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SUPT5H SPT5 homolog, DSIF elongation factor subunit [ Homo sapiens (human) ]

Gene ID: 6829, updated on 2-Nov-2024

Summary

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Official Symbol
SUPT5Hprovided by HGNC
Official Full Name
SPT5 homolog, DSIF elongation factor subunitprovided by HGNC
Primary source
HGNC:HGNC:11469
See related
Ensembl:ENSG00000196235 MIM:602102; AllianceGenome:HGNC:11469
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
SPT5; SPT5H; Tat-CT1
Summary
Enables enzyme binding activity and protein heterodimerization activity. Involved in positive regulation of macroautophagy; regulation of DNA-templated transcription; and transcription elongation by RNA polymerase II. Located in nucleoplasm. Part of DSIF complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 64.5), bone marrow (RPKM 32.4) and 25 other tissues See more
Orthologs
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Genomic context

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See SUPT5H in Genome Data Viewer
Location:
19q13.2
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (39445582..39476670)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (42249844..42280929)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (39936222..39967310)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10601 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10602 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10603 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10604 Neighboring gene pleckstrin homology and RhoGEF domain containing G2 Neighboring gene Sharpr-MPRA regulatory region 7883 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14620 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:39925783-39926362 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39928026-39928794 Neighboring gene ribosomal protein S16 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:39935465-39936262 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:39936263-39937059 Neighboring gene small nucleolar RNA, C/D box 175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10606 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:39971166-39971760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14623 Neighboring gene uncharacterized LOC124904718 Neighboring gene translocase of inner mitochondrial membrane 50 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39988291-39989283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10610 Neighboring gene delta like canonical Notch ligand 3

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 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. Loss-of-Function Variants in SUPT5H as Modifying Factors in Beta-Thalassemia. Harteveld CL, et al. Int J Mol Sci, 2024 Aug 16. PMID 39201615, Free PMC Article
  2. Isolation, sequencing, and mapping of the human homologue of the yeast transcription factor, SPT5. Chiang PW, et al. Genomics, 1996 Dec 15. PMID 8975720
  3. Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. Bernecky C, et al. Nat Struct Mol Biol, 2017 Oct. PMID 28892040
  4. Human Supt5h protein, a putative modulator of chromatin structure, is reversibly phosphorylated in mitosis. Stachora AA, et al. FEBS Lett, 1997 Jun 2. PMID 9199507
  5. Modulating HIV-1 replication by RNA interference directed against human transcription elongation factor SPT5. Ping YH, et al. Retrovirology, 2004 Dec 27. PMID 15620346, Free PMC Article

See all (207) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Loss-of-Function Variants in SUPT5H as Modifying Factors in Beta-Thalassemia.
    Title: Loss-of-Function Variants in SUPT5H as Modifying Factors in Beta-Thalassemia.
  2. RBM22 regulates RNA polymerase II 5' pausing, elongation rate, and termination by coordinating 7SK-P-TEFb complex and SPT5.
    Title: RBM22 regulates RNA polymerase II 5' pausing, elongation rate, and termination by coordinating 7SK-P-TEFb complex and SPT5.
  3. A stepwise haematological screening and whole-exome sequencing reveal multiple mutations from SUPT5H causing an elevation of Hb A2 from a cohort of 47336 individuals.
    Title: A stepwise haematological screening and whole-exome sequencing reveal multiple mutations from SUPT5H causing an elevation of Hb A(2) from a cohort of 47336 individuals.
  4. ZWC complex-mediated SPT5 phosphorylation suppresses divergent antisense RNA transcription at active gene promoters.
    Title: ZWC complex-mediated SPT5 phosphorylation suppresses divergent antisense RNA transcription at active gene promoters.
  5. SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape.
    Title: SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape.
  6. SPT5 stabilization of promoter-proximal RNA polymerase II.
    Title: SPT5 stabilization of promoter-proximal RNA polymerase II.
  7. CRISPRi-mediated depletion of Spt4 and Spt5 reveals a role for DSIF in the control of HIV latency.
    Title: CRISPRi-mediated depletion of Spt4 and Spt5 reveals a role for DSIF in the control of HIV latency.
  8. SUPT5H Post-Transcriptional Silencing Modulates PIN1 Expression, Inhibits Tumorigenicity, and Induces Apoptosis of Human Breast Cancer Cells.
    Title: SUPT5H Post-Transcriptional Silencing Modulates PIN1 Expression, Inhibits Tumorigenicity, and Induces Apoptosis of Human Breast Cancer Cells.
  9. Poly(A) site-dependent deceleration caused by PNUTS-PP1 and Spt5 dephosphorylation is required to convert Pol II into a viable target for the Xrn2 terminator exonuclease, leading to transcription termination.
    Title: Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a "Sitting Duck Torpedo" Mechanism.
  10. the solution structures of the human Spt5 KOW4 and the C-terminal domain by nuclear magnetic resonance spectroscopy, are reported.
    Title: Structure and nucleic acid binding properties of KOW domains 4 and 6-7 of human transcription elongation factor DSIF.
Submit: New GeneRIF Correction See all GeneRIFs (31)

