Human Gene SETBP1 (ENST00000649279.2_9) from GENCODE V47lift37
  Description: SET binding protein 1, transcript variant 1 (from RefSeq NM_015559.3)
Gencode Transcript: ENST00000649279.2_9
Gencode Gene: ENSG00000152217.20_17
Transcript (Including UTRs)
   Position: hg19 chr18:42,260,853-42,648,475 Size: 387,623 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr18:42,281,312-42,643,663 Size: 362,352 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:42,260,853-42,648,475)mRNA (may differ from genome)Protein (1596 aa)
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-  Comments and Description Text from UniProtKB
  ID: SETBP_HUMAN
DESCRIPTION: RecName: Full=SET-binding protein; Short=SEB;
SUBUNIT: Interacts with SET.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed in numerous tissues.
DISEASE: Defects in SETBP1 are the cause of Schinzel-Giedion midface retraction syndrome (SGMFS) [MIM:269150]. It is a disorder characterized by severe mental retardation, distinctive facial features, and multiple congenital malformations including skeletal abnormalities, genitourinary and renal malformations, cardiac defects, as well as a higher-than-normal prevalence of tumors, notably neuroepithelial neoplasia.
SIMILARITY: Contains 3 A.T hook DNA-binding domains.
SEQUENCE CAUTION: Sequence=AAI46777.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAA24826.2; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAA82444.1; 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: SETBP1
Diseases sorted by gene-association score: schinzel-giedion midface retraction syndrome* (1343), mental retardation, autosomal dominant 29* (1019), leukemia, chronic myeloid, somatic* (498), schinzel giedion syndrome* (419), intellectual disability-expressive aphasia-facial dysmorphism syndrome* (247), myelodysplastic syndrome* (130), juvenile myelomonocytic leukemia* (126), leukemia, acute myeloid* (63), atypical chronic myeloid leukemia (26), staphyloenterotoxemia (19), myelodysplastic myeloproliferative cancer (12), refractory anemia with excess blasts (11), chronic neutrophilic leukemia (10), chronic myelomonocytic leukemia (10), non-secretory myeloma (9), splenomegaly (7), commensal bacterial infectious disease (7), chromosome 15q24 deletion syndrome (6), hypomyelinating leukodystrophy (5), seborrheic dermatitis (5), intellectual disability (2)
* = 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.

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -85.60306-0.280 Picture PostScript Text
3' UTR -1277.904812-0.266 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
IPR017956 - AT_hook_DNA-bd_motif

Pfam Domains:
PF02178 - AT hook motif

ModBase Predicted Comparative 3D Structure on Q9Y6X0
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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:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0005515 protein binding

Biological Process:
GO:0006357 regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus
GO:0005829 cytosol
GO:0016604 nuclear body


-  Descriptions from all associated GenBank mRNAs
  BC062338 - Homo sapiens SET binding protein 1, mRNA (cDNA clone IMAGE:6338507), complete cds.
AB007897 - Homo sapiens KIAA0437 mRNA.
BC146776 - Homo sapiens SET binding protein 1, mRNA (cDNA clone MGC:166855 IMAGE:9007225), complete cds.
CU687538 - Synthetic construct Homo sapiens gateway clone IMAGE:100022400 5' read SETBP1 mRNA.
KJ893513 - Synthetic construct Homo sapiens clone ccsbBroadEn_02907 SETBP1 gene, encodes complete protein.
AB384479 - Synthetic construct DNA, clone: pF1KA0437, Homo sapiens SETBP1 gene for SET-binding protein, complete cds, without stop codon, in Flexi system.
AB022660 - Homo sapiens mRNA for SET-binding protein (SEB), complete cds.
JD336442 - Sequence 317466 from Patent EP1572962.
JD461206 - Sequence 442230 from Patent EP1572962.
JD404978 - Sequence 386002 from Patent EP1572962.
AK091663 - Homo sapiens cDNA FLJ34344 fis, clone FEBRA2010299, moderately similar to SET-binding protein (SEB).
JD527059 - Sequence 508083 from Patent EP1572962.
JD469895 - Sequence 450919 from Patent EP1572962.
JD469056 - Sequence 450080 from Patent EP1572962.
JD427231 - Sequence 408255 from Patent EP1572962.
JD466065 - Sequence 447089 from Patent EP1572962.
JD440041 - Sequence 421065 from Patent EP1572962.
JD465469 - Sequence 446493 from Patent EP1572962.
JD083728 - Sequence 64752 from Patent EP1572962.
AL832945 - Homo sapiens mRNA; cDNA DKFZp666J1210 (from clone DKFZp666J1210).
JD314030 - Sequence 295054 from Patent EP1572962.
JD077799 - Sequence 58823 from Patent EP1572962.
JD096622 - Sequence 77646 from Patent EP1572962.
JD551935 - Sequence 532959 from Patent EP1572962.
JD245398 - Sequence 226422 from Patent EP1572962.
JD512329 - Sequence 493353 from Patent EP1572962.
JD166347 - Sequence 147371 from Patent EP1572962.
JD555984 - Sequence 537008 from Patent EP1572962.
JD237879 - Sequence 218903 from Patent EP1572962.
JD243086 - Sequence 224110 from Patent EP1572962.
JD059936 - Sequence 40960 from Patent EP1572962.
JD556930 - Sequence 537954 from Patent EP1572962.
JD228096 - Sequence 209120 from Patent EP1572962.
JD292667 - Sequence 273691 from Patent EP1572962.
JD309031 - Sequence 290055 from Patent EP1572962.
JD285304 - Sequence 266328 from Patent EP1572962.
JD092593 - Sequence 73617 from Patent EP1572962.
JD346245 - Sequence 327269 from Patent EP1572962.
AK123972 - Homo sapiens cDNA FLJ41978 fis, clone SKNSH2000482.
JD121210 - Sequence 102234 from Patent EP1572962.
JD114543 - Sequence 95567 from Patent EP1572962.
JD521846 - Sequence 502870 from Patent EP1572962.
JD316804 - Sequence 297828 from Patent EP1572962.
JD237994 - Sequence 219018 from Patent EP1572962.
JD115900 - Sequence 96924 from Patent EP1572962.
JD159613 - Sequence 140637 from Patent EP1572962.
JD486863 - Sequence 467887 from Patent EP1572962.
JD566229 - Sequence 547253 from Patent EP1572962.
JD078918 - Sequence 59942 from Patent EP1572962.
JD273187 - Sequence 254211 from Patent EP1572962.
JD225933 - Sequence 206957 from Patent EP1572962.
JD240169 - Sequence 221193 from Patent EP1572962.
JD360939 - Sequence 341963 from Patent EP1572962.
JD504473 - Sequence 485497 from Patent EP1572962.
JD311296 - Sequence 292320 from Patent EP1572962.
JD280290 - Sequence 261314 from Patent EP1572962.
JD196976 - Sequence 178000 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6H8W5, ENST00000649279.1, KIAA0437, NM_015559, Q6P6C3, Q9UEF3, Q9Y6X0, SETBP_HUMAN, uc328pyz.1, uc328pyz.2
UCSC ID: ENST00000649279.2_9
RefSeq Accession: NM_015559.3
Protein: Q9Y6X0 (aka SETBP_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SETBP1:
schinzel-giedion (Schinzel-Giedion Syndrome)
setbp1-hd (SETBP1 Haploinsufficiency Disorder)

-  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.