Human Gene KNL1 (ENST00000346991.9_8) from GENCODE V47lift37
  Description: kinetochore scaffold 1, transcript variant 1 (from RefSeq NM_170589.5)
Gencode Transcript: ENST00000346991.9_8
Gencode Gene: ENSG00000137812.21_18
Transcript (Including UTRs)
   Position: hg19 chr15:40,886,218-40,956,540 Size: 70,323 Total Exon Count: 27 Strand: +
Coding Region
   Position: hg19 chr15:40,895,130-40,954,386 Size: 59,257 Coding Exon Count: 26 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:40,886,218-40,956,540)mRNA (may differ from genome)Protein (2342 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMalacards
MGIOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CASC5_HUMAN
DESCRIPTION: RecName: Full=Protein CASC5; AltName: Full=ALL1-fused gene from chromosome 15q14 protein; Short=AF15q14; AltName: Full=Bub-linking kinetochore protein; Short=Blinkin; AltName: Full=Cancer susceptibility candidate gene 5 protein; AltName: Full=Cancer/testis antigen 29; Short=CT29; AltName: Full=Kinetochore-null protein 1; AltName: Full=Protein D40/AF15q14;
FUNCTION: Performs two crucial functions during mitosis: it is essential for spindle-assembly checkpoint signaling and for correct chromosome alignment. Required for attachment of the kinetochores to the spindle microtubules. Directly links BUB1 and BUB1B to kinetochores. Part of the MIS12 complex, which may be fundamental for kinetochore formation and proper chromosome segregation during mitosis. Acts in coordination with CENPK to recruit the NDC80 complex to the outer kinetochore.
SUBUNIT: Interacts with DSN1, MIS12, BUB1, BUB1B, NSL1 and ZWINT.
SUBCELLULAR LOCATION: Nucleus. Chromosome, centromere, kinetochore. Note=Weakly expressed in interphase nuclei. Expression increases from prophase to late anaphase, but greatly diminishes from the telophase and cytokinesis to early G1 phase of cell cycle.
TISSUE SPECIFICITY: Highly expressed in testis, where it is localized in germ cells, in particular in spermatocytes and in the pre-acrosome of round spermatids. Detected in the acrosome of ejaculated spermatozoa. Detected in adult thymus, bone marrow, colon, small intestine, appendix and placenta, and in fetal liver and thymus.
DISEASE: Note=A chromosomal aberration involving CASC5 is associated with acute myeloblastic leukemia (AML). Translocation t(11;15)(q23;q14) with MLL/HRX. May give rise to a MLL-CASC5 fusion protein.
DISEASE: Note=Defects in CASC5 are a cause of primary microcephaly (MCPH). A rare homozygous missense mutation causing skipping of exon 18 with subsequent frameshift and protein truncation has been found in MCPH patients from three consanguineous families.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/AF15q14ID318.html";

-  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: KNL1
Diseases sorted by gene-association score: microcephaly 4, primary, autosomal recessive* (1329), median neuropathy (17), microcephaly (15), autosomal recessive primary microcephaly (8), mononeuritis of upper limb and mononeuritis multiplex (8)
* = Manually curated disease association

+  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: 11.26 RPKM in Testis
Total median expression: 25.30 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 -132.70390-0.340 Picture PostScript Text
3' UTR -753.802154-0.350 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
  Pfam Domains:
PF18210 - Knl1 RWD C-terminal domain
PF19221 - MELT motif

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3SI5 - X-ray MuPIT 4A1G - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q8NG31
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0001675 acrosome assembly
GO:0007049 cell cycle
GO:0007059 chromosome segregation
GO:0008608 attachment of spindle microtubules to kinetochore
GO:0010923 negative regulation of phosphatase activity
GO:0034080 CENP-A containing nucleosome assembly
GO:0034501 protein localization to kinetochore
GO:0051301 cell division

Cellular Component:
GO:0000775 chromosome, centromeric region
GO:0000776 kinetochore
GO:0000777 condensed chromosome kinetochore
GO:0001669 acrosomal vesicle
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005829 cytosol
GO:0016604 nuclear body


