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SP3 Sp3 transcription factor [ Homo sapiens (human) ]

Gene ID: 6670, updated on 6-Jan-2019

Summary

Official Symbol
SP3provided by HGNC
Official Full Name
Sp3 transcription factorprovided by HGNC
Primary source
HGNC:HGNC:11208
See related
Ensembl:ENSG00000172845 MIM:601804
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SPR2
Summary
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]
Expression
Ubiquitous expression in bone marrow (RPKM 21.0), thyroid (RPKM 19.7) and 25 other tissues See more
Orthologs

Genomic context

See SP3 in Genome Data Viewer
Location:
2q31.1
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (173906459..173965702, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (174771187..174830430, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373745 Neighboring gene ribosomal protein L5 pseudogene 7 Neighboring gene long intergenic non-protein coding RNA 1960 Neighboring gene ribosomal protein SA pseudogene 24

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study of chronic otitis media with effusion and recurrent otitis media identifies a novel susceptibility locus on chromosome 2.
NHGRI GWA Catalog
Chromosome 2q31.1 associates with ESRD in women with type 1 diabetes.
NHGRI GWA Catalog
Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Pol gag-pol Transcription factors Oct-1, Oct-2, PU.1, Sp1, and Sp3 are recruited to the HS7 regulatory site in the pol coding region, suggesting that Oct-1, Oct-2, PU.1, Sp1, and Sp3 indirectly interact with HIV-1 Pol PubMed
Tat tat HIV-1 Tat downregulates SOD2 expression by interacting with Sp1 and Sp3 to increase the Sp3-containing complexes on the basal SOD2 promoter PubMed
tat In hepatic cells, HIV-1 Tat expression upregulates Sp1 and Sp3, which play different roles in regulating MnSOD transcription (overexpression of Sp1 stimulates, while overexpression of Sp3 represses transcriptional activity) PubMed
tat Sp3 represses basal expression from the HIV-1 LTR promoter, and overexpression of Sp3 inhibits HIV-1 Tat-mediated transactivation of the HIV-1 LTR promoter PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • MECP2 and Associated Rett Syndrome, organism-specific biosystem (from WikiPathways)
    MECP2 and Associated Rett Syndrome, organism-specific biosystemMecp2 is in many mammals an important regulator of neuronal function and development. It affects all cell types, especially neurons but also astrocytes, oligodendrocytes, and glial cells. Mecp2 plays...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Regulation of Telomerase, organism-specific biosystem (from Pathway Interaction Database)
    Regulation of Telomerase, organism-specific biosystem
    Regulation of Telomerase
  • SUMO E3 ligases SUMOylate target proteins, organism-specific biosystem (from REACTOME)
    SUMO E3 ligases SUMOylate target proteins, organism-specific biosystemSUMO proteins are conjugated to lysine residues of target proteins via an isopeptide bond with the C-terminal glycine of SUMO (reviewed in Zhao 2007, Gareau and Lima 2010, Hannoun et al. 2010, Citro ...
  • SUMOylation, organism-specific biosystem (from REACTOME)
    SUMOylation, organism-specific biosystemSmall Ubiquitin-like MOdifiers (SUMOs) are a family of 3 proteins (SUMO1,2,3) that are reversibly conjugated to lysine residues of target proteins via a glycine-lysine isopeptide bond (reviewed in Ha...
  • SUMOylation of transcription factors, organism-specific biosystem (from REACTOME)
    SUMOylation of transcription factors, organism-specific biosystemProteins classified as transcription factors constitute a disproportionate number of SUMOylation targets. In most cases SUMOylation inhibits transcriptional activation, however in some cases such as ...
  • Selenium Metabolism and Selenoproteins, organism-specific biosystem (from WikiPathways)
    Selenium Metabolism and Selenoproteins, organism-specific biosystem* Comments belonging to specific genes on the Selenoprotein pathway ** TRXND3 gene: Although the geneID is correct, the sequence of this gene was guessed by analogy. ** Cystathionine gamma-lyase is t...
  • Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways, organism-specific biosystem (from WikiPathways)
    Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways, organism-specific biosystemIn this model, we provide an integrated view of Sudden Infant Death Syndrome (SIDS) at the level of implicated tissues, signaling networks and genetics. The purpose of this model is to serve as an ov...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp686O1631

Gene Ontology Provided by GOA

Process Evidence Code Pubs
B cell differentiation IEA
Inferred from Electronic Annotation
more info
 
T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
definitive hemopoiesis IEA
Inferred from Electronic Annotation
more info
 
embryonic camera-type eye morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic placenta development IEA
Inferred from Electronic Annotation
more info
 
embryonic process involved in female pregnancy IEA
Inferred from Electronic Annotation
more info
 
embryonic skeletal system development IEA
Inferred from Electronic Annotation
more info
 
enucleate erythrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
granulocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
liver development IEA
Inferred from Electronic Annotation
more info
 
lung development IEA
Inferred from Electronic Annotation
more info
 
megakaryocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
monocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
natural killer cell differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
ossification IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
trophectodermal cell differentiation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
PML body IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IC
Inferred by Curator
more info
PubMed 
protein-DNA complex ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
transcriptional repressor complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
transcription factor Sp3
Names
GC-binding transcription factor Sp3
specificity protein 3

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029153.1 RefSeqGene

    Range
    5001..64244
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001017371.4NP_001017371.3  transcription factor Sp3 isoform 2

    See identical proteins and their annotated locations for NP_001017371.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) is missing exons 1 and 2 found in transcript variant 1, and has a different 5' end. It initiates translation from a non-AUG (AUA) start site, and encodes an isoform (2) with a shorter N-terminus compared to isoform 1. Alternative translation initiation from downstream, in-frame AUG start codons produces shorter isoforms.
    Source sequence(s)
    AB209334, AY070137, BQ010796, M97191
    Consensus CDS
    CCDS46452.1
    UniProtKB/Swiss-Prot
    Q02447
    UniProtKB/TrEMBL
    Q59FX5
    Related
    ENSP00000406140.2, ENST00000418194.6
    Conserved Domains (4) summary
    COG5048
    Location:568650
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:555577
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:613635
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:599622
    zf-H2C2_2; Zinc-finger double domain
  2. NM_001172712.1NP_001166183.1  transcription factor Sp3 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1. Alternative translation initiation from downstream, in-frame start codons produces shorter isoforms.
    Source sequence(s)
    AB209334, AY441957, BC143928, BQ010796, M97191
    UniProtKB/Swiss-Prot
    Q02447
    UniProtKB/TrEMBL
    B7ZLN9, Q59FX5
    Related
    ENSP00000413665.1, ENST00000416195.1
    Conserved Domains (4) summary
    COG5048
    Location:633715
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:620642
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:678700
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:664687
    zf-H2C2_2; Zinc-finger double domain
  3. NM_003111.4NP_003102.1  transcription factor Sp3 isoform 1

    See identical proteins and their annotated locations for NP_003102.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Alternative translation initiation from downstream, in-frame start codons produces shorter isoforms.
    Source sequence(s)
    AC093399, AY070137, AY441957, BC042945, M97191
    Consensus CDS
    CCDS2254.1
    UniProtKB/Swiss-Prot
    Q02447
    UniProtKB/TrEMBL
    Q86TP0
    Related
    ENSP00000310301.6, ENST00000310015.10
    Conserved Domains (4) summary
    COG5048
    Location:636718
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:623645
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:681703
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:667690
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    173906459..173965702 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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