Human Gene SET (uc022bol.1) Description and Page Index
  Description: Homo sapiens SET nuclear oncogene (SET), transcript variant 3, mRNA.
RefSeq Summary (NM_001248000): The protein encoded by this gene inhibits acetylation of nucleosomes, especially histone H4, by histone acetylases (HAT). This inhibition is most likely accomplished by masking histone lysines from being acetylated, and the consequence is to silence HAT-dependent transcription. The encoded protein is part of a complex localized to the endoplasmic reticulum but is found in the nucleus and inhibits apoptosis following attack by cytotoxic T lymphocytes. This protein can also enhance DNA replication of the adenovirus genome. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BU543146.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968540, SAMEA1968832 [ECO:0000348] ##Evidence-Data-END##
Transcript (Including UTRs)
   Position: hg19 chr9:131,447,365-131,458,675 Size: 11,311 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr9:131,447,447-131,456,943 Size: 9,497 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr9:131,447,365-131,458,675)mRNA (may differ from genome)Protein (268 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
Stanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: SubName: Full=Protein SET; SubName: Full=SET nuclear oncogene;
SIMILARITY: Belongs to the nucleosome assembly protein (NAP) family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SET
CDC HuGE Published Literature: SET
Positive Disease Associations: Macular Degeneration
Related Studies:
  1. Macular Degeneration
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: SET
Diseases sorted by gene-association score: leukemia, acute myeloid (4), leukoencephalopathy with vanishing white matter (1)

-  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: 147.68 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 2482.49 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 -27.3082-0.333 Picture PostScript Text
3' UTR -473.751732-0.274 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
IPR002164 - NAP_family

Pfam Domains:
PF00956 - Nucleosome assembly protein (NAP)

ModBase Predicted Comparative 3D Structure on Q5VXV2
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 Details   Gene Details 
Gene Sorter   Gene Sorter 
    Protein Sequence 

