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SPOCD1 SPOC domain containing 1 [ Homo sapiens (human) ]

Gene ID: 90853, updated on 2-Nov-2024

Summary

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Official Symbol
SPOCD1provided by HGNC
Official Full Name
SPOC domain containing 1provided by HGNC
Primary source
HGNC:HGNC:26338
See related
Ensembl:ENSG00000134668 MIM:619038; AllianceGenome:HGNC:26338
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
PPP1R146
Summary
This gene encodes a protein that belongs to the TFIIS family of transcription factors. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
Expression
Biased expression in testis (RPKM 4.6), urinary bladder (RPKM 3.3) and 7 other tissues See more
Orthologs
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Genomic context

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See SPOCD1 in Genome Data Viewer
Location:
1p35.2
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (31790422..31816022, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (31648071..31674002, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32256023..32281623, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene adhesion G protein-coupled receptor B2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 574 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32227559-32228412 Neighboring gene uncharacterized LOC124903930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 576 Neighboring gene microRNA 4254 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32253763-32254538 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 578 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 579 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:32303933-32304116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 655 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 656 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 657 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 658 Neighboring gene uncharacterized LOC128031832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32389035-32389578 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 659 Neighboring gene protein tyrosine phosphatase 4A2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 660 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:32403472-32403643 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 581 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 661 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32409768-32410302 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32419864-32420642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32420643-32421419 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32421420-32422197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 667 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:32473819-32474378 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32479704-32480274 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 583 Neighboring gene KH RNA binding domain containing, signal transduction associated 1 Neighboring gene VISTA enhancer hs645 Neighboring gene NANOG hESC enhancer GRCh37_chr1:32526442-32527054

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Haplotype phasing of a bipolar disorder pedigree revealed rare multiple mutations of SPOCD1 gene in the 1p36-35 susceptibility locus. Takamatsu G, et al. J Affect Disord, 2022 Aug 1. PMID 35504398
  2. SPOCD1 promotes cell proliferation and inhibits cell apoptosis in human osteosarcoma. Liang J, et al. Mol Med Rep, 2018 Feb. PMID 29257309
  3. LncRNA SPOCD1-AS from ovarian cancer extracellular vesicles remodels mesothelial cells to promote peritoneal metastasis via interacting with G3BP1. Wang C, et al. J Exp Clin Cancer Res, 2021 Mar 16. PMID 33726799, Free PMC Article
  4. Exome Array Analysis Identifies Variants in SPOCD1 and BTN3A2 That Affect Risk for Gastric Cancer. Zhu M, et al. Gastroenterology, 2017 Jun. PMID 28246015
  5. C19ORF84 connects piRNA and DNA methylation machineries to defend the mammalian germ line. Zoch A, et al. Mol Cell, 2024 Mar 21. PMID 38359823,

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Haplotype phasing of a bipolar disorder pedigree revealed rare multiple mutations of SPOCD1 gene in the 1p36-35 susceptibility locus.
    Title: Haplotype phasing of a bipolar disorder pedigree revealed rare multiple mutations of SPOCD1 gene in the 1p36-35 susceptibility locus.
  2. LncRNA SPOCD1-AS from ovarian cancer extracellular vesicles remodels mesothelial cells to promote peritoneal metastasis via interacting with G3BP1.
    Title: LncRNA SPOCD1-AS from ovarian cancer extracellular vesicles remodels mesothelial cells to promote peritoneal metastasis via interacting with G3BP1.
  3. SPOCD1 promoted cell proliferation and inhibited cell apoptosis through regulation of VEGFA in osteosarcoma.
    Title: SPOCD1 promotes cell proliferation and inhibits cell apoptosis in human osteosarcoma.
  4. SPOCD1 genetic variants have role in gastric carcinogenesis.
    Title: Exome Array Analysis Identifies Variants in SPOCD1 and BTN3A2 That Affect Risk for Gastric Cancer.
  5. SPOCD1 expression is significantly upregulated in human masticatory mucosa during wound healing
    Title: Human gingiva transcriptome during wound healing.
Submit: New GeneRIF Correction

Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ25348, FLJ38873, FLJ39908

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in piRNA-mediated retrotransposon silencing by heterochromatin formation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in spermatogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
SPOC domain-containing protein 1
Names
protein phosphatase 1, regulatory subunit 146

