Human Gene SUPT4H1 (uc002iwe.2) Description and Page Index
  Description: Homo sapiens suppressor of Ty 4 homolog 1 (S. cerevisiae) (SUPT4H1), transcript variant 1, mRNA.
RefSeq Summary (NM_003168): 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].
Transcript (Including UTRs)
   Position: hg19 chr17:56,422,536-56,429,599 Size: 7,064 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr17:56,423,607-56,429,496 Size: 5,890 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:56,422,536-56,429,599)mRNA (may differ from genome)Protein (117 aa)
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Wikipedia

-  Comments and Description Text from UniProtKB
  ID: SPT4H_HUMAN
DESCRIPTION: RecName: Full=Transcription elongation factor SPT4; Short=hSPT4; AltName: Full=DRB sensitivity-inducing factor 14 kDa subunit; Short=DSIF p14; AltName: Full=DRB sensitivity-inducing factor small subunit; Short=DSIF small subunit;
FUNCTION: Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates mRNA processing and transcription elongation by RNA polymerase II. DSIF positively regulates mRNA capping by stimulating the mRNA guanylyltransferase activity of RNGTT/CAP1A. DSIF also acts cooperatively with the negative elongation factor complex (NELF complex) to enhance transcriptional pausing at sites proximal to the promoter. Transcriptional pausing may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF and NELF promote pausing by inhibition of the transcription elongation factor TFIIS/S-II. TFIIS/S-II binds to RNA polymerase II at transcription pause sites and stimulates the weak intrinsic nuclease activity of the enzyme. Cleavage of blocked transcripts by RNA polymerase II promotes the resumption of transcription from the new 3' terminus and may allow repeated attempts at transcription through natural pause sites. DSIF can also positively regulate transcriptional elongation and is required for the efficient activation of transcriptional elongation by the HIV- 1 nuclear transcriptional activator, Tat. DSIF acts to suppress transcriptional pausing in transcripts derived from the HIV-1 LTR and blocks premature release of HIV-1 transcripts at terminator sequences.
SUBUNIT: Interacts with SUPT5H to form DSIF. DSIF interacts with the positive transcription elongation factor b complex (P-TEFb complex), which is composed of CDK9 and cyclin-T (CCNT1 or CCNT2). DSIF interacts with RNA polymerase II, and this interaction is reduced by phosphorylation of the C-terminal domain (CTD) of POLR2A by P-TEFb. DSIF also interacts with the NELF complex, which is composed of WHSC2/NELFA, COBRA1/NELFB, TH1L/NELFD and RDBP/NELFE, and this interaction occurs following prior binding of DSIF to RNA polymerase II. DSIF also interacts with HRMT1L2/PRMT1, HTATSF1/TATSF1, RNGTT/CAP1A, SKB1/PRMT5, SUPT6H, and can interact with PIN1.
INTERACTION: O00267:SUPT5H; NbExp=3; IntAct=EBI-727250, EBI-710464;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Widely expressed.
SIMILARITY: Belongs to the SPT4 family.

-  MalaCards Disease Associations
  MalaCards Gene Search: SUPT4H1
Diseases sorted by gene-association score: hiv-1 (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 43.39 RPKM in Whole Blood
Total median expression: 1292.25 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -31.60103-0.307 Picture PostScript Text
3' UTR -320.511071-0.299 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR009287 - Spt4
IPR016046 - Spt4-like
IPR022800 - Spt4/RpoE2_Znf

Pfam Domains:
PF06093 - Spt4/RpoE2 zinc finger

SCOP Domains:
63393 - RNA polymerase subunits

Protein Data Bank (PDB) 3-D Structure
MuPIT help

3H7H
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P63272
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
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  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000993 RNA polymerase II core binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003727 single-stranded RNA binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0046872 metal ion binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0006368 transcription elongation from RNA polymerase II promoter
GO:0006397 mRNA processing
GO:0032785 negative regulation of DNA-templated transcription, elongation
GO:0032786 positive regulation of DNA-templated transcription, elongation
GO:0034243 regulation of transcription elongation from RNA polymerase II promoter
GO:0034244 negative regulation of transcription elongation from RNA polymerase II promoter
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0032044 DSIF complex


