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

    Gene ID: 6829, updated on 7-Jan-2024

    Summary

    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 RNA metabolic process; and transcription elongation from RNA polymerase II promoter. Located in nucleoplasm. Part of DSIF complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 64.5), bone marrow (RPKM 32.4) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See SUPT5H in Genome Data Viewer
    Location:
    19q13.2
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (39445582..39476670)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (42249844..42280929)
    105.20220307 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

    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?

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 
    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

    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)

    NEW Try the new Transcript table

    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_001111020.3NP_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:178265
      NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
      COG5164
      Location:334965
      SPT5; Transcription elongation factor [Transcription]
      cd06081
      Location:276313
      KOW_Spt5_1; KOW domain of Spt5, repeat 1
      cd06086
      Location:10281084
      KOW_Spt5_6; KOW domain of Spt5, repeat 6
      pfam11942
      Location:93172
      Spt5_N; Spt5 transcription elongation factor, acidic N-terminal
    2. NM_001130824.2NP_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:178265
      NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
      COG5164
      Location:334965
      SPT5; Transcription elongation factor [Transcription]
      cd06081
      Location:276313
      KOW_Spt5_1; KOW domain of Spt5, repeat 1
      cd06086
      Location:10281084
      KOW_Spt5_6; KOW domain of Spt5, repeat 6
      pfam11942
      Location:93172
      Spt5_N; Spt5 transcription elongation factor, acidic N-terminal
    3. NM_001130825.2NP_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:171312
      nusG; transcription antitermination protein NusG; Validated
      cd09888
      Location:174261
      NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
      COG5164
      Location:330961
      SPT5; Transcription elongation factor [Transcription]
      cd06081
      Location:272309
      KOW_Spt5_1; KOW domain of Spt5, repeat 1
      cd06082
      Location:416466
      KOW_Spt5_2; KOW domain of Spt5, repeat 2
      cd06083
      Location:467517
      KOW_Spt5_3; KOW domain of Spt5, repeat 3
      cd06084
      Location:593635
      KOW_Spt5_4; KOW domain of Spt5, repeat 4
      cd06085
      Location:698747
      KOW_Spt5_5; KOW domain of Spt5, repeat 5
      cd06086
      Location:10241080
      KOW_Spt5_6; KOW domain of Spt5, repeat 6
      pfam04731
      Location:843972
      Caudal_act; Caudal like protein activation region
      pfam11942
      Location:75167
      Spt5_N; Spt5 transcription elongation factor, acidic N-terminal
      pfam12815
      Location:762818
      CTD; Spt5 C-terminal nonapeptide repeat binding Spt4
    4. NM_001319990.2NP_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:178265
      NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
      COG5164
      Location:334965
      SPT5; Transcription elongation factor [Transcription]
      cd06081
      Location:276313
      KOW_Spt5_1; KOW domain of Spt5, repeat 1
      cd06086
      Location:10281084
      KOW_Spt5_6; KOW domain of Spt5, repeat 6
      pfam11942
      Location:93172
      Spt5_N; Spt5 transcription elongation factor, acidic N-terminal
    5. NM_001319991.2NP_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:171312
      nusG; transcription antitermination protein NusG; Validated
      cd09888
      Location:174261
      NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
      COG5164
      Location:330961
      SPT5; Transcription elongation factor [Transcription]
      cd06081
      Location:272309
      KOW_Spt5_1; KOW domain of Spt5, repeat 1
      cd06082
      Location:416466
      KOW_Spt5_2; KOW domain of Spt5, repeat 2
      cd06083
      Location:467517
      KOW_Spt5_3; KOW domain of Spt5, repeat 3
      cd06084
      Location:593635
      KOW_Spt5_4; KOW domain of Spt5, repeat 4
      cd06085
      Location:698747
      KOW_Spt5_5; KOW domain of Spt5, repeat 5
      cd06086
      Location:10241080
      KOW_Spt5_6; KOW domain of Spt5, repeat 6
      pfam04731
      Location:843972
      Caudal_act; Caudal like protein activation region
      pfam11942
      Location:75167
      Spt5_N; Spt5 transcription elongation factor, acidic N-terminal
      pfam12815
      Location:762818
      CTD; Spt5 C-terminal nonapeptide repeat binding Spt4
    6. NM_003169.4NP_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:178265
      NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
      COG5164
      Location:334965
      SPT5; Transcription elongation factor [Transcription]
      cd06081
      Location:276313
      KOW_Spt5_1; KOW domain of Spt5, repeat 1
      cd06086
      Location:10281084
      KOW_Spt5_6; KOW domain of Spt5, repeat 6
      pfam11942
      Location:93172
      Spt5_N; Spt5 transcription elongation factor, acidic N-terminal

    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_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)