Human Gene SETD2 (ENST00000409792.4_10) from GENCODE V47lift37
  Description: SET domain containing 2, histone lysine methyltransferase, transcript variant 3 (from RefSeq NR_146158.3)
Gencode Transcript: ENST00000409792.4_10
Gencode Gene: ENSG00000181555.22_23
Transcript (Including UTRs)
   Position: hg19 chr3:47,057,926-47,205,603 Size: 147,678 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr3:47,058,583-47,205,414 Size: 146,832 Coding Exon Count: 21 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:47,057,926-47,205,603)mRNA (may differ from genome)Protein (2564 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SETD2_HUMAN
DESCRIPTION: RecName: Full=Histone-lysine N-methyltransferase SETD2; EC=2.1.1.43; AltName: Full=HIF-1; AltName: Full=Huntingtin yeast partner B; AltName: Full=Huntingtin-interacting protein 1; Short=HIP-1; AltName: Full=Huntingtin-interacting protein B; AltName: Full=Lysine N-methyltransferase 3A; AltName: Full=SET domain-containing protein 2; Short=hSET2; AltName: Full=p231HBP;
FUNCTION: Histone methyltransferase that methylates 'Lys-36' of histone H3. H3 'Lys-36' methylation represents a specific tag for epigenetic transcriptional activation. Probably plays a role in chromatin structure modulation during elongation via its interaction with hyperphosphorylated POLR2A. Binds DNA at promoters. May also act as a transcription activator that binds to promoters. Binds to the promoters of adenovirus 12 E1A gene in case of infection, possibly leading to regulate its expression.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
SUBUNIT: Specifically interacts with hyperphosphorylated C- terminal domain (CTD) of RNA polymerase II large subunit (POLR2A). Binds specifically to CTD heptad repeats doubly phosphorylated on 'Ser-2' and 'Ser-5' of each heptad. Interacts with HTT.
INTERACTION: P84022:SMAD3; NbExp=2; IntAct=EBI-945869, EBI-347161;
SUBCELLULAR LOCATION: Nucleus (Probable). Chromosome (Probable).
TISSUE SPECIFICITY: Ubiquitously expressed.
DOMAIN: The low charge region mediates the transcriptional activation activity.
PTM: May be automethylated.
SIMILARITY: Belongs to the histone-lysine methyltransferase family. SET2 subfamily.
SIMILARITY: Contains 1 AWS domain.
SIMILARITY: Contains 1 post-SET domain.
SIMILARITY: Contains 1 SET domain.
SIMILARITY: Contains 1 WW domain.
SEQUENCE CAUTION: Sequence=AAF29041.1; Type=Frameshift; Positions=Several; Sequence=AAH72440.1; Type=Erroneous termination; Positions=463; Note=Translated as Glu; Sequence=AAI17163.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAI17165.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAT77612.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAT77613.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB15367.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB15367.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=BAC87131.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAC28349.1; Type=Erroneous termination; Positions=385; Note=Translated as Arg; Sequence=CAD38601.2; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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: SETD2
Diseases sorted by gene-association score: luscan-lumish syndrome* (929), sotos syndrome 1* (251), renal cell carcinoma* (96), retinal ischemia (17), clear cell renal cell carcinoma (15), autoinflammation, lipodystrophy, and dermatosis syndrome (13), renal clear cell carcinoma (11), collecting duct carcinoma (10), autism spectrum disorder (8), cerebritis (8), chronic ulcer of skin (7), decubitus ulcer (7), huntington disease (4), kidney cancer (4), intellectual disability (1)
* = Manually curated disease association

-  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: 16.75 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 511.10 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 -110.10189-0.583 Picture PostScript Text
3' UTR -181.10657-0.276 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
IPR006560 - AWS
IPR009078 - Ferritin/RNR-like
IPR003616 - Post-SET_dom
IPR001214 - SET_dom
IPR013257 - SRI
IPR001202 - WW_Rsp5_WWP

Pfam Domains:
PF00397 - WW domain
PF00856 - SET domain
PF08236 - SRI (Set2 Rpb1 interacting) domain
PF17907 - AWS domain

SCOP Domains:
47240 - Ferritin-like
51045 - WW domain
82199 - SET domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2A7O - NMR MuPIT 4FMU - X-ray MuPIT 4H12 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9BYW2
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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 BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGD  WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0016279 protein-lysine N-methyltransferase activity
GO:0016740 transferase activity
GO:0018024 histone-lysine N-methyltransferase activity
GO:0043014 alpha-tubulin binding
GO:0046872 metal ion binding
GO:0046975 histone methyltransferase activity (H3-K36 specific)

