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

Gene ID: 54908, updated on 19-Sep-2024

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
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Genomic context

See SPDL1 in Genome Data Viewer
Location:
5q35.1
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (169583773..169604778)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (170119147..170140150)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (169010777..169031782)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901131 Neighboring gene uncharacterized LOC105377714 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:168884987-168885782 Neighboring gene uncharacterized LOC105377715 Neighboring gene RNA, U6 small nuclear 477, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:169010404-169011404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16601 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23593 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23595 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23596 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:169122482-169123681 Neighboring gene dedicator of cytokinesis 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23597 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23598 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23599 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23601 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:169235189-169235766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23603 Neighboring gene NANOG hESC enhancer GRCh37_chr5:169334064-169334793 Neighboring gene inhibitory synaptic factor family member 2B Neighboring gene Sharpr-MPRA regulatory region 8772 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:169403516-169404715 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:169407449-169408187 Neighboring gene microRNA 378e

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ20364, FLJ40690

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
 
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
 
involved_in establishment of mitotic spindle orientation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in mitotic metaphase chromosome alignment IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in mitotic metaphase chromosome alignment 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
 
involved_in protein localization to kinetochore IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in centrosome IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol TAS
Traceable Author Statement
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
 
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
 
located_in spindle pole IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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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

  1. NG_051238.1 RefSeqGene

    Range
    5140..26145
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001329639.2NP_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:351417
    GrpE; nucleotide exchange factor GrpE
  2. NM_001329640.2NP_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:351417
    GrpE; nucleotide exchange factor GrpE
  3. NM_001329641.2NP_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
    B4E393, C9JS47, Q8TEC8, Q96EA4, Q9HD44, Q9NX97
  4. NM_001329642.2NP_001316571.1  protein Spindly isoform c

    Status: REVIEWED

    Source sequence(s)
    AC008680, BU616897
    Conserved Domains (1) summary
    cl03075
    Location:280346
    GrpE; nucleotide exchange factor GrpE
  5. NM_001329643.2NP_001316572.1  protein Spindly isoform d

    Status: REVIEWED

    Source sequence(s)
    AC008680, BU616897
  6. NM_017785.5NP_060255.3  protein Spindly isoform b

    See identical proteins and their annotated locations for NP_060255.3

    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
    B4E393, C9JS47, Q8TEC8, Q96EA4, Q9HD44, Q9NX97
    Related
    ENSP00000265295.4, ENST00000265295.9
    Conserved Domains (1) summary
    cl03075
    Location:351417
    GrpE; nucleotide exchange factor GrpE

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    169583773..169604778
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047417344.1XP_047273300.1  protein Spindly isoform X2

    UniProtKB/Swiss-Prot
    B4E393, C9JS47, Q8TEC8, Q96EA4, Q9HD44, Q9NX97
  2. XM_047417345.1XP_047273301.1  protein Spindly isoform X2

    UniProtKB/Swiss-Prot
    B4E393, C9JS47, Q8TEC8, Q96EA4, Q9HD44, Q9NX97
  3. XM_047417346.1XP_047273302.1  protein Spindly isoform X2

    UniProtKB/Swiss-Prot
    B4E393, C9JS47, Q8TEC8, Q96EA4, Q9HD44, Q9NX97
  4. XM_011534587.3XP_011532889.1  protein Spindly isoform X1

    See identical proteins and their annotated locations for XP_011532889.1

    Conserved Domains (1) summary
    cl03075
    Location:351417
    GrpE; nucleotide exchange factor GrpE
  5. XM_011534588.3XP_011532890.1  protein Spindly isoform X1

    See identical proteins and their annotated locations for XP_011532890.1

    Conserved Domains (1) summary
    cl03075
    Location:351417
    GrpE; nucleotide exchange factor GrpE
  6. XM_011534589.3XP_011532891.1  protein Spindly isoform X1

    See identical proteins and their annotated locations for XP_011532891.1

    Conserved Domains (1) summary
    cl03075
    Location:351417
    GrpE; nucleotide exchange factor GrpE
  7. XM_047417347.1XP_047273303.1  protein Spindly isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    170119147..170140150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054352872.1XP_054208847.1  protein Spindly isoform X2

  2. XM_054352873.1XP_054208848.1  protein Spindly isoform X2

  3. XM_054352874.1XP_054208849.1  protein Spindly isoform X2

  4. XM_054352869.1XP_054208844.1  protein Spindly isoform X1

  5. XM_054352870.1XP_054208845.1  protein Spindly isoform X1

  6. XM_054352871.1XP_054208846.1  protein Spindly isoform X1

  7. XM_054352875.1XP_054208850.1  protein Spindly isoform X3