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

Gene ID: 11198, updated on 3-May-2020

Summary

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
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

Genomic context

See SUPT16H in Genome Data Viewer
Location:
14q11.2
Exon count:
27
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (21351472..21384019, 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 Neighboring gene mitochondrial ribosomal protein S17 pseudogene 6 Neighboring gene RPGR interacting protein 1 Neighboring gene uncharacterized LOC107984643 Neighboring gene chromodomain helicase DNA binding protein 8 Neighboring gene small nucleolar RNA, C/D box 9

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10857, FLJ14010, FLJ34357

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
histone binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleosome binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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
PubMed 
regulation of signal transduction by p53 class mediator TAS
Traceable Author Statement
more info
 
transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
transcription elongation from RNA polymerase II promoter IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription elongation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
FACT complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromosome IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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
    5248..37791
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_007192.4NP_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, ENST00000216297.7
    Conserved Domains (1) summary
    cl25953
    Location:51001
    SPT16; FACT complex subunit (SPT16/CDC68)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

    Range
    21351472..21384019 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
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