-  Descriptions from all associated GenBank mRNAs
  LF384793 - JP 2014500723-A/192296: Polycomb-Associated Non-Coding RNAs.
U43923 - Human transcription factor SUPT4H mRNA, complete cds.
AK129758 - Homo sapiens cDNA FLJ26247 fis, clone DMC01574.
U38818 - Human SUPT4H mRNA, complete cds.
JD251243 - Sequence 232267 from Patent EP1572962.
JD486605 - Sequence 467629 from Patent EP1572962.
JD067844 - Sequence 48868 from Patent EP1572962.
JD556599 - Sequence 537623 from Patent EP1572962.
JD161797 - Sequence 142821 from Patent EP1572962.
JD258536 - Sequence 239560 from Patent EP1572962.
JD435094 - Sequence 416118 from Patent EP1572962.
JD290522 - Sequence 271546 from Patent EP1572962.
JD312678 - Sequence 293702 from Patent EP1572962.
U38817 - Human SUPT4H mRNA, complete cds.
BC002802 - Homo sapiens suppressor of Ty 4 homolog 1 (S. cerevisiae), mRNA (cDNA clone MGC:3864 IMAGE:3636217), complete cds.
JD172331 - Sequence 153355 from Patent EP1572962.
JD565218 - Sequence 546242 from Patent EP1572962.
JD156917 - Sequence 137941 from Patent EP1572962.
JD332797 - Sequence 313821 from Patent EP1572962.
KJ892229 - Synthetic construct Homo sapiens clone ccsbBroadEn_01623 SUPT4H1 gene, encodes complete protein.
AK311986 - Homo sapiens cDNA, FLJ92259, Homo sapiens suppressor of Ty 4 homolog 1 (S. cerevisiae)(SUPT4H1), mRNA.
EU446710 - Synthetic construct Homo sapiens clone IMAGE:100069796; IMAGE:100011919; FLH258568.01L suppressor of Ty 4 homolog 1 (S. cerevisiae) (SUPT4H1) gene, encodes complete protein.
AB527904 - Synthetic construct DNA, clone: pF1KB0917, Homo sapiens SUPT4H1 gene for suppressor of Ty 4 homolog 1, without stop codon, in Flexi system.
CR407663 - Homo sapiens full open reading frame cDNA clone RZPDo834E017D for gene SUPT4H1, suppressor of Ty 4 homolog 1 (S. cerevisiae) complete cds, without stopcodon.
LF327232 - JP 2014500723-A/134735: Polycomb-Associated Non-Coding RNAs.
JD545966 - Sequence 526990 from Patent EP1572962.
MA620370 - JP 2018138019-A/192296: Polycomb-Associated Non-Coding RNAs.
MA562809 - JP 2018138019-A/134735: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P63272 (Reactome details) participates in the following event(s):

