Human Gene SPDL1 (ENST00000265295.9_6) from GENCODE V47lift37
  Description: spindle apparatus coiled-coil protein 1, transcript variant 3 (from RefSeq NM_017785.5)
Gencode Transcript: ENST00000265295.9_6
Gencode Gene: ENSG00000040275.17_15
Transcript (Including UTRs)
   Position: hg19 chr5:169,010,777-169,031,782 Size: 21,006 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr5:169,015,421-169,031,211 Size: 15,791 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene 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 (chr5:169,010,777-169,031,782)mRNA (may differ from genome)Protein (605 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SPDLY_HUMAN
DESCRIPTION: RecName: Full=Protein Spindly; Short=hSpindly; AltName: Full=Arsenite-related gene 1 protein; AltName: Full=Coiled-coil domain-containing protein 99; AltName: Full=Rhabdomyosarcoma antigen MU-RMS-40.4A; AltName: Full=Spindle apparatus coiled-coil domain-containing protein 1;
FUNCTION: Required for the localization of dynein and dynactin to the mitotic kintochore. Dynein is believed to control the initial lateral interaction between the kinetochore and spindle microtubules and to facilitate the subsequent formation of end-on kinetochore-microtubule attachments mediated by the NDC80 complex. Also required for correct spindle orientation. Does not appear to be required for the removal of spindle assembly checkpoint (SAC) proteins from the kinetochore upon bipolar spindle attachment.
SUBUNIT: Interacts with KNTC1 and ZW10. These interactions appear weak and may be transient or indirect.
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton, centrosome. Chromosome, centromere, kinetochore. Nucleus. Cytoplasm, cytoskeleton, spindle pole. Note=Localizes to the nucleus in interphase and to the kinetochore in early prometaphase. Relocalizes to the mitotic spindle pole before metaphase and is subsequently lost from the spindle poles after chromosome congression is completed. Removal of this protein from the kinetochore requires the dynein/dynactin complex.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the Spindly family.
SEQUENCE CAUTION: Sequence=AAG01408.1; Type=Frameshift; Positions=604; Sequence=BAA91119.1; Type=Frameshift; Positions=412; Sequence=BAB85022.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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           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: 10.27 RPKM in Testis
Total median expression: 108.35 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 -49.40140-0.353 Picture PostScript Text
3' UTR -118.80571-0.208 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 Q96EA4
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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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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0019899 enzyme binding
GO:0043515 kinetochore binding

Biological Process:
GO:0000132 establishment of mitotic spindle orientation
GO:0007049 cell cycle
GO:0007080 mitotic metaphase plate congression
GO:0031577 spindle checkpoint
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:0000922 spindle pole
GO:0000940 condensed chromosome outer kinetochore
GO:0005634 nucleus
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0005856 cytoskeleton


-  Descriptions from all associated GenBank mRNAs
  LF209033 - JP 2014500723-A/16536: Polycomb-Associated Non-Coding RNAs.
AK304623 - Homo sapiens cDNA FLJ55024 complete cds.
AF269167 - Homo sapiens arsenite related gene 1 mRNA, complete cds.
AK310442 - Homo sapiens cDNA, FLJ17484.
AK308835 - Homo sapiens cDNA, FLJ98876.
BC012568 - Homo sapiens coiled-coil domain containing 99, mRNA (cDNA clone MGC:13437 IMAGE:4102558), complete cds.
AY517557 - Homo sapiens hypothetical rhabdomyosarcoma antigen MU-RMS-40.4A mRNA, complete cds.
LF325409 - JP 2014500723-A/132912: Polycomb-Associated Non-Coding RNAs.
JD466222 - Sequence 447246 from Patent EP1572962.
JD543748 - Sequence 524772 from Patent EP1572962.
AK000371 - Homo sapiens cDNA FLJ20364 fis, clone HEP17854.
JD040538 - Sequence 21562 from Patent EP1572962.
CU680366 - Synthetic construct Homo sapiens gateway clone IMAGE:100020720 5' read CCDC99 mRNA.
JF432342 - Synthetic construct Homo sapiens clone IMAGE:100073530 coiled-coil domain containing 99 (CCDC99) gene, encodes complete protein.
KJ899035 - Synthetic construct Homo sapiens clone ccsbBroadEn_08429 CCDC99-like gene, encodes complete protein.
LF325406 - JP 2014500723-A/132909: Polycomb-Associated Non-Coding RNAs.
AK074227 - Homo sapiens cDNA FLJ23647 fis, clone COL04258.
LF325403 - JP 2014500723-A/132906: Polycomb-Associated Non-Coding RNAs.
LF325402 - JP 2014500723-A/132905: Polycomb-Associated Non-Coding RNAs.
LF325401 - JP 2014500723-A/132904: Polycomb-Associated Non-Coding RNAs.
LF325398 - JP 2014500723-A/132901: Polycomb-Associated Non-Coding RNAs.
AK098009 - Homo sapiens cDNA FLJ40690 fis, clone THYMU2024616.
JD391232 - Sequence 372256 from Patent EP1572962.
MA560986 - JP 2018138019-A/132912: Polycomb-Associated Non-Coding RNAs.
MA560983 - JP 2018138019-A/132909: Polycomb-Associated Non-Coding RNAs.
MA560980 - JP 2018138019-A/132906: Polycomb-Associated Non-Coding RNAs.
MA560979 - JP 2018138019-A/132905: Polycomb-Associated Non-Coding RNAs.
MA560978 - JP 2018138019-A/132904: Polycomb-Associated Non-Coding RNAs.
MA560975 - JP 2018138019-A/132901: Polycomb-Associated Non-Coding RNAs.
MA444610 - JP 2018138019-A/16536: Polycomb-Associated Non-Coding RNAs.

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

Protein Q96EA4 (Reactome details) participates in the following event(s):

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-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-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-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-68882 Mitotic Anaphase
R-HSA-69618 Mitotic Spindle Checkpoint
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-194315 Signaling by Rho GTPases
R-HSA-2555396 Mitotic Metaphase and Anaphase
R-HSA-69620 Cell Cycle Checkpoints
R-HSA-1640170 Cell Cycle
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B4E393, C9JS47, CCDC99 , ENST00000265295.1, ENST00000265295.2, ENST00000265295.3, ENST00000265295.4, ENST00000265295.5, ENST00000265295.6, ENST00000265295.7, ENST00000265295.8, NM_017785, Q8TEC8, Q96EA4, Q9HD44, Q9NX97, SPDL1 , SPDLY_HUMAN, uc317iab.1, uc317iab.2
UCSC ID: ENST00000265295.9_6
RefSeq Accession: NM_017785.5
Protein: Q96EA4 (aka SPDLY_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.