
    C,F,A,H--21727567(-) GAAGGC/TGTAGT 2 -- ds500118Minor allele frequency- T:0.12NS EA NA WA CSA 799
    rs341057511,2
    C--21727638(+) CTCAGC/GTGTTT 2 -- ds50012Minor allele frequency- G:0.00NA 4
    rs1507681881,2
    --21727713(+) AACATC/TGACTT 2 -- ds50010--------
    rs1410671421,2
    C--21727823(+) CTGGC-/CTCTT 
            
    CTCAG
    2 -- ut310--------
    rs619503331,2
    C--21727828(+) CCTCAG/CTCTCC 2 -- ut311Minor allele frequency- C:0.50NA 2

    HapMap Linkage Disequilibrium report for SKA3 (21727734 - 21750741 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 15 variations for SKA3
         8 CNVs: 39124 39126 39128 66395 39127 39125 7003 5701
         7 Indels: 39957 45142 39955 11074 39956 61297 25210

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    (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.)
    About This Section

    SKA3 for disorders           About GeneDecksing

    3 diseases for SKA3:    About MalaCards
    acute poststreptococcal glomerulonephritis    rheumatic fever    glomerulonephritis

    1 disease from the University of Copenhagen DISEASES database for SKA3:
    Acute poststreptococcal glomerulonephritis

    Export disorders for SKA3 gene to outside databases

    (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)
    About This Section

    PubMed articles for SKA3 gene, integrated from 9 sources (see all 28):
    (articles sorted by number of sources associating them with SKA3)
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    1. Stable kinetochore-microtubule interactions depend on the Ska complex and its new component Ska3/C13Orf3. (PubMed id 19360002)1, 2, 3 Gaitanos T.N....Nigg E.A. (2009)
    2. The human kinetochore Ska1 complex facilitates microtubule depolymerization-coupled motility. (PubMed id 19289083)1, 2, 3 Welburn J.P.I.... Cheeseman I.M. (2009)
    3. Comparative profiling identifies C13orf3 as a component of the Ska complex required for mammalian cell division. (PubMed id 19387489)1, 3 Theis M....Buchholz F. (2009)
    4. Ska3 is required for spindle checkpoint silencing and the maintenance of chromosome cohesion in mitosis. (PubMed id 19646878)1, 3 Daum J.R....Gorbsky G.J. (2009)
    5. The DNA sequence and analysis of human chromosome 13. (PubMed id 15057823)1, 2 Dunham A.... Ross M.T. (2004)
    6. Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry. (PubMed id 15144186)1, 2 Brill L.M....Peters E.C. (2004)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    9. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    10. Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (2012)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 221150 HGNC: 20262 AceView: C13orf3 Ensembl:ENSG00000165480 euGenes: HUgn221150
    ECgene: SKA3 H-InvDB: SKA3

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SKA3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SKA3 gene:
    Search GeneIP for patents involving SKA3

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