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SUPT6H SPT6 homolog, histone chaperone and transcription elongation factor [ Homo sapiens (human) ]

Gene ID: 6830, updated on 7-Apr-2024

Summary

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Official Symbol
SUPT6Hprovided by HGNC
Official Full Name
SPT6 homolog, histone chaperone and transcription elongation factorprovided by HGNC
Primary source
HGNC:HGNC:11470
See related
Ensembl:ENSG00000109111 MIM:601333; AllianceGenome:HGNC:11470
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
SPT6; SPT6H; emb-5
Summary
Enables histone binding activity. Involved in negative regulation of histone H3-K27 methylation and positive regulation of transcription elongation from RNA polymerase II promoter. Predicted to be located in nucleoplasm. Predicted to be part of transcription elongation factor complex. Predicted to be active in transcriptionally active chromatin. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 15.3), ovary (RPKM 14.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
17q11.2
Exon count:
42
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (28662205..28702679)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (29604969..29645463)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (26989223..27029697)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene SPAG5 antisense RNA 1 Neighboring gene bridge-like lipid transfer protein family member 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:26954912-26955086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8346 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8347 Neighboring gene stromal cell derived factor 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:26988611-26989810 Neighboring gene ribosomal protein S12 pseudogene 28 Neighboring gene Sharpr-MPRA regulatory region 10516 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr17:27037571-27038346 and GRCh37_chr17:27038347-27039122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11936 Neighboring gene protein interacting with cyclin A1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8349 Neighboring gene RAB34, member RAS oncogene family

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
  • 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. Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination. Narain A, et al. Mol Cell, 2021 Aug 5. PMID 34233157, Free PMC Article
  2. SPT6 promotes epidermal differentiation and blockade of an intestinal-like phenotype through control of transcriptional elongation. Li J, et al. Nat Commun, 2021 Feb 4. PMID 33542242, Free PMC Article
  3. SPT6-driven error-free DNA repair safeguards genomic stability of glioblastoma cancer stem-like cells. Obara EAA, et al. Nat Commun, 2020 Sep 18. PMID 32948765, Free PMC Article
  4. Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence. Nojima T, et al. Mol Cell, 2018 Dec 20. PMID 30449723, Free PMC Article
  5. The cellular protein SPT6 is required for efficient replication of human cytomegalovirus. Cygnar D, et al. J Virol, 2012 Feb. PMID 22171252, Free PMC Article

See all (113) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Insights into Spt6: a histone chaperone that functions in transcription, DNA replication, and genome stability.
    Title: Insights into Spt6: a histone chaperone that functions in transcription, DNA replication, and genome stability.
  2. Hypermethylation-Mediated lncRNA MAGI2-AS3 Downregulation Facilitates Malignant Progression of Laryngeal Squamous Cell Carcinoma via Interacting With SPT6.
    Title: Hypermethylation-Mediated lncRNA MAGI2-AS3 Downregulation Facilitates Malignant Progression of Laryngeal Squamous Cell Carcinoma via Interacting With SPT6.
  3. SPT6 recruits SND1 to co-activate human telomerase reverse transcriptase to promote colon cancer progression.
    Title: SPT6 recruits SND1 to co-activate human telomerase reverse transcriptase to promote colon cancer progression.
  4. Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo.
    Title: Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo.
  5. Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination.
    Title: Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination.
  6. SPT6 promotes epidermal differentiation and blockade of an intestinal-like phenotype through control of transcriptional elongation.
    Title: SPT6 promotes epidermal differentiation and blockade of an intestinal-like phenotype through control of transcriptional elongation.
  7. SPT6-driven error-free DNA repair safeguards genomic stability of glioblastoma cancer stem-like cells.
    Title: SPT6-driven error-free DNA repair safeguards genomic stability of glioblastoma cancer stem-like cells.
  8. Spt6 is a maintenance factor for centromeric CENP-A.
    Title: Spt6 is a maintenance factor for centromeric CENP-A.
  9. SPT6 acts as a master regulator of Pol II elongation, favoring productive protein coding over non-productive and potentially deleterious lncRNA transcription.
    Title: Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence.
  10. cryo-EM structure of an activated elongation complex of Sus scrofa Pol II and Homo sapiens DSIF, PAF and SPT6 was determined at 3.1 A resolution and compared to the structure of the paused elongation complex formed by Pol II, DSIF and NELF
    Title: Structure of activated transcription complex Pol II-DSIF-PAF-SPT6.
Submit: New GeneRIF Correction See all GeneRIFs (17)

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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of SPT6 by shRNA enhances HIV-1 replication in HIV-1-infected CD4+ T-cells and latently infected cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0162, MGC87943

