This gene encodes a coiled-coil domain-containing protein that functions in mitotic spindle formation and chromosome segregation. The encoded protein plays a role in coordinating microtubule attachment by promoting recruitment of dynein proteins, and in mitotic checkpoint signaling. [provided by RefSeq, Jul 2016] See more...

Aliases for SPDL1 Gene

Aliases for SPDL1 Gene

  • Spindle Apparatus Coiled-Coil Protein 1 2 3 5
  • Coiled-Coil Domain-Containing Protein 99 3 4
  • Rhabdomyosarcoma Antigen MU-RMS-40.4A 3 4
  • Arsenite-Related Gene 1 Protein 3 4
  • Protein Spindly 3 4
  • CCDC99 3 4
  • Spindle Apparatus Coiled-Coil Domain-Containing Protein 1 4
  • Rrhabdomyosarcoma Antigen Protein MU-RMS-40.4A 3
  • Coiled-Coil Domain Containing 99 2
  • Spindly Homolog (Drosophila) 2
  • HSpindly 4

External Ids for SPDL1 Gene

Previous HGNC Symbols for SPDL1 Gene

  • CCDC99

Previous GeneCards Identifiers for SPDL1 Gene

  • GC05P169011

Summaries for SPDL1 Gene

Entrez Gene Summary for SPDL1 Gene

  • This gene encodes a coiled-coil domain-containing protein that functions in mitotic spindle formation and chromosome segregation. The encoded protein plays a role in coordinating microtubule attachment by promoting recruitment of dynein proteins, and in mitotic checkpoint signaling. [provided by RefSeq, Jul 2016]

GeneCards Summary for SPDL1 Gene

SPDL1 (Spindle Apparatus Coiled-Coil Protein 1) is a Protein Coding gene. Among its related pathways are Mitotic Metaphase and Anaphase and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include enzyme binding and kinetochore binding. An important paralog of this gene is BICDL1.

UniProtKB/Swiss-Prot Summary for SPDL1 Gene

  • 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 (PubMed:17576797, PubMed:19468067). Acts as an adapter protein linking the dynein motor complex to various cargos and converts dynein from a non-processive to a highly processive motor in the presence of dynactin. Facilitates the interaction between dynein and dynactin and activates dynein processivity (the ability to move along a microtubule for a long distance without falling off the track) (PubMed:25035494).

Additional gene information for SPDL1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPDL1 Gene

Genomics for SPDL1 Gene

GeneHancer (GH) Regulatory Elements for SPDL1 Gene

Promoters and enhancers for SPDL1 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
GH05J169582 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 546.1 +0.7 744 2.8 RXRA ZBTB40 ZNF217 SIN3A NRF1 POLR2G GTF2E2 PHF8 ZFX REST SPDL1 LOC105377714 lnc-DOCK2-2 lnc-SLIT3-1 lnc-DOCK2-1
GH05J169581 Enhancer 0.8 Ensembl ENCODE 531 -1.8 -1838 0.8 CTCF RAD21 TRIM22 MYNN SMC3 GATA3 ZNF654 GATAD1 HNF4A TEAD3 SPDL1 LOC105377714 lnc-DOCK2-2 lnc-SLIT3-1 RF00026-910 RNU6-477P
GH05J169628 Enhancer 1 FANTOM5 Ensembl ENCODE 53.3 +46.4 46364 3.6 TCF12 JUND FOS FOSL2 CEBPB CHD2 JUN STAT3 EP300 STAT1 SPDL1 SLIT3 DOCK2 piR-58308-280
GH05J169636 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 21.7 +53.9 53867 2.6 HNRNPK ZBTB40 SIN3A GTF2E2 ZNF263 CTBP1 TRIM22 POLR2A KDM4B RBM25 DOCK2 SPDL1 ENSG00000253269
GH05J169626 Enhancer 0.7 Ensembl ENCODE 32.3 +43.5 43518 1.6 JUND FOS REST FOSL2 MAFK JUN BHLHE40 NFE2L2 POLR2A TAF1 SPDL1 piR-58308-280 DOCK2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPDL1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SPDL1

