Human Gene SETD1A (ENST00000262519.14_6) from GENCODE V47lift37
  Description: SET domain containing 1A, histone lysine methyltransferase (from RefSeq NM_014712.3)
Gencode Transcript: ENST00000262519.14_6
Gencode Gene: ENSG00000099381.20_9
Transcript (Including UTRs)
   Position: hg19 chr16:30,969,075-30,995,985 Size: 26,911 Total Exon Count: 19 Strand: +
Coding Region
   Position: hg19 chr16:30,970,053-30,995,344 Size: 25,292 Coding Exon Count: 18 

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 (chr16:30,969,075-30,995,985)mRNA (may differ from genome)Protein (1707 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SET1A_HUMAN
DESCRIPTION: RecName: Full=Histone-lysine N-methyltransferase SETD1A; EC=2.1.1.43; AltName: Full=Lysine N-methyltransferase 2F; AltName: Full=SET domain-containing protein 1A; Short=hSET1A; AltName: Full=Set1/Ash2 histone methyltransferase complex subunit SET1;
FUNCTION: Histone methyltransferase that specifically methylates 'Lys-4' of histone H3, when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys- 9' residue is already methylated. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. The non-overalpping localization with SETD1B suggests that SETD1A and SETD1B make non-redundant contributions to the epigenetic control of chromatin structure and gene expression.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
SUBUNIT: Component of the SET1 complex, at least composed of the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30. Interacts with HCFC1. Interacts with ASH2/ASH2L, CXXC1/CFP1, WDR5 and RBBP5. Interacts (via the RRM domain) with WDR82. Interacts (via the RRM domain) with hyperphosphorylated C-terminal domain (CTD) of RNA polymerase II large subunit (POLR2A) only in the presence of WDR82. Binds specifically to CTD heptad repeats phosphorylated on 'Ser-5' of each heptad.
INTERACTION: P51610:HCFC1; NbExp=2; IntAct=EBI-540779, EBI-396176;
SUBCELLULAR LOCATION: Nucleus speckle. Chromosome. Note=Localizes to a largely non-overlapping set of euchromatic nuclear speckles with SETD1B, suggesting that SETD1A and SETD1B each bind to a unique set of target genes.
SIMILARITY: Contains 1 post-SET domain.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SIMILARITY: Contains 1 SET domain.
SEQUENCE CAUTION: Sequence=AAH35795.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=BAA20797.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  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: SETD1A
Diseases sorted by gene-association score: schizophrenia* (145), cerebritis (10), hemometra (7), cerebral lymphoma (6), anus cancer (5)
* = Manually curated disease association

-  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: 22.47 RPKM in Testis
Total median expression: 379.53 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 -96.30226-0.426 Picture PostScript Text
3' UTR -265.30641-0.414 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
IPR024657 - COMPASS_Set1_N-SET
IPR015722 - Histone-lysine_MeTfrase
IPR012677 - Nucleotide-bd_a/b_plait
IPR003616 - Post-SET_dom
IPR000504 - RRM_dom
IPR001214 - SET_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF00856 - SET domain
PF11764 - COMPASS (Complex proteins associated with Set1p) component N

SCOP Domains:
82199 - SET domain
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3S8S - X-ray MuPIT 3UVN - X-ray MuPIT 4EWR - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O15047
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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 orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008013 beta-catenin binding
GO:0008134 transcription factor binding
GO:0008168 methyltransferase activity
GO:0016740 transferase activity
GO:0018024 histone-lysine N-methyltransferase activity
GO:0042800 histone methyltransferase activity (H3-K4 specific)

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0032259 methylation
GO:0034968 histone lysine methylation
GO:0045652 regulation of megakaryocyte differentiation
GO:0051568 histone H3-K4 methylation
GO:1902036 regulation of hematopoietic stem cell differentiation
GO:1902275 regulation of chromatin organization

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0016607 nuclear speck
GO:0035097 histone methyltransferase complex
GO:0048188 Set1C/COMPASS complex