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.

mRNA and Protein(s)

  1. NM_001281987.3 → NP_001268916.1  SPOC domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001268916.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' terminal exon compared to variant 1. This results in a shorter protein (isoform 2) compared to isoform 1.
    Source sequence(s)
    AL354919
    Consensus CDS
    CCDS60066.1
    UniProtKB/Swiss-Prot
    Q6ZMY3
    Related
    ENSP00000435851.1, ENST00000533231.5
    Conserved Domains (2) summary
    pfam07500
    Location:608 → 717
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:867 → 965
    SPOC; SPOC domain

  2. NM_001281988.3 → NP_001268917.1  SPOC domain-containing protein 1 isoform 3

    See identical proteins and their annotated locations for NP_001268917.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' terminal exon, lacks an alternate exon in the 5' region and uses a downstream start codon compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AL354919
    Consensus CDS
    CCDS72748.1
    UniProtKB/TrEMBL
    E9PPM7
    Related
    ENSP00000257100.3, ENST00000257100.7
    Conserved Domains (2) summary
    pfam07500
    Location:101 → 211
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:353 → 497
    SPOC; SPOC domain

  3. NM_001394397.1 → NP_001381326.1  SPOC domain-containing protein 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL354919

  4. NM_001394398.1 → NP_001381327.1  SPOC domain-containing protein 1 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL354919

  5. NM_001394399.1 → NP_001381328.1  SPOC domain-containing protein 1 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AL354919

  6. NM_144569.7 → NP_653170.3  SPOC domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_653170.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL354919
    Consensus CDS
    CCDS347.1
    UniProtKB/Swiss-Prot
    Q24JU3, Q6PI90, Q6ZMY3, Q8N869, Q8N8U0, Q8NBC6, Q96LN6
    Related
    ENSP00000353670.2, ENST00000360482.7
    Conserved Domains (2) summary
    pfam07500
    Location:608 → 717
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:867 → 965
    SPOC; SPOC domain

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    31790422..31816022 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011542413.3 → XP_011540715.1  SPOC domain-containing protein 1 isoform X6

    See identical proteins and their annotated locations for XP_011540715.1

    UniProtKB/TrEMBL
    E9PPM7
    Conserved Domains (2) summary
    pfam07500
    Location:101 → 211
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:353 → 497
    SPOC; SPOC domain

  2. XM_047433825.1 → XP_047289781.1  SPOC domain-containing protein 1 isoform X5

  3. XM_047433811.1 → XP_047289767.1  SPOC domain-containing protein 1 isoform X2

  4. XM_017002782.2 → XP_016858271.1  SPOC domain-containing protein 1 isoform X4

    Conserved Domains (2) summary
    pfam07500
    Location:351 → 460
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:610 → 708
    SPOC; SPOC domain

  5. XM_017002781.2 → XP_016858270.1  SPOC domain-containing protein 1 isoform X3

    Conserved Domains (2) summary
    pfam07500
    Location:608 → 715
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:825 → 923
    SPOC; SPOC domain

  6. XM_017002779.2 → XP_016858268.1  SPOC domain-containing protein 1 isoform X1

    Conserved Domains (2) summary
    pfam07500
    Location:608 → 717
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:866 → 964
    SPOC; SPOC domain

  7. XM_047433838.1 → XP_047289794.1  SPOC domain-containing protein 1 isoform X7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    31648071..31674002 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054339531.1 → XP_054195506.1  SPOC domain-containing protein 1 isoform X6

  2. XM_054339530.1 → XP_054195505.1  SPOC domain-containing protein 1 isoform X5

  3. XM_054339527.1 → XP_054195502.1  SPOC domain-containing protein 1 isoform X2

  4. XM_054339529.1 → XP_054195504.1  SPOC domain-containing protein 1 isoform X4

  5. XM_054339528.1 → XP_054195503.1  SPOC domain-containing protein 1 isoform X3

  6. XM_054339526.1 → XP_054195501.1  SPOC domain-containing protein 1 isoform X1

  7. XM_054339532.1 → XP_054195507.1  SPOC domain-containing protein 1 isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZMY3.1 GenPept UniProtKB/Swiss-Prot:Q6ZMY3

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