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    SPTY2D1 SPT2 chromatin protein domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 144108, updated on 5-May-2024

    Summary

    Official Symbol
    SPTY2D1provided by HGNC
    Official Full Name
    SPT2 chromatin protein domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:26818
    See related
    Ensembl:ENSG00000179119 AllianceGenome:HGNC:26818
    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
    Spt2
    Summary
    Enables DNA binding activity and histone binding activity. Involved in nucleosome organization; regulation of chromatin assembly; and regulation of transcription, DNA-templated. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in bone marrow (RPKM 18.4), gall bladder (RPKM 8.3) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    Location:
    11p15.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (18606403..18634342, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (18704496..18732445, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (18627950..18655889, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene UEV and lactate/malate dehyrogenase domains Neighboring gene ReSE screen-validated silencer GRCh37_chr11:18600575-18600756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4505 Neighboring gene Sharpr-MPRA regulatory region 13786 Neighboring gene uncharacterized LOC112268073 Neighboring gene MTCH1 pseudogene 2 Neighboring gene Sharpr-MPRA regulatory region 7651 Neighboring gene mitochondrial sheath formation associated Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:18637160-18638359 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3192 Neighboring gene uncharacterized LOC105376578 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4507 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:18670593-18671313 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:18671314-18672033 Neighboring gene SRSF3 pseudogene 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    Phenotypes

    EBI GWAS Catalog

    Description
    Biological, clinical and population relevance of 95 loci for blood lipids.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ39441, DKFZp686I068, DKFZp686F1942

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase I core binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone chaperone activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nucleosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in nucleosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in transcription by RNA polymerase I IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleolus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    protein SPT2 homolog
    Names
    SPT2 domain-containing protein 1
    SPT2, Suppressor of Ty, domain containing 1

    NCBI Reference Sequences (RefSeq)

    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_194285.3NP_919261.2  protein SPT2 homolog

      See identical proteins and their annotated locations for NP_919261.2

      Status: VALIDATED

      Source sequence(s)
      AF086471, AF452716, AK096760, AL834393, BC036844, BC056261, BX538046, BX641102, BX647798, BX648114, BX648478
      Consensus CDS
      CCDS31441.1
      UniProtKB/Swiss-Prot
      Q68D10, Q6AWA5, Q6MZI5, Q7Z390, Q7Z470, Q86VG8, Q8N3E7, Q8N417, Q8N8I3
      UniProtKB/TrEMBL
      B4E223
      Related
      ENSP00000337991.5, ENST00000336349.6
      Conserved Domains (1) summary
      pfam08243
      Location:604667
      SPT2; SPT2 chromatin protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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
      18606403..18634342 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      18704496..18732445 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)