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    SPINDOC spindlin interactor and repressor of chromatin binding [ Homo sapiens (human) ]

    Gene ID: 144097, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SPINDOCprovided by HGNC
    Official Full Name
    spindlin interactor and repressor of chromatin bindingprovided by HGNC
    Primary source
    HGNC:HGNC:25115
    See related
    Ensembl:ENSG00000168005 AllianceGenome:HGNC:25115
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    C11orf84; SPIN-DOC
    Summary
    Involved in DNA damage response and negative regulation of DNA-templated transcription. Is active in nucleus and site of DNA damage. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in testis (RPKM 9.7), placenta (RPKM 7.2) and 23 other tissues See more
    Orthologs
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    Genomic context

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    See SPINDOC in Genome Data Viewer
    Location:
    11q13.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (63813456..63827716)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (63802814..63817077)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (63580928..63595188)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:63529087-63529846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3442 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3443 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3445 Neighboring gene zinc finger translocation associated Neighboring gene RNA, 7SL, cytoplasmic 596, pseudogene Neighboring gene Sharpr-MPRA regulatory region 949 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3446 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:63598793-63599010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63599819-63600638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63605268-63606256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4875 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3447 Neighboring gene ATP synthase membrane subunit g pseudogene 1 Neighboring gene microtubule affinity regulating kinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4877 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:63642729-63643230 Neighboring gene RNA, U6 small nuclear 1306, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Molecular Basis for SPINDOC-Spindlin1 Engagement and Its Role in Transcriptional Attenuation. Zhao F, et al. J Mol Biol, 2024 Apr 1. PMID 37977297
    2. Spindlin docking protein (SPIN.DOC) interaction with SPIN1 (a histone code reader) regulates Wnt signaling. Devi MS, et al. Biochem Biophys Res Commun, 2019 Apr 9. PMID 30803761
    3. SPINDOC binds PARP1 to facilitate PARylation. Yang F, et al. Nat Commun, 2021 Nov 4. PMID 34737271, Free PMC Article
    4. Family-based genome-wide association study of frontal θ oscillations identifies potassium channel gene KCNJ6. Kang SJ, et al. Genes Brain Behav, 2012 Aug. PMID 22554406, Free PMC Article
    5. A transcriptional coregulator, SPIN·DOC, attenuates the coactivator activity of Spindlin1. Bae N, et al. J Biol Chem, 2017 Dec 22. PMID 29061846, Free PMC Article

    See all (50) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Molecular Basis for SPINDOC-Spindlin1 Engagement and Its Role in Transcriptional Attenuation.
      Title: Molecular Basis for SPINDOC-Spindlin1 Engagement and Its Role in Transcriptional Attenuation.
    2. SPINDOC binds PARP1 to facilitate PARylation.
      Title: SPINDOC binds PARP1 to facilitate PARylation.
    3. SPINDOC Interacts with SPIN1 in DNA independent manner. SPINDOC regulates expression and chromatin loading of SPIN1.
      Title: Spindlin docking protein (SPIN.DOC) interaction with SPIN1 (a histone code reader) regulates Wnt signaling.
    4. identified SPIN.DOC as a transcriptional repressor that binds SPIN1 and masks its ability to engage the H3-Lys-4 trimethylation activation mark
      Title: A transcriptional coregulator, SPIN·DOC, attenuates the coactivator activity of Spindlin1.
    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

    EBI GWAS Catalog

    Description
    Family-based genome-wide association study of frontal θ oscillations identifies potassium channel gene KCNJ6.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp762N0114

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein 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 DNA damage response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of protein ADP-ribosylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in site of DNA damage IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    spindlin interactor and repressor of chromatin-binding protein
    Names
    SPIN1 docking protein
    hypothetical protein BC007540
    uncharacterized protein C11orf84

    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_138471.3 → NP_612480.1  spindlin interactor and repressor of chromatin-binding protein

      See identical proteins and their annotated locations for NP_612480.1

      Status: VALIDATED

      Source sequence(s)
      BC002782, HY013538
      Consensus CDS
      CCDS31594.1
      UniProtKB/Swiss-Prot
      Q68CV7, Q6PHS2, Q96IH0, Q9BUA3
      Related
      ENSP00000294244.3, ENST00000294244.9

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      63813456..63827716
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006718437.2 → XP_006718500.1  spindlin interactor and repressor of chromatin-binding protein isoform X2

      Conserved Domains (1) summary
      pfam18658
      Location:70 → 134
      zf-C2H2_12; Zinc-finger C2H2-type

    2. XM_011544770.2 → XP_011543072.1  spindlin interactor and repressor of chromatin-binding protein isoform X1

      Conserved Domains (1) summary
      pfam18658
      Location:70 → 134
      zf-C2H2_12; Zinc-finger C2H2-type

    3. XM_011544772.2 → XP_011543074.1  spindlin interactor and repressor of chromatin-binding protein isoform X4

      Conserved Domains (1) summary
      pfam18658
      Location:70 → 134
      zf-C2H2_12; Zinc-finger C2H2-type

    4. XM_011544771.2 → XP_011543073.1  spindlin interactor and repressor of chromatin-binding protein isoform X3

      Conserved Domains (1) summary
      pfam18658
      Location:70 → 134
      zf-C2H2_12; Zinc-finger C2H2-type

    5. XM_047426423.1 → XP_047282379.1  spindlin interactor and repressor of chromatin-binding protein isoform X5

    6. XM_047426424.1 → XP_047282380.1  spindlin interactor and repressor of chromatin-binding protein isoform X7

    7. XM_005273782.4 → XP_005273839.1  spindlin interactor and repressor of chromatin-binding protein isoform X6

      Conserved Domains (1) summary
      pfam18658
      Location:70 → 134
      zf-C2H2_12; Zinc-finger C2H2-type

    8. XM_047426425.1 → XP_047282381.1  spindlin interactor and repressor of chromatin-binding protein isoform X8

    RNA

    1. XR_007062453.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      63802814..63817077
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367768.1 → XP_054223743.1  spindlin interactor and repressor of chromatin-binding protein isoform X1

    2. XM_054367771.1 → XP_054223746.1  spindlin interactor and repressor of chromatin-binding protein isoform X4

    3. XM_054367770.1 → XP_054223745.1  spindlin interactor and repressor of chromatin-binding protein isoform X3

    4. XM_054367774.1 → XP_054223749.1  spindlin interactor and repressor of chromatin-binding protein isoform X7

    5. XM_054367769.1 → XP_054223744.1  spindlin interactor and repressor of chromatin-binding protein isoform X2

    6. XM_054367772.1 → XP_054223747.1  spindlin interactor and repressor of chromatin-binding protein isoform X5

    7. XM_054367773.1 → XP_054223748.1  spindlin interactor and repressor of chromatin-binding protein isoform X6

    8. XM_054367775.1 → XP_054223750.1  spindlin interactor and repressor of chromatin-binding protein isoform X8

    RNA

    1. XR_008488345.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BUA3.3 GenPept UniProtKB/Swiss-Prot:Q9BUA3

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