Genomic Locations for SPDL1 Gene

Genomic Locations for SPDL1 Gene
chr5:169,583,634-169,604,778
(GRCh38/hg38)
Size:
21,145 bases
Orientation:
Plus strand
chr5:169,010,638-169,031,782
(GRCh37/hg19)
Size:
21,145 bases
Orientation:
Plus strand

Genomic View for SPDL1 Gene

Genes around SPDL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPDL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPDL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPDL1 Gene

Proteins for SPDL1 Gene

  • Protein details for SPDL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96EA4-SPDLY_HUMAN
    Recommended name:
    Protein Spindly
    Protein Accession:
    Q96EA4
    Secondary Accessions:
    • B4E393
    • C9JS47
    • Q8TEC8
    • Q9HD44
    • Q9NX97

    Protein attributes for SPDL1 Gene

    Size:
    605 amino acids
    Molecular mass:
    70172 Da
    Quaternary structure:
    • Interacts with KNTC1 and ZW10. These interactions appear weak and may be transient or indirect (PubMed:19468067). Interacts with dynein intermediate chain and dynactin (DCTN1) (PubMed:25035494).
    SequenceCaution:
    • Sequence=AAG01408.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=BAA91119.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=BAB85022.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for SPDL1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPDL1 Gene

Post-translational modifications for SPDL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SPDL1 Gene

Domains & Families for SPDL1 Gene

Gene Families for SPDL1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SPDL1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SPDL1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ55024 (B4E393_HUMAN)
  • Rhabdomyosarcoma antigen MU-RMS-40.4A (SPDLY_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96EA4

UniProtKB/Swiss-Prot:

SPDLY_HUMAN :
  • Belongs to the Spindly family.
Family:
  • Belongs to the Spindly family.
genes like me logo Genes that share domains with SPDL1: view

Function for SPDL1 Gene

Molecular function for SPDL1 Gene

UniProtKB/Swiss-Prot 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 (PubMed:17576797, PubMed:19468067). Acts as an adapter protein linking the dynein motor complex to various cargos and converts dynein from a non-processive to a highly processive motor in the presence of dynactin. Facilitates the interaction between dynein and dynactin and activates dynein processivity (the ability to move along a microtubule for a long distance without falling off the track) (PubMed:25035494).

Phenotypes From GWAS Catalog for SPDL1 Gene

Gene Ontology (GO) - Molecular Function for SPDL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19468067
GO:0019899 enzyme binding IPI 23382074
GO:0043515 kinetochore binding IBA,IDA 19468067
genes like me logo Genes that share ontologies with SPDL1: view
genes like me logo Genes that share phenotypes with SPDL1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPDL1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SPDL1 Gene

Localization for SPDL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPDL1 Gene

Cytoplasm, cytoskeleton, microtubule organizing center, 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.

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 SPDL1 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 5
plasma membrane 1
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SPDL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000775 chromosome, centromeric region IEA --
GO:0000776 kinetochore IEA --
GO:0000777 condensed chromosome kinetochore IEA --
GO:0000922 spindle pole IDA,IBA 19468067
GO:0000940 condensed chromosome outer kinetochore IBA,IDA 19468067
genes like me logo Genes that share ontologies with SPDL1: view

Pathways & Interactions for SPDL1 Gene

genes like me logo Genes that share pathways with SPDL1: view

Pathways by source for SPDL1 Gene

Gene Ontology (GO) - Biological Process for SPDL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000132 establishment of mitotic spindle orientation IMP 19468067
GO:0007049 cell cycle IEA --
GO:0007080 mitotic metaphase plate congression IBA,IMP 19468067
GO:0007094 mitotic spindle assembly checkpoint IEA --
GO:0034501 protein localization to kinetochore IBA,IMP 19468067
genes like me logo Genes that share ontologies with SPDL1: view