-  Descriptions from all associated GenBank mRNAs
  AK300794 - Homo sapiens cDNA FLJ51749 complete cds, highly similar to Protein SET.
D45198 - Homo sapiens set mRNA for template acyivating factor-I alpha, complete cds.
AB464200 - Synthetic construct DNA, clone: pF1KB6336, Homo sapiens SET gene for SET translocation, without stop codon, in Flexi system.
AM393022 - Synthetic construct Homo sapiens clone IMAGE:100002298 for hypothetical protein (SET gene).
JF729356 - Homo sapiens SET mRNA, complete cds.
BC056245 - Homo sapiens cDNA clone IMAGE:6698185, partial cds.
AK223556 - Homo sapiens mRNA for SET translocation (myeloid leukemia-associated) variant, clone: FCC127D11.
BC014567 - Homo sapiens cDNA clone IMAGE:3010577, containing frame-shift errors.
AK315313 - Homo sapiens cDNA, FLJ96345, Homo sapiens SET translocation (myeloid leukemia-associated) (SET),mRNA.
BC032749 - Homo sapiens SET nuclear oncogene, mRNA (cDNA clone MGC:45315 IMAGE:5587291), complete cds.
X75091 - H.sapiens mRNA for HLA-DR associated protein II (PHAPII).
EF534308 - Homo sapiens SET mRNA, complete cds.
AM392720 - Synthetic construct Homo sapiens clone IMAGE:100002122 for hypothetical protein (SET gene).
AM392742 - Synthetic construct Homo sapiens clone IMAGE:100002121 for hypothetical protein (SET gene).
AM393175 - Synthetic construct Homo sapiens clone IMAGE:100002126 for hypothetical protein (SET gene).
AM393446 - Synthetic construct Homo sapiens clone IMAGE:100002125 for hypothetical protein (SET gene).
DQ894408 - Synthetic construct Homo sapiens clone IMAGE:100008868; FLH170300.01L; RZPDo839D1297D SET translocation (myeloid leukemia-associated) (SET) gene, encodes complete protein.
EU176263 - Synthetic construct Homo sapiens clone IMAGE:100006375; FLH170307.01X; RZPDo839D10250D SET translocation (myeloid leukemia-associated) (SET) gene, encodes complete protein.
CU689520 - Synthetic construct Homo sapiens gateway clone IMAGE:100016619 5' read SET mRNA.
KJ892125 - Synthetic construct Homo sapiens clone ccsbBroadEn_01519 SET gene, encodes complete protein.
M93651 - Human set gene, complete cds.
CR542050 - Homo sapiens full open reading frame cDNA clone RZPDo834A0736D for gene SET, SET translocation (myeloid leukemia-associated); complete cds, without stopcodon.
AY349172 - Homo sapiens inhibitor-2 of protein phosphatase-2A mRNA, complete cds.
U51924 - Human phosphatase 2A inhibitor I2PP2A mRNA, complete cds.
CR536543 - Homo sapiens full open reading frame cDNA clone RZPDo834H0620D for gene SET, SET translocation (myeloid leukemia-associated); complete cds, incl. stopcodon.
AK300609 - Homo sapiens cDNA FLJ59759 complete cds, highly similar to Protein SET.
AK311346 - Homo sapiens cDNA, FLJ18388.
LF358860 - JP 2014500723-A/166363: Polycomb-Associated Non-Coding RNAs.
LF358859 - JP 2014500723-A/166362: Polycomb-Associated Non-Coding RNAs.
JD073747 - Sequence 54771 from Patent EP1572962.
LF358858 - JP 2014500723-A/166361: Polycomb-Associated Non-Coding RNAs.
JD309052 - Sequence 290076 from Patent EP1572962.
JD267851 - Sequence 248875 from Patent EP1572962.
JD471200 - Sequence 452224 from Patent EP1572962.
JD073880 - Sequence 54904 from Patent EP1572962.
JD363425 - Sequence 344449 from Patent EP1572962.
JD297856 - Sequence 278880 from Patent EP1572962.
JD164004 - Sequence 145028 from Patent EP1572962.
JD563157 - Sequence 544181 from Patent EP1572962.
JD498950 - Sequence 479974 from Patent EP1572962.
JD267289 - Sequence 248313 from Patent EP1572962.
JD539047 - Sequence 520071 from Patent EP1572962.
JD232148 - Sequence 213172 from Patent EP1572962.
JD044645 - Sequence 25669 from Patent EP1572962.
JD286105 - Sequence 267129 from Patent EP1572962.
JD061000 - Sequence 42024 from Patent EP1572962.
JD181986 - Sequence 163010 from Patent EP1572962.
JD240327 - Sequence 221351 from Patent EP1572962.
JD139966 - Sequence 120990 from Patent EP1572962.
JD293056 - Sequence 274080 from Patent EP1572962.
JD359021 - Sequence 340045 from Patent EP1572962.
JD537012 - Sequence 518036 from Patent EP1572962.
JD324380 - Sequence 305404 from Patent EP1572962.
JD338371 - Sequence 319395 from Patent EP1572962.
JD267090 - Sequence 248114 from Patent EP1572962.
MA594437 - JP 2018138019-A/166363: Polycomb-Associated Non-Coding RNAs.
MA594436 - JP 2018138019-A/166362: Polycomb-Associated Non-Coding RNAs.
MA594435 - JP 2018138019-A/166361: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_setPathway - Granzyme A mediated Apoptosis Pathway

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001248000, NP_001234929, Q5VXV2, Q5VXV2_HUMAN, RP11-216B9.3-003
UCSC ID: uc022bol.1
RefSeq Accession: NM_001248000
Protein: Q5VXV2 CCDS: CCDS59149.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001248000.1
exon count: 8CDS single in 3' UTR: no RNA size: 2638
ORF size: 807CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1813.00frame shift in genome: no % Coverage: 99.36
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
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.