Human Gene SUPT6H (ENST00000314616.11_4) from GENCODE V47lift37
  Description: SPT6 homolog, histone chaperone and transcription elongation factor, transcript variant 2 (from RefSeq NM_003170.5)
Gencode Transcript: ENST00000314616.11_4
Gencode Gene: ENSG00000109111.15_8
Transcript (Including UTRs)
   Position: hg19 chr17:26,989,223-27,029,697 Size: 40,475 Total Exon Count: 37 Strand: +
Coding Region
   Position: hg19 chr17:27,000,420-27,028,643 Size: 28,224 Coding Exon Count: 36 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:26,989,223-27,029,697)mRNA (may differ from genome)Protein (1726 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SPT6H_HUMAN
DESCRIPTION: RecName: Full=Transcription elongation factor SPT6; Short=hSPT6; AltName: Full=Tat-cotransactivator 2 protein; Short=Tat-CT2 protein;
FUNCTION: Acts to stimulate transcriptional elongation by RNA polymerase II.
SUBUNIT: Interacts with RNA polymerase II and the DRB sensitivity- inducing factor complex (DSIF complex), which is composed of SUPT5H and SUPT4H1. Interacts with human cytomegalovirus/HHV-5 protein UL69.
SUBCELLULAR LOCATION: Nucleus (Probable).
TISSUE SPECIFICITY: Ubiquitously expressed.
SIMILARITY: Belongs to the SPT6 family.
SIMILARITY: Contains 1 S1 motif domain.
SIMILARITY: Contains 1 SH2 domain.
SEQUENCE CAUTION: Sequence=AAB18949.1; Type=Frameshift; Positions=988; Sequence=AAC50821.1; Type=Erroneous initiation; Sequence=AAH33074.1; Type=Erroneous initiation; Sequence=BAA11479.2; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SUPT6H
Diseases sorted by gene-association score: chromosome 17q11.2 deletion syndrome, 1.4-mb (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 32.75 RPKM in Pituitary
Total median expression: 1133.45 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 -60.00169-0.355 Picture PostScript Text
3' UTR -394.801054-0.375 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
IPR012340 - NA-bd_OB-fold
IPR016027 - NA-bd_OB-fold-like
IPR003029 - Rbsml_prot_S1_RNA-bd_dom
IPR022967 - RNA-binding_domain_S1
IPR000980 - SH2
IPR023323 - Tex-like_dom
IPR023097 - Tex_RuvX-like_dom
IPR017072 - TF_Spt6
IPR006641 - YqgF/RNaseH-like_dom

Pfam Domains:
PF00017 - SH2 domain
PF00575 - S1 RNA binding domain
PF12836 - Helix-hairpin-helix motif
PF14632 - Acidic N-terminal SPT6
PF14633 - SH2 domain
PF14635 - Helix-hairpin-helix motif
PF14639 - Holliday-junction resolvase-like of SPT6
PF14641 - Helix-turn-helix DNA-binding domain of SPT6
PF17674 - HHH domain

SCOP Domains:
158832 - Tex N-terminal region-like
47781 - RuvA domain 2-like
50249 - Nucleic acid-binding proteins
53098 - Ribonuclease H-like
55550 - SH2 domain

ModBase Predicted Comparative 3D Structure on Q7KZ85
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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 orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000991 transcription factor activity, core RNA polymerase II binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0031491 nucleosome binding
GO:0042393 histone binding

Biological Process:
GO:0006139 nucleobase-containing compound metabolic process
GO:0006338 chromatin remodeling
GO:0006342 chromatin silencing
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:0008380 RNA splicing
GO:0010793 regulation of mRNA export from nucleus
GO:0016032 viral process
GO:0032784 regulation of DNA-templated transcription, elongation
GO:0032968 positive regulation of transcription elongation from RNA polymerase II promoter
GO:0034728 nucleosome organization
GO:0042789 mRNA transcription from RNA polymerase II promoter
GO:0045191 regulation of isotype switching
GO:0050684 regulation of mRNA processing
GO:0051028 mRNA transport
GO:0051147 regulation of muscle cell differentiation
GO:0061086 negative regulation of histone H3-K27 methylation
GO:0070827 chromatin maintenance

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0008023 transcription elongation factor complex
GO:0035327 transcriptionally active chromatin


