SUPT4H1 SPT4 homolog, DSIF elongation factor subunit [Homo sapiens (human)] - Gene

Summary

Official Symbol: SUPT4H1provided by HGNC
Official Full Name: SPT4 homolog, DSIF elongation factor subunitprovided by HGNC
Primary source: HGNC:HGNC:11467
See related: Ensembl:ENSG00000213246 MIM:603555; AllianceGenome:HGNC:11467
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SPT4; SPT4H; SUPT4H; Supt4a
Summary: This gene encodes the small subunit of DRB (5,6-dichloro-1-beta-d-ribofuranosylbenzimidazole) sensitivity-inducing factor (DSIF) complex, which regulates mRNA processing and transcription elongation by RNA polymerase II. The encoded protein is localized to the nucleus and interacts with the large subunit (SUPT5H) to form the DSIF complex. Related pseudogenes have been identified on chromosomes 2 and 12. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2012]
Expression: Ubiquitous expression in bone marrow (RPKM 34.4), brain (RPKM 26.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q22

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (58345178..58352201, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (59213053..59220076, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (56422539..56429562, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Authors depleted SUPT4H1 by RNA interference to inhibit the function of the SUPT4H1/SUPT5H transcription elongation complex. Depletion of SUPT4H1 leads to a global reduction in all cellular RNA.
Title: SUPT4H1 Depletion Leads to a Global Reduction in RNA.
Chimeric transcript resulting from the fusion of RNF43 and SUPT4H1 was found to occur frequently in primary colorectal carcinoma.
Title: Transcriptome analysis of paired primary colorectal carcinoma and liver metastases reveals fusion transcripts and similar gene expression profiles in primary carcinoma and liver metastases.
Knockdown of SUPT4H1, the human Spt4 ortholog, similarly decreased production of sense and antisense RNA foci, as well as dipeptide repeat proteins, in patient cells.
Title: Spt4 selectively regulates the expression of C9orf72 sense and antisense mutant transcripts.
crystal structure of hSpt4 in complex with the dimerization region of hSpt5
Title: Crystal structure of the human transcription elongation factor DSIF hSpt4 subunit in complex with the hSpt5 dimerization interface.
he Paf1 complex (Paf1C) and Tat-SF1, two factors implicated previously in elongation control, collaborate with DSIF to facilitate efficient elongation
Title: DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation.
These findings reveal a dynamic regulation of DSIF involving either E-box or NF-kappaB depending on the physiological circumstances.
Title: Interplay between E-box and NF-kappaB in regulation of A20 gene by DRB sensitivity-inducing factor (DSIF).
These results suggest that one of the functions of Spt5 is to suppress senescence and apoptosis, and that this function is exerted through its association with Spt4 and Pol II.
Title: Role of human transcription elongation factor DSIF in the suppression of senescence and apoptosis.
Spt4 was purified and characterized.
Title: The small hSpt4 subunit of the human transcription elongation factor DSIF is a Zn-finger protein with alpha/beta type topology.
Upon induction of NF-kappaB, a subset of target genes is regulated differentially by either P-TEFb or DSIF.[P-TEFb, DSIF]
Title: Differential regulation of NF-kappaB by elongation factors is determined by core promoter type.

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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)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	The SPT5/SPT4 complex, DSIF, associates with the HIV-1 transcription elongation complex (TEC) and are involved in the activation of transcriptional elongation by HIV-1 Tat	PubMed

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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

WI-11652 (e-PCR)
- UniSTS:81424

RH35987 (e-PCR)
- UniSTS:8224

RH98919 (e-PCR)
- UniSTS:84783

D12S1371 (e-PCR)
- UniSTS:153655

RH45569 (e-PCR)
- UniSTS:70968

D17S1419E (e-PCR)
- UniSTS:14910

STS-H72889 (e-PCR)
- UniSTS:74849

RH68148 (e-PCR)
- UniSTS:77415

RH70634 (e-PCR)
- UniSTS:64151

MARC_4325-4326:991938466:1 (e-PCR)
- UniSTS:231081

MARC_4325-4326:996679570:1 (e-PCR)
- UniSTS:231081

WI-21001 (e-PCR)
- UniSTS:79542

MARC_3557-3558:966881413:1 (e-PCR)
- UniSTS:269274

RH93017 (e-PCR)
- UniSTS:87791

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA polymerase II complex 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
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

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 transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription elongation by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription, elongation	IDA Inferred from Direct Assay 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 DNA-templated transcription	TAS Traceable Author Statement 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-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 SPT4

Names: DRB sensitivity-inducing factor 14 kDa subunit; DSIF p14; small hSpt4 subunit; suppressor of Ty 4 homolog 1

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)

NM_003168.3 → NP_003159.1 transcription elongation factor SPT4

See identical proteins and their annotated locations for NP_003159.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the shorter transcript and encodes the functional protein.

Source sequence(s)

BG026473, U43923

Consensus CDS

CCDS11606.1

UniProtKB/Swiss-Prot

B2R4X8, D3DTZ4, P63272, Q16550, Q62387, Q6ZP89

UniProtKB/TrEMBL

J3QSB9

Related

ENSP00000225504.3, ENST00000225504.8

Conserved Domains (1) summary

cd07973
Location:11 → 108

Spt4; Transcription elongation factor Spt4

RNA

NR_073470.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 5' exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AI735030, BP318625, BX331655, U43923

Related

ENST00000577396.5