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 200... See more...

Aliases for SKA3 Gene

Aliases for SKA3 Gene

  • Spindle And Kinetochore Associated Complex Subunit 3 2 3 5
  • Spindle And Kinetochore-Associated Protein 3 3 4
  • C13orf3 3 4
  • RAMA1 3 4
  • Chromosome 13 Open Reading Frame 3 2

External Ids for SKA3 Gene

Previous HGNC Symbols for SKA3 Gene

  • C13orf3

Previous GeneCards Identifiers for SKA3 Gene

  • GC13M020626
  • GC13M021728
  • GC13M002529

Summaries for SKA3 Gene

Entrez Gene Summary for SKA3 Gene

  • 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]

GeneCards Summary for SKA3 Gene

SKA3 (Spindle And Kinetochore Associated Complex Subunit 3) is a Protein Coding gene. Diseases associated with SKA3 include Uterine Adnexa Cancer.

UniProtKB/Swiss-Prot Summary for SKA3 Gene

  • Component of the SKA1 complex, a microtubule-binding subcomplex of the outer kinetochore that is essential for proper chromosome segregation (PubMed:19289083, PubMed:19360002, PubMed:23085020). The SKA1 complex is a direct component of the kinetochore-microtubule interface and directly associates with microtubules as oligomeric assemblies (PubMed:19289083, PubMed:19360002). The complex facilitates the processive movement of microspheres along a microtubule in a depolymerization-coupled manner (PubMed:19289083). In the complex, it mediates the microtubule-stimulated oligomerization (PubMed:19289083). Affinity for microtubules is synergistically enhanced in the presence of the ndc-80 complex and may allow the ndc-80 complex to track depolymerizing microtubules (PubMed:23085020).

Additional gene information for SKA3 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SKA3 Gene

Genomics for SKA3 Gene

GeneHancer (GH) Regulatory Elements for SKA3 Gene

Promoters and enhancers for SKA3 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
GH13J021668 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 500 -496.5 -496516 8.9 HNRNPK EP300 CTCF NRF1 SP1 ZNF639 ZIC2 ZBTB10 POLR2A ZNF423 FGF9 SKA3 lnc-MICU2-1 HSALNG0095624
GH13J021174 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +0.3 301 3.8 ZNF217 EP300 SIN3A MYC NRF1 USF1 POLR2G SP1 GTF2E2 JUND MRPL57 SKA3 piR-61101-131 EEF1AKMT1 SAP18
GH13J021139 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 12.6 +35.5 35518 3.4 ZBTB40 ZNF217 SIN3A NRF1 POLR2G PHF8 ZFX ZNF639 POLR2A CLOCK SAP18 DQ866754 ENSG00000252128 lnc-SKA3-1 MRPL57 SKA3
GH13J021296 Promoter/Enhancer 1.9 Ensembl ENCODE CraniofacialAtlas 10.8 -121.9 -121887 3 ZNF217 EP300 CTCF SIN3A POLR2G USF1 SP1 PHF8 FOS TEAD4 MIPEPP3 LOC101928764 lnc-MRPL57-5 MRPL57 SKA3 GRK6P1 LINC00539 lnc-ZDHHC20-3 RF00017-1361
GH13J021217 Enhancer 1 Ensembl ENCODE dbSUPER 12.3 -42.4 -42442 3.1 TCF12 CBFB SRF IKZF1 ATF2 TBX21 POLR2A PAX5 NFIC ZNF366 MRPL57 SKA3 SAP18 ENSG00000271250 LINC01046
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SKA3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SKA3

Genomic Locations for SKA3 Gene

Genomic Locations for SKA3 Gene
chr13:21,153,595-21,176,602
(GRCh38/hg38)
Size:
23,008 bases
Orientation:
Minus strand
chr13:21,727,734-21,750,741
(GRCh37/hg19)
Size:
23,008 bases
Orientation:
Minus strand

Genomic View for SKA3 Gene

Genes around SKA3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SKA3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SKA3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SKA3 Gene

Proteins for SKA3 Gene

  • Protein details for SKA3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IX90-SKA3_HUMAN
    Recommended name:
    Spindle and kinetochore-associated protein 3
    Protein Accession:
    Q8IX90
    Secondary Accessions:
    • A2A330
    • A2A331
    • B2RBY2
    • Q5VZV5
    • Q86WR2
    • Q8NBG1
    • Q96D22

