SPDL1 spindle apparatus coiled-coil protein 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPDL1provided by HGNC
Official Full Name: spindle apparatus coiled-coil protein 1provided by HGNC
Primary source: HGNC:HGNC:26010
See related: Ensembl:ENSG00000040275 MIM:616401; AllianceGenome:HGNC:26010
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CCDC99
Summary: 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]
Expression: Broad expression in testis (RPKM 14.1), lymph node (RPKM 4.5) and 21 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 5q35.1

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (169583773..169604778)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (170119147..170140150)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (169010777..169031782)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of a missense variant in SPDL1 associated with idiopathic pulmonary fibrosis.
Title: Identification of a missense variant in SPDL1 associated with idiopathic pulmonary fibrosis.
[Expression and clinical significance of Spindly and Bub3 in oral squamous cell carcinoma].
Title: [Expression and clinical significance of Spindly and Bub3 in oral squamous cell carcinoma].
SPDL1 knockdown in human CRC cells significantly increased invasion and migration of tumor cells. Lower SPDL1 expression levels are significantly associated with reduced survival in CRC patients. SPDL1 depletion in human CRC cells significantly increases tumor development in xenograft assays. SPDL1 is a human CRC tumor-suppressor genes that acts downstream of MRTFB to regulate CRC growth and survival.
Title: MRTFB suppresses colorectal cancer development through regulating SPDL1 and MCAM.
Using mass spectrometry this study identified CCDC99 as a new target of USP45. The data showed that CCDC99 and USP45 are part of the same complex and that their interaction specifically depends on the catalytic activity of USP45.
Title: USP45 and Spindly are part of the same complex implicated in cell migration.
Farnesylation of Spindly is essential for its localization, & thus for proper localization of dynein & dynactin, to prometaphase kinetochores. Both Spindly and CENP-E farnesylation are required for efficient chromosome congression
Title: Preventing farnesylation of the dynein adaptor Spindly contributes to the mitotic defects caused by farnesyltransferase inhibitors.
hSpindly is farnesylated in vivo and farnesylation is essential for its interaction with the RZZ complex and hence Kinetochore localization.
Title: A novel role of farnesylation in targeting a mitotic checkpoint protein, human Spindly, to kinetochores.
Spindly is not only required for kinetochore localization of dynein but is a functional component of a mechanism that couples dynein-dependent poleward movement of chromosomes to their efficient attachment to microtubules.
Title: Spindly/CCDC99 is required for efficient chromosome congression and mitotic checkpoint regulation.
dynein-mediated removal of Spindly from microtubule-attached kinetochores, rather than poleward transport per se, is the critical reaction in checkpoint silencing
Title: Removal of Spindly from microtubule-attached kinetochores controls spindle checkpoint silencing in human cells.
[hSpindly] Localization of human Spindly (hSpindly) to kinetochores is controlled by the Rod/Zw10/Zwilch (RZZ) complex and Aurora B.
Title: Mitotic control of kinetochore-associated dynein and spindle orientation by human Spindly.

Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

RH48014 (e-PCR)
- UniSTS:42853

RH78613 (e-PCR)
- UniSTS:25025

SHGC-110560 (e-PCR)
- UniSTS:167899

Homology

Homologs of the SPDL1 gene: The SPDL1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 495 organisms have orthologs with human gene SPDL1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables kinetochore binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables kinetochore binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in establishment of mitotic spindle orientation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in establishment of mitotic spindle orientation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic metaphase plate congression	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in mitotic metaphase plate congression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic spindle assembly checkpoint signaling	IEA Inferred from Electronic Annotation more info
involved_in protein localization to kinetochore	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in protein localization to kinetochore	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	TAS Traceable Author Statement more info
located_in microtubule organizing center	IEA Inferred from Electronic Annotation more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of outer kinetochore	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of outer kinetochore	IDA Inferred from Direct Assay more info	PubMed
is_active_in spindle pole	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in spindle pole	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: protein Spindly

Names: arsenite-related gene 1 protein; coiled-coil domain-containing protein 99; rhabdomyosarcoma antigen MU-RMS-40.4A; rrhabdomyosarcoma antigen protein MU-RMS-40.4A

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_051238.1 RefSeqGene

Range

5140..26145

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001329639.2 → NP_001316568.1 protein Spindly isoform a

Status: REVIEWED

Description

Transcript Variant: Variants 1 and 2 encode the same isoform (a).

Source sequence(s)

AC008680, BU616897

Conserved Domains (1) summary

cl03075
Location:351 → 417

GrpE; nucleotide exchange factor GrpE
NM_001329640.2 → NP_001316569.1 protein Spindly isoform a

Status: REVIEWED

Description

Transcript Variant: Variants 1 and 2 encode the same isoform (a).

Source sequence(s)

AC008680, BU616897

Conserved Domains (1) summary

cl03075
Location:351 → 417

GrpE; nucleotide exchange factor GrpE
NM_001329641.2 → NP_001316570.1 protein Spindly isoform b

Status: REVIEWED

Description

Transcript Variant: Variants 3 and 4 encode the same isoform (b).

Source sequence(s)

AC008680, BU616897

Consensus CDS

CCDS4370.1

UniProtKB/Swiss-Prot

Q96EA4, Q9NX97
NM_001329642.2 → NP_001316571.1 protein Spindly isoform c

Status: REVIEWED

Source sequence(s)

AC008680, BU616897

Conserved Domains (1) summary

cl03075
Location:280 → 346

GrpE; nucleotide exchange factor GrpE
NM_001329643.2 → NP_001316572.1 protein Spindly isoform d

Status: REVIEWED

Source sequence(s)

AC008680, BU616897
NM_017785.5 → NP_060255.3 protein Spindly isoform b

Status: REVIEWED

Description

Transcript Variant: Variants 3 and 4 encode the same isoform (b).

Source sequence(s)

BC012568, BP295943, BU166207, CA417197, CD653505, DC379275

Consensus CDS

CCDS4370.1

UniProtKB/Swiss-Prot

Q96EA4, Q9NX97

Related

ENSP00000265295.4, ENST00000265295.9

Conserved Domains (1) summary

cl03075
Location:351 → 417

GrpE; nucleotide exchange factor GrpE

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

169583773..169604778

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047417344.1 → XP_047273300.1 protein Spindly isoform X2

UniProtKB/Swiss-Prot

Q9NX97
XM_047417345.1 → XP_047273301.1 protein Spindly isoform X2

UniProtKB/Swiss-Prot

Q9NX97
XM_047417346.1 → XP_047273302.1 protein Spindly isoform X2

UniProtKB/Swiss-Prot

Q9NX97
XM_011534587.3 → XP_011532889.1 protein Spindly isoform X1

Conserved Domains (1) summary

cl03075
Location:351 → 417

GrpE; nucleotide exchange factor GrpE
XM_011534588.3 → XP_011532890.1 protein Spindly isoform X1

Conserved Domains (1) summary

cl03075
Location:351 → 417

GrpE; nucleotide exchange factor GrpE
XM_011534589.3 → XP_011532891.1 protein Spindly isoform X1

Conserved Domains (1) summary

cl03075
Location:351 → 417

GrpE; nucleotide exchange factor GrpE
XM_047417347.1 → XP_047273303.1 protein Spindly isoform X3