Human Gene SP3 (ENST00000310015.12_8) from GENCODE V47lift37
  Description: Sp3 transcription factor, transcript variant 1 (from RefSeq NM_003111.5)
Gencode Transcript: ENST00000310015.12_8
Gencode Gene: ENSG00000172845.18_11
Transcript (Including UTRs)
   Position: hg19 chr2:174,765,503-174,830,101 Size: 64,599 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr2:174,774,669-174,829,899 Size: 55,231 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:174,765,503-174,830,101)mRNA (may differ from genome)Protein (781 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SP3_HUMAN
DESCRIPTION: RecName: Full=Transcription factor Sp3; AltName: Full=SPR-2;
FUNCTION: Transcriptional factor that can act as an activator or repressor depending on isoform and/or post-translational modifications. Binds to GT and GC boxes promoter elements. Competes with SP1 for the GC-box promoters. Weak activator of transcription but can activate a number of genes involved in different processes such as cell-cycle regulation, hormone- induction and house-keeping.
SUBUNIT: Interacts with HLTF; the interaction may be required for basal transcriptional activity of HLTF. Interacts with HDAC1; the interaction deacetylates SP3 and regulates its transcriptional activity. Interacts with HDAC2 (preferably the CK2-phosphorylated form); the interaction deacetylates SP3 and regulates its transcriptional activity.
INTERACTION: P03372:ESR1; NbExp=2; IntAct=EBI-348158, EBI-78473;
SUBCELLULAR LOCATION: Nucleus. Nucleus, PML body. Note=Localizes to the nuclear periphery and in nuclear dots when sumoylated. Some localization in PML nuclear bodies.
TISSUE SPECIFICITY: Ubiquitously expressed.
PTM: Not glycosylated.
PTM: Acetylated by histone acetyltransferase p300, deacetylated by HDACs. Acetylation/deacetylation states regulate transcriptional activity. Acetylation appears to activate transcription. Alternate sumoylation and acetylation at Lys-551 also control transcriptional activity. Ceramides can also regulate acetylation/deacetylation events through altering the interaction of HDAC with SP3. In vitro, C(18)-ceramides, but not C(16)- ceramides, increase the interaction of HDAC1 with SP3 and enhance the deacetylation of SP3 and the subsequent repression of the TERT promoter.
PTM: Sumoylated on all isoforms. Sumoylated on 2 sites in longer isoforms with Lys-551 being the major site. Sumoylation at this site promotes nuclear localization to the nuclear periphery, nuclear dots and PML nuclear bodies. Sumoylation on Lys-551 represses the transactivation activity, except for the largest isoform, L-Sp3, which has little effect on transactivation. Alternate sumoylation and acetylation at Lys-551 also control transcriptional activity.
SIMILARITY: Belongs to the Sp1 C2H2-type zinc-finger protein family.
SIMILARITY: Contains 3 C2H2-type zinc fingers.

-  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


-  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: 19.20 RPKM in Cervix - Endocervix
Total median expression: 494.75 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 -66.00202-0.327 Picture PostScript Text
3' UTR -2317.579166-0.253 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
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd

Pfam Domains:
PF00096 - Zinc finger, C2H2 type
PF13912 - C2H2-type zinc finger

SCOP Domains:
57667 - beta-beta-alpha zinc fingers

ModBase Predicted Comparative 3D Structure on Q02447
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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:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0000987 core promoter proximal region sequence-specific DNA binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003690 double-stranded DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001503 ossification
GO:0001701 in utero embryonic development
GO:0001779 natural killer cell differentiation
GO:0001829 trophectodermal cell differentiation
GO:0001889 liver development
GO:0001892 embryonic placenta development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0030183 B cell differentiation
GO:0030217 T cell differentiation
GO:0030218 erythrocyte differentiation
GO:0030219 megakaryocyte differentiation
GO:0030224 monocyte differentiation
GO:0030324 lung development
GO:0030851 granulocyte differentiation
GO:0043353 enucleate erythrocyte differentiation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048596 embryonic camera-type eye morphogenesis
GO:0048706 embryonic skeletal system development
GO:0060136 embryonic process involved in female pregnancy
GO:0060216 definitive hemopoiesis

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016605 PML body
GO:0017053 transcriptional repressor complex
GO:0032993 protein-DNA complex


