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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
    mouse all
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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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