    Protein attributes for SKA3 Gene

    Size:
    412 amino acids
    Molecular mass:
    46359 Da
    Quaternary structure:
    • Component of the SKA1 complex, composed of SKA1, SKA2 and SKA3 (PubMed:19289083, PubMed:19360002). The core SKA1 complex is composed of 2 SKA1-SKA2 heterodimers, each heterodimer interacting with a molecule of the SKA3 homodimer (PubMed:19289083, PubMed:19360002). The core SKA1 complex associates with microtubules and forms oligomeric assemblies (PubMed:19289083, PubMed:19360002, PubMed:23085020). Interacts with SKA1; the interaction is direct (PubMed:19289083, PubMed:23085020).
    Miscellaneous:
    • [Isoform 2]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
    SequenceCaution:
    • Sequence=AAH13418.1; Type=Erroneous translation; Note=Wrong choice of frame.; Evidence={ECO:0000305}; Sequence=BAG37379.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAG37379.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=EAX08294.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SKA3 Gene

    Alternative splice isoforms for SKA3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SKA3 Gene

Post-translational modifications for SKA3 Gene

  • Glycosylation at Asn316
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SKA3 Gene

Domains & Families for SKA3 Gene

Gene Families for SKA3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SKA3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SKA3 Gene

GenScript: Design optimal peptide antigens:
  • Spindle and kinetochore-associated protein 3 (SKA3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IX90

UniProtKB/Swiss-Prot:

SKA3_HUMAN :
  • Belongs to the SKA3 family.
Family:
  • Belongs to the SKA3 family.
genes like me logo Genes that share domains with SKA3: view

Function for SKA3 Gene

Molecular function for SKA3 Gene

UniProtKB/Swiss-Prot Function:
Component of the SKA1 complex, a microtubule-binding subcomplex of the outer kinetochore that is essential for proper chromosome segregation (PubMed:19289083, PubMed:19360002, PubMed:23085020). The SKA1 complex is a direct component of the kinetochore-microtubule interface and directly associates with microtubules as oligomeric assemblies (PubMed:19289083, PubMed:19360002). The complex facilitates the processive movement of microspheres along a microtubule in a depolymerization-coupled manner (PubMed:19289083). In the complex, it mediates the microtubule-stimulated oligomerization (PubMed:19289083). Affinity for microtubules is synergistically enhanced in the presence of the ndc-80 complex and may allow the ndc-80 complex to track depolymerizing microtubules (PubMed:23085020).

Gene Ontology (GO) - Molecular Function for SKA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19289083
genes like me logo Genes that share ontologies with SKA3: view
genes like me logo Genes that share phenotypes with SKA3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SKA3

Clone Products

  • Addgene plasmids for SKA3

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SKA3 Gene

Localization for SKA3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SKA3 Gene

Cytoplasm, cytoskeleton, spindle. Chromosome, centromere, kinetochore. Note=Localizes to the outer kinetochore and spindle microtubules during mitosis in a NDC80 complex-dependent manner. {ECO:0000269 PubMed:19360002}.

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 SKA3 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
nucleus 3
plasma membrane 2
mitochondrion 0
golgi apparatus 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centrosome (4)
  • Cytosol (4)
  • Microtubules (4)
  • Mitotic spindle (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SKA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000775 chromosome, centromeric region IEA --
GO:0000776 kinetochore IDA,IEA 20813266
GO:0000777 condensed chromosome kinetochore IEA --
GO:0000940 condensed chromosome outer kinetochore IEA,IDA 19289083
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with SKA3: view

Pathways & Interactions for SKA3 Gene

PathCards logo

SuperPathways for SKA3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SKA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000278 mitotic cell cycle IMP 19289083
GO:0007049 cell cycle IEA --
GO:0007059 chromosome segregation IEA,IMP 19289083
GO:0031110 regulation of microtubule polymerization or depolymerization IDA 19289083
GO:0051301 cell division IEA --
genes like me logo Genes that share ontologies with SKA3: view

No data available for Pathways by source and SIGNOR curated interactions for SKA3 Gene

Drugs & Compounds for SKA3 Gene

No Compound Related Data Available

Transcripts for SKA3 Gene

mRNA/cDNA for SKA3 Gene

2 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SKA3

Clone Products

  • Addgene plasmids for SKA3

Alternative Splicing Database (ASD) splice patterns (SP) for SKA3 Gene

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

Relevant External Links for SKA3 Gene

GeneLoc Exon Structure for
SKA3

Expression for SKA3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SKA3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SKA3 Gene

This gene is overexpressed in Testis (x6.7) and Esophagus - Mucosa (x4.1).