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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Protein interactions

Protein Gene Interaction Pubs
Tat tat SPT5 associates with the HIV-1 Tat cofactor Tat-SF1 and the RNA polymerase II holoenzyme and stimulates Tat-mediated transcriptional activation of the HIV-1 LTR promoter PubMed
tat HIV-1 Tat induces the phosphorylation of the SPT5 CTR1 domain (amino acids 754-817) by CDK9/P-TEFb PubMed
tat The SPT5/SPT4 complex, DSIF, associates with the HIV-1 transcription elongation complex (TEC) and SPT5 cooperates with HIV-1 Tat by preventing premature RNA release from the TEC at terminator sequences and reducing polymerase pausing at arrest sites 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

  • FLJ34157

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
  
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of DNA-templated transcription, elongation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription, elongation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription, elongation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of macroautophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription elongation by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in transcription elongation by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transcription elongation by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in transcription elongation by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in transcription elongation-coupled chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of DSIF complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of DSIF complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of DSIF complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
transcription elongation factor SPT5
Names
DRB sensitivity-inducing factor 160 kDa subunit
DRB sensitivity-inducing factor large subunit
DSIF large subunit
DSIF p160
Tat-cotransactivator 1 protein
hSPT5
suppressor of Ty 5 homolog

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_001111020.3 → NP_001104490.1  transcription elongation factor SPT5 isoform a

    See identical proteins and their annotated locations for NP_001104490.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 5 all encode the same isoform (a).
    Source sequence(s)
    AF040253, DB097498
    Consensus CDS
    CCDS12536.1
    UniProtKB/Swiss-Prot
    O00267, O43279, Q59G52, Q99639
    UniProtKB/TrEMBL
    B4DZJ7
    Related
    ENSP00000404029.4, ENST00000432763.7
    Conserved Domains (5) summary
    cd09888
    Location:178 → 265
    NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
    COG5164
    Location:334 → 965
    SPT5; Transcription elongation factor [Transcription]
    cd06081
    Location:276 → 313
    KOW_Spt5_1; KOW domain of Spt5, repeat 1
    cd06086
    Location:1028 → 1084
    KOW_Spt5_6; KOW domain of Spt5, repeat 6
    pfam11942
    Location:93 → 172
    Spt5_N; Spt5 transcription elongation factor, acidic N-terminal

  2. NM_001130824.2 → NP_001124296.1  transcription elongation factor SPT5 isoform a

    See identical proteins and their annotated locations for NP_001124296.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 5 all encode the same isoform (a).
    Source sequence(s)
    AF040253, BC024203, DB097498, Y12790
    Consensus CDS
    CCDS12536.1
    UniProtKB/Swiss-Prot
    O00267, O43279, Q59G52, Q99639
    UniProtKB/TrEMBL
    B4DZJ7
    Conserved Domains (5) summary
    cd09888
    Location:178 → 265
    NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
    COG5164
    Location:334 → 965
    SPT5; Transcription elongation factor [Transcription]
    cd06081
    Location:276 → 313
    KOW_Spt5_1; KOW domain of Spt5, repeat 1
    cd06086
    Location:1028 → 1084
    KOW_Spt5_6; KOW domain of Spt5, repeat 6
    pfam11942
    Location:93 → 172
    Spt5_N; Spt5 transcription elongation factor, acidic N-terminal

