This gene belongs to a family of Sp1 related genes that encode transcription factors that regulate transcription by binding to consensus GC- and GT-box regulatory elements in target genes. This protein contains a zinc finger DNA-binding domain and several transactivation domains, and has been reported to function as a bifunctional transcription factor that either stimulates or ... See more...

Aliases for SP3 Gene

Aliases for SP3 Gene

  • Sp3 Transcription Factor 2 3 5
  • Transcription Factor Sp3 3 4
  • SPR-2 2 4
  • GC-Binding Transcription Factor Sp3 3
  • Specificity Protein 3 3
  • SPR2 3
  • SP3 5

External Ids for SP3 Gene

Previous GeneCards Identifiers for SP3 Gene

  • GC02M172825
  • GC02M173434
  • GC02M174737
  • GC02M174975
  • GC02M174598
  • GC02M174481
  • GC02M174771
  • GC02M166650
  • GC02M173906

Summaries for SP3 Gene

Entrez Gene Summary for SP3 Gene

  • This gene belongs to a family of Sp1 related genes that encode transcription factors that regulate transcription by binding to consensus GC- and GT-box regulatory elements in target genes. This protein contains a zinc finger DNA-binding domain and several transactivation domains, and has been reported to function as a bifunctional transcription factor that either stimulates or represses the transcription of numerous genes. Transcript variants encoding different isoforms have been described for this gene, and one has been reported to initiate translation from a non-AUG (AUA) start codon. Additional isoforms, resulting from the use of alternate downstream translation initiation sites, have also been noted. A related pseudogene has been identified on chromosome 13. [provided by RefSeq, Feb 2010]

GeneCards Summary for SP3 Gene

SP3 (Sp3 Transcription Factor) is a Protein Coding gene. Diseases associated with SP3 include Petrositis and Ischiocoxopodopatellar Syndrome With Or Without Pulmonary Arterial Hypertension. Among its related pathways are G-Beta Gamma Signaling and Transcription Ligand-dependent activation of the ESR1/SP pathway. Gene Ontology (GO) annotations related to this gene include chromatin binding and double-stranded DNA binding. An important paralog of this gene is SP4.

UniProtKB/Swiss-Prot Summary for SP3 Gene

  • 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.

Gene Wiki entry for SP3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SP3 Gene

Genomics for SP3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SP3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SP3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SP3

Top Transcription factor binding sites by QIAGEN in the SP3 gene promoter:
  • AP-2alpha
  • AP-2alpha isoform 2
  • AP-2alpha isoform 3
  • AP-2alphaA

Genomic Locations for SP3 Gene

Latest Assembly
chr2:173,880,850-173,965,702
(GRCh38/hg38)
Size:
84,853 bases
Orientation:
Minus strand

Previous Assembly
chr2:174,765,503-174,830,430
(GRCh37/hg19 by Entrez Gene)
Size:
64,928 bases
Orientation:
Minus strand

chr2:174,771,187-174,830,430
(GRCh37/hg19 by Ensembl)
Size:
59,244 bases
Orientation:
Minus strand

Genomic View for SP3 Gene

Genes around SP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SP3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SP3 Gene

Proteins for SP3 Gene

  • Protein details for SP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q02447-SP3_HUMAN
    Recommended name:
    Transcription factor Sp3
    Protein Accession:
    Q02447
    Secondary Accessions:
    • A0AVL9
    • B4E2B7
    • Q69B26
    • Q69B27
    • Q8TD56
    • Q8WWU4
    • Q9BQR1

    Protein attributes for SP3 Gene

    Size:
    781 amino acids
    Molecular mass:
    81925 Da
    Quaternary structure:
    • 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. Interacts with MEIS2 isoform 4 and PBX1 isoform PBX1a.
    Miscellaneous:
    • [Isoform 2]: Produced by alternative initiation at Met-13 of isoform 1.
    • [Isoform 3]: Produced by alternative initiation at Met-286 of isoform 1.
    • [Isoform 4]: Produced by alternative initiation at Met-303 of isoform 1.
    • [Isoform 5]: Produced by alternative splicing. An AUA codon is translated into Met and used as a translation initiation site (in vitro).
    • [Isoform 6]: Produced by alternative splicing.

