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Aliases for SPDEF Gene

Aliases for SPDEF Gene

  • SAM Pointed Domain Containing ETS Transcription Factor 2 3 5
  • Prostate Epithelium-Specific Ets Transcription Factor 3 4
  • Prostate-Derived Ets Factor 3 4
  • Prostate-Specific Ets 3 4
  • PDEF 3 4
  • SAM Pointed Domain-Containing Ets Transcription Factor 3
  • SAM Pointed Domain Containing Ets Transcription Factor 2
  • BA375E1.3 3
  • PSE 4

External Ids for SPDEF Gene

Previous GeneCards Identifiers for SPDEF Gene

  • GC06M034552
  • GC06M034613
  • GC06M034505
  • GC06M034228
  • GC06M034625
  • GC06M035571
  • GC06M036288
  • GC06M036657
  • GC06M037010
  • GC06M037360
  • GC06M037716
  • GC06M038062

Summaries for SPDEF Gene

Entrez Gene Summary for SPDEF Gene

  • The protein encoded by this gene belongs to the ETS family of transcription factors. It is highly expressed in the prostate epithelial cells, and functions as an androgen-independent transactivator of prostate-specific antigen (PSA) promoter. Higher expression of this protein has also been reported in brain, breast, lung and ovarian tumors, compared to the corresponding normal tissues, and it shows better tumor-association than other cancer-associated molecules, making it a more suitable target for developing specific cancer therapies. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

GeneCards Summary for SPDEF Gene

SPDEF (SAM Pointed Domain Containing ETS Transcription Factor) is a Protein Coding gene. Diseases associated with SPDEF include Prostate Cancer. Among its related pathways are Regulation of Androgen receptor activity. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and RNA polymerase II transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is ETV6.

UniProtKB/Swiss-Prot for SPDEF Gene

  • May function as an androgen-independent transactivator of the prostate-specific antigen (PSA) promoter. Binds to 5-GGAT-3 DNA sequences. May play a role in the regulation of the prostate gland and/or prostate cancer development. Acts as a transcriptional activator for SERPINB5 promoter.

Gene Wiki entry for SPDEF Gene

Additional gene information for SPDEF Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SPDEF Gene

Genomics for SPDEF Gene

GeneHancer (GH) Regulatory Elements for SPDEF Gene

Promoters and enhancers for SPDEF Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J034555 Promoter/Enhancer 1.4 EPDnew ENCODE dbSUPER 650.7 +0.3 263 1.7 BCOR CTCF PTBP1 FOXA2 ZSCAN4 ZMYM3 PAX8 ZBTB7B GTF3C2 GATA3 SPDEF TAF11 LEMD2 ITPR3 ENSG00000219023 FANCE RPS10 RPL10A UHRF1BP1 PACSIN1
GH06J034554 Enhancer 0.9 FANTOM5 dbSUPER 652.5 +1.3 1342 0.3 ZNF687 ZSCAN4 PAX8 MNT ZBTB7B ZNF217 ZFHX2 ZNF184 CREB1 ZNF444 SPDEF UHRF1BP1 PACSIN1
GH06J034557 Enhancer 0.9 ENCODE dbSUPER 650.7 -0.8 -830 0.3 TAL1 TCF12 CTBP1 GATA2 NCOR1 CBFA2T2 TRIM24 PRDM10 ZNF263 ZBTB2 SPDEF LEMD2 TAF11 GC06M038956
GH06J034608 Enhancer 1.2 Ensembl ENCODE 11.4 -54.0 -53982 2.7 HDGF PKNOX1 FOXA2 MLX ARNT ZNF2 YY1 ZNF213 E2F8 ZNF143 UHRF1BP1 RPL10A SPDEF ENSG00000219023 RPS10 ENSG00000220643 C6orf106 LEMD2 GRM4 ANKS1A
GH06J034602 Enhancer 1 ENCODE dbSUPER 12 -46.6 -46604 0.6 FOXA2 ARID4B ZNF48 RAD21 YY1 SLC30A9 RXRA REST TGIF2 SP1 UHRF1BP1 SPDEF GRM4 GC06P043181 RPL7P25 C6orf106
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SPDEF on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SPDEF gene promoter:
  • SRF (504 AA)
  • SRF
  • Max1
  • c-Myc
  • NF-1/L
  • NF-1
  • NF-kappaB
  • NF-kappaB1
  • NF-kappaB2