-  Descriptions from all associated GenBank mRNAs
  AF173994 - Homo sapiens AF15q14 mRNA, complete cds.
BC043597 - Homo sapiens cancer susceptibility candidate 5, mRNA (cDNA clone IMAGE:6013959), containing frame-shift errors.
BC014306 - Homo sapiens cancer susceptibility candidate 5, mRNA (cDNA clone IMAGE:3683505), with apparent retained intron.
AB022190 - Homo sapiens D40 mRNA, complete cds.
LF383717 - JP 2014500723-A/191220: Polycomb-Associated Non-Coding RNAs.
AK307605 - Homo sapiens cDNA, FLJ97553.
AK307996 - Homo sapiens cDNA, FLJ97944.
AF248041 - Homo sapiens AF15q14 protein mRNA, complete cds.
AF461041 - Homo sapiens AF15q14 isoform 2 mRNA, complete cds; alternatively spliced.
BC029373 - Homo sapiens cancer susceptibility candidate 5, mRNA (cDNA clone IMAGE:4611681), partial cds.
MA619294 - JP 2018138019-A/191220: Polycomb-Associated Non-Coding RNAs.
JD080544 - Sequence 61568 from Patent EP1572962.
JD241918 - Sequence 222942 from Patent EP1572962.
JD065201 - Sequence 46225 from Patent EP1572962.
LF348815 - JP 2014500723-A/156318: Polycomb-Associated Non-Coding RNAs.
BC172422 - Synthetic construct Homo sapiens clone IMAGE:100069116, MGC:199127 cancer susceptibility candidate 5 (CASC5) mRNA, encodes complete protein.
LF348818 - JP 2014500723-A/156321: Polycomb-Associated Non-Coding RNAs.
LF348819 - JP 2014500723-A/156322: Polycomb-Associated Non-Coding RNAs.
LF348820 - JP 2014500723-A/156323: Polycomb-Associated Non-Coding RNAs.
JD322273 - Sequence 303297 from Patent EP1572962.
JD221152 - Sequence 202176 from Patent EP1572962.
LF348821 - JP 2014500723-A/156324: Polycomb-Associated Non-Coding RNAs.
LF348822 - JP 2014500723-A/156325: Polycomb-Associated Non-Coding RNAs.
LF348823 - JP 2014500723-A/156326: Polycomb-Associated Non-Coding RNAs.
AB046790 - Homo sapiens mRNA for KIAA1570 protein, partial cds.
LF348824 - JP 2014500723-A/156327: Polycomb-Associated Non-Coding RNAs.
LF348825 - JP 2014500723-A/156328: Polycomb-Associated Non-Coding RNAs.
LF348826 - JP 2014500723-A/156329: Polycomb-Associated Non-Coding RNAs.
LF348827 - JP 2014500723-A/156330: Polycomb-Associated Non-Coding RNAs.
LF348828 - JP 2014500723-A/156331: Polycomb-Associated Non-Coding RNAs.
U52052 - Human S6 A-8 mRNA expressed in chromosome 6-suppressed melanoma cells.
JD068033 - Sequence 49057 from Patent EP1572962.
JD212369 - Sequence 193393 from Patent EP1572962.
JD512655 - Sequence 493679 from Patent EP1572962.
JD118063 - Sequence 99087 from Patent EP1572962.
JD387970 - Sequence 368994 from Patent EP1572962.
JD118061 - Sequence 99085 from Patent EP1572962.
JD319807 - Sequence 300831 from Patent EP1572962.
JD455201 - Sequence 436225 from Patent EP1572962.
JD387969 - Sequence 368993 from Patent EP1572962.
JD118062 - Sequence 99086 from Patent EP1572962.
LF212910 - JP 2014500723-A/20413: Polycomb-Associated Non-Coding RNAs.
MA584392 - JP 2018138019-A/156318: Polycomb-Associated Non-Coding RNAs.
MA584395 - JP 2018138019-A/156321: Polycomb-Associated Non-Coding RNAs.
MA584396 - JP 2018138019-A/156322: Polycomb-Associated Non-Coding RNAs.
MA584397 - JP 2018138019-A/156323: Polycomb-Associated Non-Coding RNAs.
MA584398 - JP 2018138019-A/156324: Polycomb-Associated Non-Coding RNAs.
MA584399 - JP 2018138019-A/156325: Polycomb-Associated Non-Coding RNAs.
MA584400 - JP 2018138019-A/156326: Polycomb-Associated Non-Coding RNAs.
MA584401 - JP 2018138019-A/156327: Polycomb-Associated Non-Coding RNAs.
MA584402 - JP 2018138019-A/156328: Polycomb-Associated Non-Coding RNAs.
MA584403 - JP 2018138019-A/156329: Polycomb-Associated Non-Coding RNAs.
MA584404 - JP 2018138019-A/156330: Polycomb-Associated Non-Coding RNAs.
MA584405 - JP 2018138019-A/156331: Polycomb-Associated Non-Coding RNAs.
MA448487 - JP 2018138019-A/20413: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8NG31 (Reactome details) participates in the following event(s):