    Alternative splice isoforms for SP3 Gene

neXtProt entry for SP3 Gene

Post-translational modifications for SP3 Gene

  • Not glycosylated.
  • 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.
  • 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.
  • Ubiquitination at Lys593
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SP3 Gene

Domains & Families for SP3 Gene

Gene Families for SP3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for SP3 Gene

Suggested Antigen Peptide Sequences for SP3 Gene

GenScript: Design optimal peptide antigens:
  • SP3 protein (B7ZLN9_HUMAN)
  • SP3 protein (Q86TP0_HUMAN)
  • Transcription factor SP3 (Q8TE45_HUMAN)
  • Specificity protein 3 internally initiated isoform 2 (Q8WWU2_HUMAN)
  • Specificity protein 3 internally initiated isoform 1 (Q8WWU3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q02447

UniProtKB/Swiss-Prot:

SP3_HUMAN :
  • The 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors.
  • Belongs to the Sp1 C2H2-type zinc-finger protein family.
Domain:
  • The 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors.
Family:
  • Belongs to the Sp1 C2H2-type zinc-finger protein family.
genes like me logo Genes that share domains with SP3: view

Function for SP3 Gene

Molecular function for SP3 Gene

UniProtKB/Swiss-Prot 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.
GENATLAS Biochemistry:
transcription factor SP-3,activator,GT box binding protein

Phenotypes From GWAS Catalog for SP3 Gene

Gene Ontology (GO) - Molecular Function for SP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IEA,IDA 14979875
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA,IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0000987 proximal promoter sequence-specific DNA binding IEA,ISS 10362258
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IEA --
genes like me logo Genes that share ontologies with SP3: view
genes like me logo Genes that share phenotypes with SP3: view

Animal Models for SP3 Gene

MGI Knock Outs for SP3:
  • Sp3 Sp3<tm1Sus>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SP3

Clone products for research

  • Addgene plasmids for SP3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SP3 Gene

Localization for SP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SP3 Gene

Nucleus. Nucleus, PML body. Note=Localizes to the nuclear periphery and in nuclear dots when sumoylated. Some localization in PML nuclear bodies.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SP3 gene
Compartment Confidence
nucleus 5
plasma membrane 3
cytosol 3
extracellular 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
golgi apparatus 2
peroxisome 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IEA,IC 12560508
GO:0005654 nucleoplasm TAS --
GO:0016605 PML body IEA --
GO:0017053 transcriptional repressor complex IEA --
genes like me logo Genes that share ontologies with SP3: view

Pathways & Interactions for SP3 Gene

PathCards logo

SuperPathways for SP3 Gene

genes like me logo Genes that share pathways with SP3: view

Pathways by source for SP3 Gene

5 GeneGo (Thomson Reuters) pathways for SP3 Gene
  • Development VEGF signaling and activation
  • G-protein signaling_Rac2 regulation pathway
  • Mechanisms of CFTR activation by S-nitrosoglutathione (normal and CF)
  • Proteolysis Putative SUMO-1 pathway
  • Transcription Ligand-dependent activation of the ESR1/SP pathway
1 Qiagen pathway for SP3 Gene
  • Signaling in Gap Junctions

SIGNOR curated interactions for SP3 Gene

Activates:
Inactivates:
Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for SP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0001503 ossification IEA --
GO:0001701 in utero embryonic development IEA --
GO:0001779 natural killer cell differentiation IEA --
GO:0001829 trophectodermal cell differentiation IEA --
genes like me logo Genes that share ontologies with SP3: view

Drugs & Compounds for SP3 Gene

(20) Drugs for SP3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(16) Additional Compounds for SP3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SP3: view

Transcripts for SP3 Gene

mRNA/cDNA for SP3 Gene

3 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SP3

Clone products for research

  • Addgene plasmids for SP3

Alternative Splicing Database (ASD) splice patterns (SP) for SP3 Gene

No ASD Table

Relevant External Links for SP3 Gene

GeneLoc Exon Structure for
SP3

Expression for SP3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SP3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SP3 Gene

This gene is overexpressed in CD8 Tcells (15.9), Lymph node (13.3), CD4 Tcells (10.2), and NK cells (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SP3 Gene



Protein tissue co-expression partners for SP3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SP3

SOURCE GeneReport for Unigene cluster for SP3 Gene:

Hs.531587

mRNA Expression by UniProt/SwissProt for SP3 Gene:

Q02447-SP3_HUMAN
Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for SP3 Gene

  • Blood(4.6)
  • Liver(4.5)
  • Lung(4.5)
  • Nervous system(3.4)
  • Skin(2.8)
  • Intestine(2.6)
  • Kidney(2.5)
  • Muscle(2.4)
  • Spleen(2.4)
  • Lymph node(2.4)
  • Heart(2.4)
  • Stomach(2.3)
  • Bone marrow(2.3)
  • Thyroid gland(2.2)
  • Gall bladder(2.2)
genes like me logo Genes that share expression patterns with SP3: view