Biological Process:
GO:0001525 angiogenesis
GO:0001570 vasculogenesis
GO:0001763 morphogenesis of a branching structure
GO:0001843 neural tube closure
GO:0002376 immune system process
GO:0006281 DNA repair
GO:0006298 mismatch repair
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006368 transcription elongation from RNA polymerase II promoter
GO:0006974 cellular response to DNA damage stimulus
GO:0007275 multicellular organism development
GO:0010452 histone H3-K36 methylation
GO:0010468 regulation of gene expression
GO:0010569 regulation of double-strand break repair via homologous recombination
GO:0010793 regulation of mRNA export from nucleus
GO:0018023 peptidyl-lysine trimethylation
GO:0018026 peptidyl-lysine monomethylation
GO:0030154 cell differentiation
GO:0030900 forebrain development
GO:0032259 methylation
GO:0032465 regulation of cytokinesis
GO:0032727 positive regulation of interferon-alpha production
GO:0034340 response to type I interferon
GO:0034728 nucleosome organization
GO:0034968 histone lysine methylation
GO:0035441 cell migration involved in vasculogenesis
GO:0035987 endodermal cell differentiation
GO:0045087 innate immune response
GO:0048332 mesoderm morphogenesis
GO:0048568 embryonic organ development
GO:0048701 embryonic cranial skeleton morphogenesis
GO:0048863 stem cell differentiation
GO:0048864 stem cell development
GO:0051607 defense response to virus
GO:0060039 pericardium development
GO:0060669 embryonic placenta morphogenesis
GO:0060977 coronary vasculature morphogenesis
GO:0097198 histone H3-K36 trimethylation
GO:0097676 histone H3-K36 dimethylation
GO:1902850 microtubule cytoskeleton organization involved in mitosis
GO:1905634 regulation of protein localization to chromatin

