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    SUPT16H SPT16 homolog, facilitates chromatin remodeling subunit [ Homo sapiens (human) ]

    Gene ID: 11198, updated on 5-Nov-2017
    Official Symbol
    SUPT16Hprovided by HGNC
    Official Full Name
    SPT16 homolog, facilitates chromatin remodeling subunitprovided by HGNC
    Primary source
    HGNC:HGNC:11465
    See related
    Ensembl:ENSG00000092201 MIM:605012; Vega:OTTHUMG00000029685
    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
    CDC68; SPT16; FACTP140; SPT16/CDC68
    Summary
    Transcription of protein-coding genes can be reconstituted on naked DNA with only the general transcription factors and RNA polymerase II. However, this minimal system cannot transcribe DNA packaged into chromatin, indicating that accessory factors may facilitate access to DNA. One such factor, FACT (facilitates chromatin transcription), interacts specifically with histones H2A/H2B to effect nucleosome disassembly and transcription elongation. FACT is composed of an 80 kDa subunit and a 140 kDa subunit; this gene encodes the 140 kDa subunit. [provided by RefSeq, Feb 2009]
    Expression
    Ubiquitous expression in testis (RPKM 30.8), lymph node (RPKM 27.6) and 25 other tissues See more
    Orthologs
    Location:
    14q11.2
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 14 NC_000014.9 (21351472..21384266, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (21819631..21852425, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene heterogeneous nuclear ribonucleoprotein C (C1/C2) Neighboring gene RPGR interacting protein 1 Neighboring gene mitochondrial ribosomal protein S17 pseudogene 6 Neighboring gene uncharacterized LOC107984643 Neighboring gene chromodomain helicase DNA binding protein 8 Neighboring gene small nucleolar RNA, C/D box 9 Neighboring gene small nucleolar RNA, C/D box 8

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated (2012-05-09)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated (2012-05-09)

    ClinGen Genome Curation Page

    Replication interactions

    Interaction Pubs
    shRNA knockdown of SUPT16H increases HIV-1 LTR-driven gene expression in HEK293 cells transduced with VSV-G pseudo-typed HIV-1 NL4-3-Luc construct; i.e. HIV-1 is restricted by SUPT16H PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, suppressor of Ty 16 homolog (SUPT16H), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with SUPT16H is increased by RRE PubMed
    Tat tat The heterodimeric complex FACT proteins SPT16 and SSRP1 are recognized to interact with HIV-1 in Jurkat cell PubMed
    tat HIV-1 Tat activated transcription facilitates removal of histones H2A and H2B at the LTR, and that the FACT complex, at least consisting of SPT16 and SSRP1, may be responsible for their removal PubMed

    Go to the HIV-1, Human Interaction Database

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ10857, FLJ14010, FLJ34357

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    nucleosome binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    DNA repair IEA
    Inferred from Electronic Annotation
    more info
     
    DNA replication IEA
    Inferred from Electronic Annotation
    more info
     
    DNA replication-independent nucleosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    nucleosome disassembly TAS
    Traceable Author Statement
    more info
    PubMed 
    positive regulation of DNA-templated transcription, elongation TAS
    Traceable Author Statement
    more info
    PubMed 
    positive regulation of transcription elongation from RNA polymerase II promoter IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    regulation of signal transduction by p53 class mediator TAS
    Traceable Author Statement
    more info
     
    transcription elongation from RNA polymerase II promoter IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    transcription elongation from RNA polymerase II promoter TAS
    Traceable Author Statement
    more info
     
    transcription from RNA polymerase II promoter TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    FACT complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
     
    Preferred Names
    FACT complex subunit SPT16
    Names
    FACT 140 kDa subunit
    chromatin-specific transcription elongation factor 140 kDa subunit
    facilitates chromatin remodeling 140 kDa subunit
    facilitates chromatin transcription complex subunit SPT16
    hSPT16
    suppressor of Ty 16 homolog

    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_009932.1 RefSeqGene

      Range
      5001..37795
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_007192.3NP_009123.1  FACT complex subunit SPT16

      See identical proteins and their annotated locations for NP_009123.1

      Status: REVIEWED

      Source sequence(s)
      AK001719, AK024072, AL135744, BC014046, BP872403
      Consensus CDS
      CCDS9569.1
      UniProtKB/Swiss-Prot
      Q9Y5B9
      Related
      ENSP00000216297.2, OTTHUMP00000028337, ENST00000216297.6, OTTHUMT00000074025
      Conserved Domains (5) summary
      COG5406
      Location:51001
      COG5406; Nucleosome binding factor SPN, SPT16 subunit [Transcription, Replication, recombination and repair, Chromatin structure and dynamics]
      cd01091
      Location:180420
      CDC68-like; Related to aminopeptidase P and aminopeptidase M, a member of this domain family is present in cell division control protein 68, a transcription factor.
      pfam08512
      Location:813889
      Rtt106; Histone chaperone Rttp106-like
      pfam08644
      Location:534689
      SPT16; FACT complex subunit (SPT16/CDC68)
      pfam14826
      Location:5166
      FACT-Spt16_Nlob; FACT complex subunit SPT16 N-terminal lobe domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p7 Primary Assembly

      Range
      21351472..21384266 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011536381.2XP_011534683.1  FACT complex subunit SPT16 isoform X1

      Conserved Domains (5) summary
      COG5406
      Location:5936
      COG5406; Nucleosome binding factor SPN, SPT16 subunit [Transcription, Replication, recombination and repair, Chromatin structure and dynamics]
      cd01091
      Location:115355
      CDC68-like; Related to aminopeptidase P and aminopeptidase M, a member of this domain family is present in cell division control protein 68, a transcription factor.
      pfam08512
      Location:748824
      Rtt106; Histone chaperone Rttp106-like
      pfam08644
      Location:469624
      SPT16; FACT complex subunit (SPT16/CDC68)
      pfam14826
      Location:1101
      FACT-Spt16_Nlob; FACT complex subunit SPT16 N-terminal lobe domain

    Alternate CHM1_1.1

    Genomic

    1. NC_018925.2 Alternate CHM1_1.1

      Range
      21821298..21854094 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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