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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
    mouse all
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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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    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.

    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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