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome


-  Descriptions from all associated GenBank mRNAs
  AB384629 - Synthetic construct DNA, clone: pF1KA1732, Homo sapiens SETD2 gene for SET domain-containing protein 2, complete cds, without stop codon, in Flexi system.
AK131371 - Homo sapiens cDNA FLJ16420 fis, clone BRACE3003053.
AK128096 - Homo sapiens cDNA FLJ46217 fis, clone TESTI4012960.
AL831959 - Homo sapiens mRNA; cDNA DKFZp313O1417 (from clone DKFZp313O1417).
AK095494 - Homo sapiens cDNA FLJ38175 fis, clone FCBBF1000063, weakly similar to Homo sapiens huntingtin interacting protein HYPB mRNA.
AL049470 - Homo sapiens mRNA; cDNA DKFZp586L012 (from clone DKFZp586L012).
AK026837 - Homo sapiens cDNA: FLJ23184 fis, clone LNG11527, highly similar to AF049103 Homo sapiens Huntingtin interacting protein mRNA.
AB051519 - Homo sapiens mRNA for KIAA1732 protein, partial cds.
AL713692 - Homo sapiens mRNA; cDNA DKFZp547I2310 (from clone DKFZp547I2310).
BX649110 - Homo sapiens mRNA; cDNA DKFZp686C14109 (from clone DKFZp686C14109).
BC090954 - Homo sapiens SET domain containing 2, mRNA (cDNA clone IMAGE:4397772), partial cds.
JD537667 - Sequence 518691 from Patent EP1572962.
BC117162 - Homo sapiens SET domain containing 2, mRNA (cDNA clone MGC:150771 IMAGE:40125713), complete cds.
BC117164 - Homo sapiens SET domain containing 2, mRNA (cDNA clone MGC:150773 IMAGE:40125715), complete cds.
AJ238403 - Homo sapiens mRNA for huntingtin interacting protein 1.
AY576987 - Homo sapiens HSPC069 isoform a (HSPC069) mRNA, complete cds.
AY576988 - Homo sapiens HSPC069 isoform b (HSPC069) mRNA, complete cds.
AF049103 - Homo sapiens Huntingtin interacting protein mRNA, partial cds.
JD369033 - Sequence 350057 from Patent EP1572962.
JD197112 - Sequence 178136 from Patent EP1572962.
JD393615 - Sequence 374639 from Patent EP1572962.
JD283028 - Sequence 264052 from Patent EP1572962.
JD427520 - Sequence 408544 from Patent EP1572962.
JD373787 - Sequence 354811 from Patent EP1572962.
JD294402 - Sequence 275426 from Patent EP1572962.
JD507640 - Sequence 488664 from Patent EP1572962.
JD171619 - Sequence 152643 from Patent EP1572962.
JD063146 - Sequence 44170 from Patent EP1572962.
JD042860 - Sequence 23884 from Patent EP1572962.
AF049610 - Homo sapiens huntingtin interacting protein HYPB mRNA, partial cds.
JD257501 - Sequence 238525 from Patent EP1572962.
JD149755 - Sequence 130779 from Patent EP1572962.
JD102635 - Sequence 83659 from Patent EP1572962.
JD063945 - Sequence 44969 from Patent EP1572962.
JD522038 - Sequence 503062 from Patent EP1572962.
JD202908 - Sequence 183932 from Patent EP1572962.
JD308728 - Sequence 289752 from Patent EP1572962.
JD494343 - Sequence 475367 from Patent EP1572962.
JD380046 - Sequence 361070 from Patent EP1572962.
JD303718 - Sequence 284742 from Patent EP1572962.
JD297477 - Sequence 278501 from Patent EP1572962.
JD081791 - Sequence 62815 from Patent EP1572962.
JD112847 - Sequence 93871 from Patent EP1572962.
JD202991 - Sequence 184015 from Patent EP1572962.
JD354727 - Sequence 335751 from Patent EP1572962.
JD206843 - Sequence 187867 from Patent EP1572962.
JD094768 - Sequence 75792 from Patent EP1572962.
JD392063 - Sequence 373087 from Patent EP1572962.
JD464471 - Sequence 445495 from Patent EP1572962.
AF161554 - Homo sapiens HSPC069 mRNA, complete cds.
AL833394 - Homo sapiens mRNA; cDNA DKFZp762K209 (from clone DKFZp762K209).
AK091413 - Homo sapiens cDNA FLJ34094 fis, clone FCBBF3007150.
AX746966 - Sequence 491 from Patent EP1308459.
AK026125 - Homo sapiens cDNA: FLJ22472 fis, clone HRC10558.
BC072440 - Homo sapiens SET domain containing 2, mRNA (cDNA clone IMAGE:6045080), partial cds.
AK127782 - Homo sapiens cDNA FLJ45883 fis, clone OCBBF3021086.
JD321674 - Sequence 302698 from Patent EP1572962.
JD139492 - Sequence 120516 from Patent EP1572962.
JD271291 - Sequence 252315 from Patent EP1572962.
JD458510 - Sequence 439534 from Patent EP1572962.
JD406055 - Sequence 387079 from Patent EP1572962.
JD271292 - Sequence 252316 from Patent EP1572962.
JD458514 - Sequence 439538 from Patent EP1572962.
JD057274 - Sequence 38298 from Patent EP1572962.
JD406801 - Sequence 387825 from Patent EP1572962.
JD461601 - Sequence 442625 from Patent EP1572962.
JD056228 - Sequence 37252 from Patent EP1572962.
JD458513 - Sequence 439537 from Patent EP1572962.
JD056229 - Sequence 37253 from Patent EP1572962.
JD458511 - Sequence 439535 from Patent EP1572962.
JD458512 - Sequence 439536 from Patent EP1572962.
JD200352 - Sequence 181376 from Patent EP1572962.
JD272537 - Sequence 253561 from Patent EP1572962.
JD200351 - Sequence 181375 from Patent EP1572962.
JD272536 - Sequence 253560 from Patent EP1572962.

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

Protein Q9BYW2 (Reactome details) participates in the following event(s):

R-HSA-5638141 SETD2 (KMT3A) methylates dimethyl-lysine-37 of histone H3 (H3K36)
R-HSA-3214841 PKMTs methylate histone lysines
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000409792.1, ENST00000409792.2, ENST00000409792.3, HIF1, HSPC069, HYPB , KIAA1732 , KMT3A , NR_146158, O75397, O75405, Q17RW8, Q5BKS9, Q5QGN2, Q69YI5, Q6IN64, Q6ZN53, Q6ZS25, Q8N3R0, Q8TCN0, Q9BYW2, Q9C0D1, Q9H696, Q9NZW9, SET2 , SETD2_HUMAN, uc319gej.1, uc319gej.2
UCSC ID: ENST00000409792.4_10
RefSeq Accession: NM_014159.7
Protein: Q9BYW2 (aka SETD2_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SETD2:
setd2-ndd (SETD2 Neurodevelopmental Disorders)

-  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.