-  Descriptions from all associated GenBank mRNAs
  AB002337 - Homo sapiens KIAA0339 mRNA for KIAA0339 protein.
BC035795 - Homo sapiens SET domain containing 1A, mRNA (cDNA clone IMAGE:5737791), partial cds.
JD376546 - Sequence 357570 from Patent EP1572962.
JD462467 - Sequence 443491 from Patent EP1572962.
JD393354 - Sequence 374378 from Patent EP1572962.
JD425693 - Sequence 406717 from Patent EP1572962.
JD278122 - Sequence 259146 from Patent EP1572962.
BC108673 - Homo sapiens cDNA clone IMAGE:6019468, partial cds.
JD461178 - Sequence 442202 from Patent EP1572962.
JD279966 - Sequence 260990 from Patent EP1572962.
JD531902 - Sequence 512926 from Patent EP1572962.
AB384464 - Synthetic construct DNA, clone: pF1KA0339, Homo sapiens SETD1A gene for SET domain-containing protein 1A, complete cds, without stop codon, in Flexi system.
BC027450 - Homo sapiens SET domain containing 1A, mRNA (cDNA clone IMAGE:4156088), partial cds.
JD458461 - Sequence 439485 from Patent EP1572962.
JD373316 - Sequence 354340 from Patent EP1572962.
JD232773 - Sequence 213797 from Patent EP1572962.
JD037511 - Sequence 18535 from Patent EP1572962.
JD545076 - Sequence 526100 from Patent EP1572962.
JD124545 - Sequence 105569 from Patent EP1572962.
JD138985 - Sequence 120009 from Patent EP1572962.
JD393084 - Sequence 374108 from Patent EP1572962.
JD474943 - Sequence 455967 from Patent EP1572962.
JD261040 - Sequence 242064 from Patent EP1572962.
JD151242 - Sequence 132266 from Patent EP1572962.
JD334674 - Sequence 315698 from Patent EP1572962.
JD150048 - Sequence 131072 from Patent EP1572962.
JD424721 - Sequence 405745 from Patent EP1572962.
JD125461 - Sequence 106485 from Patent EP1572962.

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

Protein O15047 (Reactome details) participates in the following event(s):

R-HSA-8935740 RUNX1 and GATA1 bind the promoter of the ITGA2B gene
R-HSA-8936616 RUNX1 and GATA1 bind the promoter of the GP1BA gene
R-HSA-8936979 RUNX1 and GATA1 bind the promoter of the THBS1 gene
R-HSA-8937037 RUNX1 and GATA1 bind the promoter of the MIR27A gene
R-HSA-8936481 Core MLL complex methylates H3K4Me2-Nucleosome at the ITGA2B gene promoter
R-HSA-8936621 Core MLL complex methylates H3K4Me2-Nucleosome at the GP1BA gene promoter
R-HSA-8937016 Core MLL complex methylates H3K4Me2-Nucleosome at the THBS1 gene promoter
R-HSA-8937050 Core MLL complex methylates H3K4Me2-Nucleosome at the MIR27A gene promoter
R-HSA-5159245 SETD3, SETD7 (KMT7), WHSC1L1 (KMT3F), Core MLL complex methylate lysine-5 of histone H3 (H3K4)
R-HSA-5244692 Core MLL complex, SMYD3, PRDM9 methylate dimethyl-lysine-5 of histone H3 (H3K4)
R-HSA-5637686 WHSC1L1 (KMT3F), Core MLL complex, SMYD3 (KMT3E) methylate methyl-lysine-5 of histone H3 (H3K4)
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-3214841 PKMTs methylate histone lysines
R-HSA-212436 Generic Transcription Pathway
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-4839726 Chromatin organization
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: A6NP62, ENST00000262519.1, ENST00000262519.10, ENST00000262519.11, ENST00000262519.12, ENST00000262519.13, ENST00000262519.2, ENST00000262519.3, ENST00000262519.4, ENST00000262519.5, ENST00000262519.6, ENST00000262519.7, ENST00000262519.8, ENST00000262519.9, KIAA0339 , KMT2F, NM_014712, O15047, Q6PIF3, Q8TAJ6, SET1, SET1A, SET1A_HUMAN, uc317hbg.1, uc317hbg.2
UCSC ID: ENST00000262519.14_6
RefSeq Accession: NM_014712.3
Protein: O15047 (aka SET1A_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.