R-HSA-112434 Formation of DSIF complex
R-HSA-113407 DSIF complex binds to RNA Pol II (hypophosphorylated)
R-HSA-167083 DSIF complex binds to RNA Pol II (hypophosphorylated)
R-HSA-113429 Elongating transcript encounters a lesion in the template
R-HSA-113402 Formation of DSIF:NELF:early elongation complex
R-HSA-112379 Recruitment of elongation factors to form elongation complex
R-HSA-112381 Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex
R-HSA-113411 2-4 nt.backtracking of Pol II complex on the template leading to elongation pausing
R-HSA-113412 Pol II elongation complex moves on the template as transcript elongates
R-HSA-113414 7-14 nt. Backtracking of Pol II complex on the template leading to elongation arrest
R-HSA-112385 Addition of nucleotides leads to transcript elongation
R-HSA-112392 Resumption of elongation after recovery from pausing
R-HSA-113413 TFIIS-mediated recovery of elongation from arrest
R-HSA-112395 Abortive termination of elongation after arrest
R-HSA-112396 Separation of elongating transcript from template
R-HSA-167085 Formation of DSIF:NELF:HIV-1 early elongation complex
R-HSA-167150 Resumption of elongation of HIV-1 transcript after recovery from pausing
R-HSA-167076 2-4 nt.backtracking of Pol II complex on the HIV-1 template leading to elongation pausing
R-HSA-167077 Recruitment of elongation factors to form HIV-1 elongation complex
R-HSA-167084 Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex
R-HSA-167282 2-4 nt.backtracking of Pol II complex on the HIV-1 template leading to elongation pausing
R-HSA-167284 7-14 nt. Backtracking of Pol II complex on the HIV-1 template leading to elongation arrest
R-HSA-167288 TFIIS-mediated recovery of HIV-1 elongation from arrest
R-HSA-167292 Resumption of elongation of HIV-1 transcript after recovery from pausing
R-HSA-167148 TFIIS-mediated recovery of elongation from arrest
R-HSA-167459 Abortive termination of HIV-1 elongation after arrest (Tat-containing elongation complex)
R-HSA-167090 7-14 nt. Backtracking of Pol II complex on the HIV-1 template leading to elongation arrest
R-HSA-170706 Phosphorylation of NEFL by the P-TEFb(Cyclin T1:Cdk9) complex
R-HSA-167191 Hyperphosphorylation (Ser2) of RNA Pol II CTD by the P-TEFb(Cyclin T1:Cdk9) complex
R-HSA-167192 Pol II elongation complex moves on the HIV-1 template as transcript elongates
R-HSA-167181 Addition of nucleotides leads to HIV-1 transcript elongation
R-HSA-167197 Separation of elongating HIV-1 transcript from template
R-HSA-167481 Abortive termination of HIV-1 elongation after arrest
R-HSA-170704 Phosphorylation of DSIF by the P-TEFb(Cyclin T1:Cdk9) complex
R-HSA-167196 Recruitment of elongation factors to form HIV-1 elongation complex
R-HSA-113409 Abortive termination of early transcription elongation by DSIF:NELF
R-HSA-167087 Limited elongation of the HIV-1 transcript
R-HSA-167478 Abortive termination of HIV-1 early transcription elongation by DSIF:NELF
R-HSA-167147 Separation of abortive HIV-1 transcript from template
R-HSA-6797616 CCNK:CDK12 binds RNA Pol II at DNA repair genes
R-HSA-6797606 CDK12 phosphorylates RNA Pol II CTD at DNA repair genes
R-HSA-674695 RNA Polymerase II Pre-transcription Events
R-HSA-113418 Formation of the Early Elongation Complex
R-HSA-167158 Formation of the HIV-1 Early Elongation Complex
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-112382 Formation of RNA Pol II elongation complex
R-HSA-75955 RNA Polymerase II Transcription Elongation
R-HSA-167238 Pausing and recovery of Tat-mediated HIV elongation
R-HSA-167152 Formation of HIV elongation complex in the absence of HIV Tat
R-HSA-167290 Pausing and recovery of HIV elongation
R-HSA-167287 HIV elongation arrest and recovery
R-HSA-167243 Tat-mediated HIV elongation arrest and recovery
R-HSA-167200 Formation of HIV-1 elongation complex containing HIV-1 Tat
R-HSA-167246 Tat-mediated elongation of the HIV-1 transcript
R-HSA-167169 HIV Transcription Elongation
R-HSA-74160 Gene expression (Transcription)
R-HSA-167242 Abortive elongation of HIV-1 transcript in the absence of Tat
R-HSA-167172 Transcription of the HIV genome
R-HSA-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-HSA-162599 Late Phase of HIV Life Cycle
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-162587 HIV Life Cycle
R-HSA-212436 Generic Transcription Pathway
R-HSA-162906 HIV Infection
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: B2R4X8, D3DTZ4, NM_003168, NP_003159, P63272, Q16550, Q62387, Q6ZP89, SPT4H, SPT4H_HUMAN, SUPT4H, uc002iwe.1
UCSC ID: uc002iwe.2
RefSeq Accession: NM_003168
Protein: P63272 (aka SPT4H_HUMAN)
CCDS: CCDS11606.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003168.2
exon count: 5CDS single in 3' UTR: no RNA size: 1545
ORF size: 354CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 908.00frame shift in genome: no % Coverage: 98.90
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.