No data available for SIGNOR curated interactions for SPDL1 Gene

Drugs & Compounds for SPDL1 Gene

No Compound Related Data Available

Transcripts for SPDL1 Gene

mRNA/cDNA for SPDL1 Gene

6 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
16 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 SPDL1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SPDL1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15
SP1: -
SP2: - - - -
SP3:
SP4:
SP5: - -
SP6:

Relevant External Links for SPDL1 Gene

GeneLoc Exon Structure for
SPDL1

Expression for SPDL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SPDL1 Gene

Protein differential expression in normal tissues from HIPED for SPDL1 Gene

This gene is overexpressed in Urinary Bladder (33.7), Testis (12.4), Bone (9.5), and Ovary (8.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SPDL1 Gene



Protein tissue co-expression partners for SPDL1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPDL1

SOURCE GeneReport for Unigene cluster for SPDL1 Gene:

Hs.368710

Evidence on tissue expression from TISSUES for SPDL1 Gene

  • Nervous system(4.5)
  • Intestine(4.3)
genes like me logo Genes that share expression patterns with SPDL1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPDL1 Gene

Orthologs for SPDL1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SPDL1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SPDL1 31 30
  • 99.39 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SPDL1 31 30
  • 90.22 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SPDL1 31 30
  • 87.4 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Spdl1 30
  • 78.28 (n)
mouse
(Mus musculus)
Mammalia Spdl1 17 31 30
  • 77.34 (n)
oppossum
(Monodelphis domestica)
Mammalia SPDL1 31
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves CCDC99 30
  • 66.94 (n)
SPDL1 31
  • 59 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SPDL1 31
  • 53 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia spdl1 30
  • 61.28 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.9016 30
zebrafish
(Danio rerio)
Actinopterygii zgc:171223 30
  • 57.07 (n)
SPDL1 31
  • 46 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 25 (a)
OneToOne
Species where no ortholog for SPDL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 SPDL1 Gene

ENSEMBL:
Gene Tree for SPDL1 (if available)
TreeFam:
Gene Tree for SPDL1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPDL1: view image

Paralogs for SPDL1 Gene

Paralogs for SPDL1 Gene

genes like me logo Genes that share paralogs with SPDL1: view

Variants for SPDL1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SPDL1 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
753082 Likely Benign: not provided 169,596,559(+) A/G SPLICE_ACCEPTOR_VARIANT
783621 Likely Benign: not provided 169,591,052(+) A/G MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT
783622 Likely Benign: not provided 169,598,497(+) T/C MISSENSE_VARIANT
790023 Benign: not provided 169,601,320(+) G/A SYNONYMOUS_VARIANT
rs730882228 Likely Pathogenic: Neonatal death; Severe primary microcephaly 169,604,101(+) GAAAAGAAACTTCAAG INFRAME_DELETION,THREE_PRIME_UTR_VARIANT

Additional dbSNP identifiers (rs#s) for SPDL1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SPDL1 Gene

Variant ID Type Subtype PubMed ID
nsv1031257 CNV gain 25217958
nsv5123 CNV insertion 18451855

Variation tolerance for SPDL1 Gene

Residual Variation Intolerance Score: 93.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.24; 52.61% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPDL1 Gene

Human Gene Mutation Database (HGMD)
SPDL1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPDL1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPDL1 Gene

Disorders for SPDL1 Gene

Additional Disease Information for SPDL1

No disorders were found for SPDL1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SPDL1 Gene

Publications for SPDL1 Gene

  1. Spindly/CCDC99 is required for efficient chromosome congression and mitotic checkpoint regulation. (PMID: 20427577) Barisic M … Geley S (Molecular biology of the cell 2010) 2 3 54
  2. Mitotic control of kinetochore-associated dynein and spindle orientation by human Spindly. (PMID: 19468067) Chan YW … Santamaria A (The Journal of cell biology 2009) 3 4 54
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  5. Nuclear actin interactome analysis links actin to KAT14 histone acetyl transferase and mRNA splicing. (PMID: 30890647) Viita T … Vartiainen MK (Journal of cell science 2019) 3 54

Products for SPDL1 Gene

Sources for SPDL1 Gene