R-HSA-606349 Mis18 complex binds the centromere
R-HSA-141409 Mad1 binds kinetochore
R-HSA-375302 Kinetochore capture of astral microtubules
R-HSA-5666129 CDC42:GTP recruits DIAPH2-2 to kinetochores
R-HSA-5666169 Kinetochore capture of astral microtubules is positively regulated by CDC42:GTP:p-S196-DIAPH2-2
R-HSA-606326 HJURP:CENPA complex localizes to the centromere
R-HSA-141431 MAD2 associates with the Mad1 kinetochore complex
R-HSA-141439 Release of activated MAD2 from kinetochores
R-HSA-2467811 Separation of sister chromatids
R-HSA-2467809 ESPL1 (Separase) cleaves centromeric cohesin
R-HSA-5666160 AURKB phosphorylates DIAPH2-2 at kinetochores
R-HSA-141422 MAD2 converted to an inhibitory state via interaction with Mad1
R-HSA-1638821 PP2A-B56 dephosphorylates centromeric cohesin
R-HSA-1638803 Phosphorylation of cohesin by PLK1 at centromeres
R-HSA-2468287 CDK1 phosphorylates CDCA5 (Sororin) at centromeres
R-HSA-606279 Deposition of new CENPA-containing nucleosomes at the centromere
R-HSA-141444 Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
R-HSA-68877 Mitotic Prometaphase
R-HSA-5663220 RHO GTPases Activate Formins
R-HSA-774815 Nucleosome assembly
R-HSA-2500257 Resolution of Sister Chromatid Cohesion
R-HSA-2467813 Separation of Sister Chromatids
R-HSA-141424 Amplification of signal from the kinetochores
R-HSA-68886 M Phase
R-HSA-195258 RHO GTPase Effectors
R-HSA-73886 Chromosome Maintenance
R-HSA-68882 Mitotic Anaphase
R-HSA-69618 Mitotic Spindle Checkpoint
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-194315 Signaling by Rho GTPases
R-HSA-1640170 Cell Cycle
R-HSA-2555396 Mitotic Metaphase and Anaphase
R-HSA-69620 Cell Cycle Checkpoints
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: CASC5, ENST00000346991.1, ENST00000346991.2, ENST00000346991.3, ENST00000346991.4, ENST00000346991.5, ENST00000346991.6, ENST00000346991.7, ENST00000346991.8, KIAA1570, KNL1 , KNL1_HUMAN, NM_170589, Q8NG31, Q8NHE1, Q8WXA6, Q9HCK2, Q9NR92, uc317xlg.1, uc317xlg.2
UCSC ID: ENST00000346991.9_8
RefSeq Accession: NM_170589.5
Protein: Q8NG31 (aka CASC5_HUMAN)

-  Gene Model Information
  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.