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding HDA PubMed 
enables histone binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables nucleosome binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA splicing IEA
Inferred from Electronic Annotation
more info
  
involved_in blastocyst formation IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA transport IEA
Inferred from Electronic Annotation
more info
  
involved_in nucleosome organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription elongation by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of isotype switching ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of mRNA export from nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of mRNA processing ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of muscle cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in transcription elongation by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transcription elongation-coupled chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of transcription elongation factor complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
transcription elongation factor SPT6
Names
histone chaperone suppressor of Ty6
suppressor of Ty 6 homolog
tat-CT2 protein
tat-cotransactivator 2 protein

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_001320755.2 → NP_001307684.1  transcription elongation factor SPT6

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AL833607, AW135492, BC150268, BM727811, DB318397
    Consensus CDS
    CCDS32596.1
    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2
    Related
    ENSP00000338143.4, ENST00000347486.8
    Conserved Domains (2) summary
    COG2183
    Location:372 → 1353
    Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
    pfam14633
    Location:1308 → 1512
    SH2_2; SH2 domain

  2. NM_003170.5 → NP_003161.2  transcription elongation factor SPT6

    See identical proteins and their annotated locations for NP_003161.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AL833607, AW135492, BC150268, BM727811
    Consensus CDS
    CCDS32596.1
    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2
    Related
    ENSP00000319104.6, ENST00000314616.11
    Conserved Domains (2) summary
    COG2183
    Location:372 → 1353
    Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
    pfam14633
    Location:1308 → 1512
    SH2_2; SH2 domain

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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    28662205..28702679
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047436596.1 → XP_047292552.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  2. XM_047436604.1 → XP_047292560.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  3. XM_047436601.1 → XP_047292557.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  4. XM_047436599.1 → XP_047292555.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  5. XM_047436605.1 → XP_047292561.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  6. XM_047436597.1 → XP_047292553.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  7. XM_047436600.1 → XP_047292556.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  8. XM_047436603.1 → XP_047292559.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  9. XM_047436595.1 → XP_047292551.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  10. XM_047436606.1 → XP_047292562.1  transcription elongation factor SPT6 isoform X3

  11. XM_047436607.1 → XP_047292563.1  transcription elongation factor SPT6 isoform X4

  12. XM_047436602.1 → XP_047292558.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  13. XM_017024980.2 → XP_016880469.1  transcription elongation factor SPT6 isoform X2

    UniProtKB/Swiss-Prot
    Q7KZ85
    Conserved Domains (10) summary
    smart00316
    Location:1104 → 1159
    S1; Ribosomal protein S1-like RNA-binding domain
    cd09918
    Location:1208 → 1292
    SH2_Nterm_SPT6_like; N-terminal Src homology 2 (SH2) domain found in Spt6
    cd09928
    Location:1301 → 1392
    SH2_Cterm_SPT6_like; C-terminal Src homology 2 (SH2) domain found in Spt6
    COG2183
    Location:249 → 1230
    Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
    pfam14639
    Location:652 → 808
    YqgF; Holliday-junction resolvase-like of SPT6
    pfam09371
    Location:442 → 500
    Tex_N; Tex-like protein N-terminal domain
    pfam14633
    Location:1181 → 1391
    SH2_2; SH2 domain
    pfam14635
    Location:812 → 915
    HHH_7; Helix-hairpin-helix motif
    pfam14641
    Location:225 → 299
    HTH_44; Helix-turn-helix DNA-binding domain of SPT6
    pfam14878
    Location:930 → 1034
    DLD; Death-like domain of SPT6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    29604969..29645463
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054317004.1 → XP_054172979.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  2. XM_054317011.1 → XP_054172986.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  3. XM_054317008.1 → XP_054172983.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  4. XM_054317006.1 → XP_054172981.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  5. XM_054317012.1 → XP_054172987.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  6. XM_054317005.1 → XP_054172980.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  7. XM_054317007.1 → XP_054172982.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  8. XM_054317010.1 → XP_054172985.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  9. XM_054317003.1 → XP_054172978.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  10. XM_054317014.1 → XP_054172989.1  transcription elongation factor SPT6 isoform X3

  11. XM_054317015.1 → XP_054172990.1  transcription elongation factor SPT6 isoform X4

  12. XM_054317009.1 → XP_054172984.1  transcription elongation factor SPT6 isoform X1

    UniProtKB/Swiss-Prot
    A7E2B4, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2

  13. XM_054317013.1 → XP_054172988.1  transcription elongation factor SPT6 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7KZ85.2 GenPept UniProtKB/Swiss-Prot:Q7KZ85

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