  3. NM_001130825.2 → NP_001124297.1  transcription elongation factor SPT5 isoform b

    See identical proteins and their annotated locations for NP_001124297.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 4 and 6 encode the same isoform (b).
    Source sequence(s)
    AB209257, AF040253, DB097498
    Consensus CDS
    CCDS46072.1
    UniProtKB/TrEMBL
    B4DZJ7
    Related
    ENSP00000384505.2, ENST00000402194.6
    Conserved Domains (12) summary
    PRK08559
    Location:171 → 312
    nusG; transcription antitermination protein NusG; Validated
    cd09888
    Location:174 → 261
    NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
    COG5164
    Location:330 → 961
    SPT5; Transcription elongation factor [Transcription]
    cd06081
    Location:272 → 309
    KOW_Spt5_1; KOW domain of Spt5, repeat 1
    cd06082
    Location:416 → 466
    KOW_Spt5_2; KOW domain of Spt5, repeat 2
    cd06083
    Location:467 → 517
    KOW_Spt5_3; KOW domain of Spt5, repeat 3
    cd06084
    Location:593 → 635
    KOW_Spt5_4; KOW domain of Spt5, repeat 4
    cd06085
    Location:698 → 747
    KOW_Spt5_5; KOW domain of Spt5, repeat 5
    cd06086
    Location:1024 → 1080
    KOW_Spt5_6; KOW domain of Spt5, repeat 6
    pfam04731
    Location:843 → 972
    Caudal_act; Caudal like protein activation region
    pfam11942
    Location:75 → 167
    Spt5_N; Spt5 transcription elongation factor, acidic N-terminal
    pfam12815
    Location:762 → 818
    CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

  4. NM_001319990.2 → NP_001306919.1  transcription elongation factor SPT5 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants Variants 1, 2, 3, and 5 all encode the same isoform (a).
    Source sequence(s)
    AF040253, DB097498, U56402, Y12790
    Consensus CDS
    CCDS12536.1
    UniProtKB/Swiss-Prot
    O00267, O43279, Q59G52, Q99639
    UniProtKB/TrEMBL
    B4DZJ7
    Conserved Domains (5) summary
    cd09888
    Location:178 → 265
    NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
    COG5164
    Location:334 → 965
    SPT5; Transcription elongation factor [Transcription]
    cd06081
    Location:276 → 313
    KOW_Spt5_1; KOW domain of Spt5, repeat 1
    cd06086
    Location:1028 → 1084
    KOW_Spt5_6; KOW domain of Spt5, repeat 6
    pfam11942
    Location:93 → 172
    Spt5_N; Spt5 transcription elongation factor, acidic N-terminal

  5. NM_001319991.2 → NP_001306920.1  transcription elongation factor SPT5 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 4 and 6 encode the same isoform (b).
    Source sequence(s)
    AB209257, AF040253, DB097498, U56402
    Consensus CDS
    CCDS46072.1
    UniProtKB/TrEMBL
    B4DZJ7
    Conserved Domains (12) summary
    PRK08559
    Location:171 → 312
    nusG; transcription antitermination protein NusG; Validated
    cd09888
    Location:174 → 261
    NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
    COG5164
    Location:330 → 961
    SPT5; Transcription elongation factor [Transcription]
    cd06081
    Location:272 → 309
    KOW_Spt5_1; KOW domain of Spt5, repeat 1
    cd06082
    Location:416 → 466
    KOW_Spt5_2; KOW domain of Spt5, repeat 2
    cd06083
    Location:467 → 517
    KOW_Spt5_3; KOW domain of Spt5, repeat 3
    cd06084
    Location:593 → 635
    KOW_Spt5_4; KOW domain of Spt5, repeat 4
    cd06085
    Location:698 → 747
    KOW_Spt5_5; KOW domain of Spt5, repeat 5
    cd06086
    Location:1024 → 1080
    KOW_Spt5_6; KOW domain of Spt5, repeat 6
    pfam04731
    Location:843 → 972
    Caudal_act; Caudal like protein activation region
    pfam11942
    Location:75 → 167
    Spt5_N; Spt5 transcription elongation factor, acidic N-terminal
    pfam12815
    Location:762 → 818
    CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

  6. NM_003169.4 → NP_003160.2  transcription elongation factor SPT5 isoform a

    See identical proteins and their annotated locations for NP_003160.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a). Variants 1, 2, 3, and 5 all encode the same isoform (a).
    Source sequence(s)
    AC011500, AF040253, BP199253
    Consensus CDS
    CCDS12536.1
    UniProtKB/Swiss-Prot
    O00267, O43279, Q59G52, Q99639
    UniProtKB/TrEMBL
    B4DZJ7
    Related
    ENSP00000469090.1, ENST00000598725.5
    Conserved Domains (5) summary
    cd09888
    Location:178 → 265
    NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
    COG5164
    Location:334 → 965
    SPT5; Transcription elongation factor [Transcription]
    cd06081
    Location:276 → 313
    KOW_Spt5_1; KOW domain of Spt5, repeat 1
    cd06086
    Location:1028 → 1084
    KOW_Spt5_6; KOW domain of Spt5, repeat 6
    pfam11942
    Location:93 → 172
    Spt5_N; Spt5 transcription elongation factor, acidic N-terminal

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    39445582..39476670
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    42249844..42280929
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O00267.1 GenPept UniProtKB/Swiss-Prot:O00267

Gene LinkOut

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