Genomic Locations for SPDEF Gene

Genomic Locations for SPDEF Gene
chr6:34,537,802-34,556,333
(GRCh38/hg38)
Size:
18,532 bases
Orientation:
Minus strand
chr6:34,505,579-34,524,110
(GRCh37/hg19)
Size:
18,532 bases
Orientation:
Minus strand

Genomic View for SPDEF Gene

Genes around SPDEF on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SPDEF Gene

Proteins for SPDEF Gene

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

    Protein Symbol:
    O95238-SPDEF_HUMAN
    Recommended name:
    SAM pointed domain-containing Ets transcription factor
    Protein Accession:
    O95238
    Secondary Accessions:
    • B4DWH8
    • F5H778

    Protein attributes for SPDEF Gene

    Size:
    335 amino acids
    Molecular mass:
    37518 Da
    Quaternary structure:
    • Interacts with the DNA-binding domain of the androgen receptor. Interacts with NKX3-1.

    Three dimensional structures from OCA and Proteopedia for SPDEF Gene

    Alternative splice isoforms for SPDEF Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPDEF Gene

Post-translational modifications for SPDEF Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SPDEF Gene

No data available for DME Specific Peptides for SPDEF Gene

Domains & Families for SPDEF Gene

Gene Families for SPDEF Gene

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

Suggested Antigen Peptide Sequences for SPDEF Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O95238

UniProtKB/Swiss-Prot:

SPDEF_HUMAN :
  • Belongs to the ETS family.
Family:
  • Belongs to the ETS family.
genes like me logo Genes that share domains with SPDEF: view

Function for SPDEF Gene

Molecular function for SPDEF Gene

UniProtKB/Swiss-Prot Function:
May function as an androgen-independent transactivator of the prostate-specific antigen (PSA) promoter. Binds to 5-GGAT-3 DNA sequences. May play a role in the regulation of the prostate gland and/or prostate cancer development. Acts as a transcriptional activator for SERPINB5 promoter.

Phenotypes From GWAS Catalog for SPDEF Gene

Gene Ontology (GO) - Molecular Function for SPDEF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS,IBA 19274049
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IC --
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IEA --
GO:0043565 sequence-specific DNA binding IDA 23332764
genes like me logo Genes that share ontologies with SPDEF: view
genes like me logo Genes that share phenotypes with SPDEF: view

Animal Models for SPDEF Gene

MGI Knock Outs for SPDEF:

Animal Model Products

CRISPR Products

miRNA for SPDEF Gene

Targeted motifs for SPDEF Gene
HOMER Transcription Factor Regulatory Elements motif SPDEF
  • Consensus sequence: ACATCCTGGT Submotif: canonical Cell Type: VCaP GEO ID: SRA014231

Inhibitory RNA Products

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

Clone Products

  • Addgene plasmids for SPDEF

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

Localization for SPDEF Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPDEF Gene

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 SPDEF gene
Compartment Confidence
nucleus 5
extracellular 2
plasma membrane 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SPDEF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
genes like me logo Genes that share ontologies with SPDEF: view

Pathways & Interactions for SPDEF Gene

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

Pathways by source for SPDEF Gene

1 BioSystems pathway for SPDEF Gene

Gene Ontology (GO) - Biological Process for SPDEF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 21656828
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA --
GO:0007275 multicellular organism development TAS 10625666
genes like me logo Genes that share ontologies with SPDEF: view

No data available for SIGNOR curated interactions for SPDEF Gene

Drugs & Compounds for SPDEF Gene

(5) Drugs for SPDEF Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with SPDEF: view

Transcripts for SPDEF Gene

mRNA/cDNA for SPDEF Gene

Unigene Clusters for SPDEF Gene

SAM pointed domain containing ets transcription factor:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

Clone Products

  • Addgene plasmids for SPDEF

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

No ASD Table

Relevant External Links for SPDEF Gene

GeneLoc Exon Structure for
SPDEF
ECgene alternative splicing isoforms for
SPDEF

Expression for SPDEF Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SPDEF Gene

This gene is overexpressed in Prostate (x17.7), Minor Salivary Gland (x11.5), Breast - Mammary Tissue (x4.6), Stomach (x4.5), and Colon - Transverse (x4.3).

Protein differential expression in normal tissues from HIPED for SPDEF Gene

This gene is overexpressed in Placenta (69.0).