Protein differential expression in normal tissues from HIPED for SKA3 Gene

This gene is overexpressed in Fetal ovary (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SKA3 Gene



Protein tissue co-expression partners for SKA3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SKA3

SOURCE GeneReport for Unigene cluster for SKA3 Gene:

Hs.88523
genes like me logo Genes that share expression patterns with SKA3: view

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SKA3 Gene

Orthologs for SKA3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SKA3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SKA3 31 30
  • 99.55 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SKA3 31 30
  • 85.76 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SKA3 31 30
  • 84.92 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Ska3 17 31 30
  • 76.01 (n)
rat
(Rattus norvegicus)
Mammalia Ska3 30
  • 74.88 (n)
oppossum
(Monodelphis domestica)
Mammalia SKA3 31
  • 49 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SKA3 31
  • 47 (a)
OneToOne
chicken
(Gallus gallus)
Aves SKA3 31 30
  • 55.01 (n)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ska3 30
  • 50.57 (n)
zebrafish
(Danio rerio)
Actinopterygii ska3 31
  • 20 (a)
OneToOne
Species where no ortholog for SKA3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for SKA3 Gene

ENSEMBL:
Gene Tree for SKA3 (if available)
TreeFam:
Gene Tree for SKA3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SKA3: view image

Paralogs for SKA3 Gene

No data available for Paralogs for SKA3 Gene

Variants for SKA3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SKA3 Gene

SNP ID Clinical significance and condition Chr 13 pos Variation AA Info Type
rs11546983 - p.Val58Ile
rs17279819 - p.Asp335Glu
rs17345690 - p.Thr254Ala

Additional dbSNP identifiers (rs#s) for SKA3 Gene

Structural Variations from Database of Genomic Variants (DGV) for SKA3 Gene

Variant ID Type Subtype PubMed ID
dgv3077n54 CNV gain 21841781
dgv3078n54 CNV gain 21841781
dgv315n67 CNV gain 20364138
dgv316n67 CNV gain 20364138
dgv924n106 CNV deletion 24896259
dgv925n106 CNV deletion 24896259
dgv960e59 CNV duplication 20981092
esv1003302 CNV deletion 20482838
esv1007120 CNV deletion 20482838
esv1249925 CNV deletion 17803354
esv2175517 CNV deletion 18987734
esv28665 CNV gain 19812545
esv3250163 CNV deletion 24192839
esv32897 CNV loss 17666407
esv33455 CNV loss 17666407
esv3550140 CNV deletion 23714750
esv3550141 CNV deletion 23714750
esv3550142 CNV deletion 23714750
esv3631454 CNV loss 21293372
esv3631455 CNV loss 21293372
esv3631456 CNV loss 21293372
esv8341 CNV loss 19470904
esv997322 CNV loss 20482838
nsv1037082 CNV gain 25217958
nsv1069734 CNV deletion 25765185
nsv1078303 OTHER inversion 25765185
nsv1115634 CNV deletion 24896259
nsv1120002 CNV deletion 24896259
nsv1120003 CNV deletion 24896259
nsv1127312 CNV deletion 24896259
nsv1140246 OTHER inversion 24896259
nsv1148852 CNV deletion 26484159
nsv1149576 CNV deletion 26484159
nsv1151909 OTHER inversion 26484159
nsv1152114 CNV deletion 26484159
nsv1152124 CNV deletion 26484159
nsv512307 CNV loss 21212237
nsv561247 CNV gain 21841781
nsv561250 CNV gain 21841781
nsv561256 CNV loss 21841781
nsv64608 CNV deletion 16902084
nsv826585 CNV gain 20364138
nsv958085 CNV deletion 24416366

Variation tolerance for SKA3 Gene

Residual Variation Intolerance Score: 90.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.61; 78.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SKA3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SKA3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SKA3 Gene

Disorders for SKA3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SKA3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
uterine adnexa cancer
- elite association - COSMIC cancer census association via MalaCards
Search SKA3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SKA3

genes like me logo Genes that share disorders with SKA3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SKA3 Gene

Publications for SKA3 Gene

  1. Stable kinetochore-microtubule interactions depend on the Ska complex and its new component Ska3/C13Orf3. (PMID: 19360002) Gaitanos TN … Nigg EA (The EMBO journal 2009) 2 3 4 54
  2. The human kinetochore Ska1 complex facilitates microtubule depolymerization-coupled motility. (PMID: 19289083) Welburn JP … Cheeseman IM (Developmental cell 2009) 2 3 4 54
  3. The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics. (PMID: 20813266) Ohta S … Rappsilber J (Cell 2010) 3 4 54
  4. Ska3 is required for spindle checkpoint silencing and the maintenance of chromosome cohesion in mitosis. (PMID: 19646878) Daum JR … Gorbsky GJ (Current biology : CB 2009) 2 3 54
  5. Comparative profiling identifies C13orf3 as a component of the Ska complex required for mammalian cell division. (PMID: 19387489) Theis M … Buchholz F (The EMBO journal 2009) 2 3 54

Products for SKA3 Gene

Sources for SKA3 Gene