-  Descriptions from all associated GenBank mRNAs
  AL833607 - Homo sapiens mRNA; cDNA DKFZp686M1767 (from clone DKFZp686M1767).
D79984 - Homo sapiens KIAA0162 mRNA.
BC150268 - Homo sapiens suppressor of Ty 6 homolog (S. cerevisiae), mRNA (cDNA clone MGC:166860 IMAGE:9007230), complete cds.
BC136522 - Homo sapiens suppressor of Ty 6 homolog (S. cerevisiae), mRNA (cDNA clone MGC:168135 IMAGE:9020512), complete cds.
BC136524 - Homo sapiens suppressor of Ty 6 homolog (S. cerevisiae), mRNA (cDNA clone MGC:168137 IMAGE:9020514), complete cds.
AB489150 - Synthetic construct DNA, clone: pF1KA0162, Homo sapiens SUPT6H gene for suppressor of Ty 6 homolog, without stop codon, in Flexi system.
LF326830 - JP 2014500723-A/134333: Polycomb-Associated Non-Coding RNAs.
MA562407 - JP 2018138019-A/134333: Polycomb-Associated Non-Coding RNAs.
U46691 - Human putative chromatin structure regulator (SUPT6H) mRNA, complete cds.
BC033074 - Homo sapiens suppressor of Ty 6 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:4877063), complete cds.
U38623 - Human chromatin structural protein (SPTH6) mRNA, partial cds.
BC003696 - Homo sapiens suppressor of Ty 6 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3456230), partial cds.
U38658 - Human chromatin structural protein (SPTH6) mRNA, partial cds.
BC017105 - Homo sapiens suppressor of Ty 6 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3533805), partial cds.
AK126585 - Homo sapiens cDNA FLJ44622 fis, clone BRACE2017359, highly similar to Mus musculus suppressor of Ty 6 homolog (S. cerevisiae) (Supt6h).
BC073963 - Homo sapiens suppressor of Ty 6 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:5587330), complete cds.
BC003692 - Homo sapiens, Similar to suppressor of Ty (S.cerevisiae) 6 homolog, clone IMAGE:3454122, mRNA, partial cds.
AF070532 - Homo sapiens clones 24605 and 24699 emb-5 mRNA, partial cds.
JD464707 - Sequence 445731 from Patent EP1572962.
JD399296 - Sequence 380320 from Patent EP1572962.
JD246222 - Sequence 227246 from Patent EP1572962.
JD463640 - Sequence 444664 from Patent EP1572962.
JD103264 - Sequence 84288 from Patent EP1572962.
JD137683 - Sequence 118707 from Patent EP1572962.
JD215045 - Sequence 196069 from Patent EP1572962.
JD481750 - Sequence 462774 from Patent EP1572962.
JD233174 - Sequence 214198 from Patent EP1572962.
JD497076 - Sequence 478100 from Patent EP1572962.
JD108461 - Sequence 89485 from Patent EP1572962.
JD411106 - Sequence 392130 from Patent EP1572962.
JD049628 - Sequence 30652 from Patent EP1572962.
JD257808 - Sequence 238832 from Patent EP1572962.
JD288245 - Sequence 269269 from Patent EP1572962.
JD068608 - Sequence 49632 from Patent EP1572962.
JD437622 - Sequence 418646 from Patent EP1572962.
JD108263 - Sequence 89287 from Patent EP1572962.
JD309557 - Sequence 290581 from Patent EP1572962.
JD537449 - Sequence 518473 from Patent EP1572962.

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

Protein Q7KZ85 (Reactome details) participates in the following event(s):

R-HSA-112379 Recruitment of elongation factors to form elongation complex
R-HSA-113429 Elongating transcript encounters a lesion in the template
R-HSA-112385 Addition of nucleotides leads to transcript elongation
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-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-112382 Formation of RNA Pol II elongation complex
R-HSA-674695 RNA Polymerase II Pre-transcription Events
R-HSA-75955 RNA Polymerase II Transcription Elongation
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: A7E2B4, ENST00000314616.1, ENST00000314616.10, ENST00000314616.2, ENST00000314616.3, ENST00000314616.4, ENST00000314616.5, ENST00000314616.6, ENST00000314616.7, ENST00000314616.8, ENST00000314616.9, KIAA0162, NM_003170, Q15737, Q6GMQ4, Q7KYW9, Q7KZ85, Q7LDK4, Q8N526, Q92775, Q96AH3, Q9BTH9, Q9BTI2, SPT6H, SPT6H_HUMAN, uc317prb.1, uc317prb.2
UCSC ID: ENST00000314616.11_4
RefSeq Accession: NM_003170.5
Protein: Q7KZ85 (aka SPT6H_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.