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



Protein tissue co-expression partners for SPDEF Gene

NURSA nuclear receptor signaling pathways regulating expression of SPDEF Gene:

SPDEF

SOURCE GeneReport for Unigene cluster for SPDEF Gene:

Hs.485158

mRNA Expression by UniProt/SwissProt for SPDEF Gene:

O95238-SPDEF_HUMAN
Tissue specificity: Expressed in a very restricted set of primarily hormone-regulated epithelial tissues with particularly high expression in the prostate gland. Significantly lower expression is seen in other hormone regulated tissues such as mammary gland, salivary gland, and ovary. Expressed in prostate carcinoma cells.

Evidence on tissue expression from TISSUES for SPDEF Gene

  • Intestine(4.5)
  • Lung(4)
  • Nervous system(2.3)
genes like me logo Genes that share expression patterns with SPDEF: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SPDEF Gene

Orthologs for SPDEF Gene

This gene was present in the common ancestor of animals.

Orthologs for SPDEF Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SPDEF 34 33
  • 99.4 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SPDEF 34 33
  • 91.24 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SPDEF 34 33
  • 89.85 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Spdef 33
  • 84.21 (n)
mouse
(Mus musculus)
Mammalia Spdef 16 34 33
  • 82.77 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SPDEF 34
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SPDEF 34
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves SPDEF 34 33
  • 76.87 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SPDEF 34
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia spdef 33
  • 65.71 (n)
Str.12237 33
zebrafish
(Danio rerio)
Actinopterygii LOC100003543 33
  • 68.76 (n)
SPDEF 34
  • 66 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Ets98B 34
  • 29 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 15 (a)
OneToOne
Species where no ortholog for SPDEF was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 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)
  • worm (Caenorhabditis elegans)

Evolution for SPDEF Gene

ENSEMBL:
Gene Tree for SPDEF (if available)
TreeFam:
Gene Tree for SPDEF (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPDEF: view image

Paralogs for SPDEF Gene

Paralogs for SPDEF Gene

(1) SIMAP similar genes for SPDEF Gene using alignment to 1 proteins:

  • SPDEF_HUMAN
genes like me logo Genes that share paralogs with SPDEF: view

Variants for SPDEF Gene

Sequence variations from dbSNP and Humsavar for SPDEF Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000035273 -- 34,539,150(-) C/T genic_downstream_transcript_variant, intron_variant
rs1000234146 -- 34,550,326(-) G/A intron_variant
rs1000387922 -- 34,539,008(-) A/G genic_downstream_transcript_variant, intron_variant
rs1000473559 -- 34,555,131(-) CACGCACGCAC/CACGCAC genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000653997 -- 34,544,620(-) G/C intron_variant

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

Variant ID Type Subtype PubMed ID
nsv516578 CNV loss 19592680
nsv1073971 CNV deletion 25765185
nsv1033534 CNV gain 25217958
nsv1026919 CNV loss 25217958
nsv1021859 CNV loss 25217958
nsv1016788 CNV loss 25217958
esv2759418 CNV gain 17122850
dgv5954n100 CNV gain 25217958
dgv5953n100 CNV loss 25217958

Variation tolerance for SPDEF Gene

Residual Variation Intolerance Score: 91% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.59; 72.37% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPDEF Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPDEF

SNP Genotyping and Copy Number Assay Products

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

Disorders for SPDEF Gene

MalaCards: The human disease database

(1) MalaCards diseases for SPDEF Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
prostate cancer
  • prostate cancer, susceptibility to
- elite association - COSMIC cancer census association via MalaCards
Search SPDEF in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SPDEF

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

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

Publications for SPDEF Gene

  1. PDEF, a novel prostate epithelium-specific ets transcription factor, interacts with the androgen receptor and activates prostate-specific antigen gene expression. (PMID: 10625666) Oettgen P … Libermann TA (The Journal of biological chemistry 2000) 2 3 4 22 58
  2. NKX-3.1 interacts with prostate-derived Ets factor and regulates the activity of the PSA promoter. (PMID: 11809674) Chen H … Bieberich CJ (Cancer research 2002) 3 4 22 58
  3. Cloning and expression of the mouse Pse gene encoding a novel Ets family member. (PMID: 10675039) Yamada N … Nozaki M (Gene 2000) 3 4 22 58
  4. SAM pointed domain ETS factor (SPDEF) regulates terminal differentiation and maturation of intestinal goblet cells. (PMID: 19786015) Noah TK … Shroyer NF (Experimental cell research 2010) 3 22 58
  5. Proteomic analysis of a PDEF Ets transcription factor-interacting protein complex. (PMID: 19203193) Cho JY … Libermann TA (Journal of proteome research 2009) 3 22 58

Products for SPDEF Gene

  • Addgene plasmids for SPDEF

Sources for SPDEF Gene

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