-  Descriptions from all associated GenBank mRNAs
  AK023489 - Homo sapiens cDNA FLJ13427 fis, clone PLACE1002477.
LF383699 - JP 2014500723-A/191202: Polycomb-Associated Non-Coding RNAs.
AB209334 - Homo sapiens mRNA for Sp3 transcription factor variant protein.
BX648857 - Homo sapiens mRNA; cDNA DKFZp686N17231 (from clone DKFZp686N17231).
X68560 - H.sapiens SPR-2 mRNA for GT box binding protein.
AY070137 - Homo sapiens specificity protein 3 (SP3) mRNA, complete cds.
AY441958 - Homo sapiens transcription factor SP3 splice variant (SP3) mRNA, complete cds; alternatively spliced.
AY441957 - Homo sapiens transcription factor SP3 large isoform (SP3) mRNA, complete cds.
CR749323 - Homo sapiens mRNA; cDNA DKFZp686O1631 (from clone DKFZp686O1631).
BC042945 - Homo sapiens Sp3 transcription factor, mRNA (cDNA clone IMAGE:4797286), partial cds.
LF347467 - JP 2014500723-A/154970: Polycomb-Associated Non-Coding RNAs.
BC126414 - Homo sapiens Sp3 transcription factor, mRNA (cDNA clone MGC:161692 IMAGE:8992130), complete cds.
BC143928 - Homo sapiens Sp3 transcription factor, mRNA (cDNA clone MGC:177463 IMAGE:9052446), complete cds.
JD559080 - Sequence 540104 from Patent EP1572962.
JD243070 - Sequence 224094 from Patent EP1572962.
JD349458 - Sequence 330482 from Patent EP1572962.
AK310663 - Homo sapiens cDNA, FLJ17705.
JD302900 - Sequence 283924 from Patent EP1572962.
JD552501 - Sequence 533525 from Patent EP1572962.
JD091740 - Sequence 72764 from Patent EP1572962.
JD058450 - Sequence 39474 from Patent EP1572962.
JD312611 - Sequence 293635 from Patent EP1572962.
AK304199 - Homo sapiens cDNA FLJ54449 complete cds, highly similar to Transcription factor Sp3.
JD315852 - Sequence 296876 from Patent EP1572962.
JD507700 - Sequence 488724 from Patent EP1572962.
M97191 - Homo sapiens Sp3 protein mRNA, partial cds.
HQ258632 - Synthetic construct Homo sapiens clone IMAGE:100073187 Sp3 transcription factor (SP3) gene, encodes complete protein.
AB528284 - Synthetic construct DNA, clone: pF1KB6278, Homo sapiens SP3 gene for Sp3 transcription factor, without stop codon, in Flexi system.
KJ904565 - Synthetic construct Homo sapiens clone ccsbBroadEn_13959 SP3 gene, encodes complete protein.
LF347468 - JP 2014500723-A/154971: Polycomb-Associated Non-Coding RNAs.
LF347469 - JP 2014500723-A/154972: Polycomb-Associated Non-Coding RNAs.
LF347474 - JP 2014500723-A/154977: Polycomb-Associated Non-Coding RNAs.
LF347477 - JP 2014500723-A/154980: Polycomb-Associated Non-Coding RNAs.
JD241318 - Sequence 222342 from Patent EP1572962.
CQ873780 - Sequence 199 from Patent WO2004076622.
DD413617 - Regulation of Mammalian Cells.
LF347478 - JP 2014500723-A/154981: Polycomb-Associated Non-Coding RNAs.
LF347479 - JP 2014500723-A/154982: Polycomb-Associated Non-Coding RNAs.
LF347480 - JP 2014500723-A/154983: Polycomb-Associated Non-Coding RNAs.
JD362524 - Sequence 343548 from Patent EP1572962.
JD362523 - Sequence 343547 from Patent EP1572962.
JD486935 - Sequence 467959 from Patent EP1572962.
JD410476 - Sequence 391500 from Patent EP1572962.
JD100084 - Sequence 81108 from Patent EP1572962.
JD506572 - Sequence 487596 from Patent EP1572962.
JD047052 - Sequence 28076 from Patent EP1572962.
JD047051 - Sequence 28075 from Patent EP1572962.
JD503820 - Sequence 484844 from Patent EP1572962.
JD318276 - Sequence 299300 from Patent EP1572962.
JD085653 - Sequence 66677 from Patent EP1572962.
JD292437 - Sequence 273461 from Patent EP1572962.
LF347481 - JP 2014500723-A/154984: Polycomb-Associated Non-Coding RNAs.
JD369657 - Sequence 350681 from Patent EP1572962.
AJ310752 - Homo sapiens partial mRNA for transcription factor SP3 (SP3 gene).
AJ430844 - Homo sapiens partial mRNA for transcription factor SP3 splice variant (SP3 gene).
JD159377 - Sequence 140401 from Patent EP1572962.
MA619276 - JP 2018138019-A/191202: Polycomb-Associated Non-Coding RNAs.
MA583044 - JP 2018138019-A/154970: Polycomb-Associated Non-Coding RNAs.
MA583045 - JP 2018138019-A/154971: Polycomb-Associated Non-Coding RNAs.
MA583046 - JP 2018138019-A/154972: Polycomb-Associated Non-Coding RNAs.
MA583051 - JP 2018138019-A/154977: Polycomb-Associated Non-Coding RNAs.
MA583054 - JP 2018138019-A/154980: Polycomb-Associated Non-Coding RNAs.
MA583055 - JP 2018138019-A/154981: Polycomb-Associated Non-Coding RNAs.
MA583056 - JP 2018138019-A/154982: Polycomb-Associated Non-Coding RNAs.
MA583057 - JP 2018138019-A/154983: Polycomb-Associated Non-Coding RNAs.
MA583058 - JP 2018138019-A/154984: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_calcineurinPathway - Effects of calcineurin in Keratinocyte Differentiation
h_tercPathway - Overview of telomerase RNA component gene hTerc Transcriptional Regulation
h_tertpathway - Overview of telomerase protein component gene hTert Transcriptional Regulation

Reactome (by CSHL, EBI, and GO)

Protein Q02447 (Reactome details) participates in the following event(s):

R-HSA-3247493 PIAS1 SUMOylates SP3 with SUMO1
R-HSA-6804468 PIAS1 SUMOylates SP3 with SUMO2
R-HSA-3232118 SUMOylation of transcription factors
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-2990846 SUMOylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A0AVL9, B4E2B7, ENST00000310015.1, ENST00000310015.10, ENST00000310015.11, ENST00000310015.2, ENST00000310015.3, ENST00000310015.4, ENST00000310015.5, ENST00000310015.6, ENST00000310015.7, ENST00000310015.8, ENST00000310015.9, NM_003111, Q02447, Q69B26, Q69B27, Q8TD56, Q8WWU4, Q9BQR1, SP3_HUMAN, uc317oqy.1, uc317oqy.2
UCSC ID: ENST00000310015.12_8
RefSeq Accession: NM_003111.5
Protein: Q02447 (aka SP3_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.