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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
    mouse all
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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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