Primer products for research

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SP3 Gene

Orthologs for SP3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SP3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SP3 30
  • 100 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia SP3 29 30
  • 96.9 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SP3 29 30
  • 96.83 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Sp3 29 16 30
  • 94.89 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sp3 29
  • 94.47 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia SP3 30
  • 92 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SP3 30
  • 91 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SP3 29 30
  • 85.34 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SP3 30
  • 84 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sp3 29
  • 75.29 (n)
Str.4059 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.5036 29
Zebrafish
(Danio rerio)
Actinopterygii sp3a 29 30
  • 60.95 (n)
OneToMany
sp3b 30
  • 57 (a)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta CG5669 31
  • 74 (a)
EP2237 31
  • 65 (a)
btd 31
  • 62 (a)
Spps 30
  • 22 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea Y40B1A.4 31
  • 67 (a)
T22C8.5 31
  • 56 (a)
sptf-3 30
  • 32 (a)
OneToMany
Species where no ortholog for SP3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SP3 Gene

ENSEMBL:
Gene Tree for SP3 (if available)
TreeFam:
Gene Tree for SP3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SP3: view image
Alliance of Genome Resources:
Additional Orthologs for SP3

Paralogs for SP3 Gene

Paralogs for SP3 Gene

(36) SIMAP similar genes for SP3 Gene using alignment to 8 proteins:

  • SP3_HUMAN
  • B7ZLN9_HUMAN
  • H0Y6K5_HUMAN
  • H0Y7L6_HUMAN
  • Q86TP0_HUMAN
  • Q8TE45_HUMAN
  • Q8WWU2_HUMAN
  • Q8WWU3_HUMAN

Pseudogenes.org Pseudogenes for SP3 Gene

genes like me logo Genes that share paralogs with SP3: view

Variants for SP3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SP3 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
932093 Uncertain Significance: See cases 173,910,181(-) TG/T
NM_003111.4(SP3):c.2105del (p.Thr702fs)
FRAMESHIFT
rs16841942 Benign: not provided 173,954,946(-) T/C
NM_003111.4(SP3):c.1566A>G (p.Gln522=)
SYNONYMOUS
rs7561583 Benign: not provided 173,910,145(-) T/G
NM_003111.4(SP3):c.2142A>C (p.Thr714=)
SYNONYMOUS
rs78928738 Benign: not provided 173,918,700(-) G/A
NM_003111.4(SP3):c.1725C>T (p.His575=)
SYNONYMOUS
rs1047640 -- p.Thr164Ala

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SP3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SP3 Gene

Variant ID Type Subtype PubMed ID
dgv751e214 CNV loss 21293372
esv2664144 CNV deletion 23128226
esv2673963 CNV deletion 23128226
esv3593394 CNV gain 21293372
esv3593395 CNV loss 21293372
esv3593396 CNV loss 21293372
nsv1112775 CNV deletion 24896259
nsv1118887 CNV deletion 24896259
nsv1152346 CNV insertion 26484159
nsv821796 CNV gain 20364138
nsv953518 CNV duplication 24416366
nsv953519 CNV deletion 24416366

Variation tolerance for SP3 Gene

Residual Variation Intolerance Score: 12.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.80; 73.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SP3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SP3
Leiden Open Variation Database (LOVD)
SP3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SP3 Gene

Disorders for SP3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for SP3 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
petrositis
  • acute petrositis
ischiocoxopodopatellar syndrome with or without pulmonary arterial hypertension
  • icpps
wolfram syndrome
  • diabetes insipidus and mellitus with optic atrophy and deafness
chondrosarcoma, extraskeletal myxoid
  • emc
- elite association - COSMIC cancer census association via MalaCards
Search SP3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SP3

genes like me logo Genes that share disorders with SP3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SP3 Gene

Publications for SP3 Gene

  1. Cloning of GT box-binding proteins: a novel Sp1 multigene family regulating T-cell receptor gene expression. (PMID: 1341900) Kingsley C … Winoto A (Molecular and cellular biology 1992) 2 3 4 22
  2. Mechanisms of ceramide-mediated repression of the human telomerase reverse transcriptase promoter via deacetylation of Sp3 by histone deacetylase 1. (PMID: 17548428) Wooten-Blanks LG … Ogretmen B (FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2007) 3 4 22
  3. Human transcription factor Sp3: genomic structure, identification of a processed pseudogene, and transcript analysis. (PMID: 15474306) Moran KM … Richert JR (Gene 2004) 3 4 22
  4. Complexity of translationally controlled transcription factor Sp3 isoform expression. (PMID: 15247228) Sapetschnig A … Suske G (The Journal of biological chemistry 2004) 3 4 22
  5. Acetylated sp3 is a transcriptional activator. (PMID: 12837748) Ammanamanchi S … Brattain MG (The Journal of biological chemistry 2003) 3 4 22

Products for SP3 Gene

Sources for SP3 Gene