Human Gene SPDEF (uc011dsq.2)
  Description: Homo sapiens SAM pointed domain containing ets transcription factor (SPDEF), transcript variant 2, mRNA.
RefSeq Summary (NM_001252294): 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].
Transcript (Including UTRs)
   Position: hg19 chr6:34,505,579-34,524,110 Size: 18,532 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr6:34,506,051-34,512,232 Size: 6,182 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:34,505,579-34,524,110)mRNA (may differ from genome)Protein (319 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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H-INVHGNCLynxMalacardsMGIOMIM
PubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: F5H778_HUMAN
DESCRIPTION: SubName: Full=SAM pointed domain-containing Ets transcription factor;
SIMILARITY: Belongs to the ETS family.
SIMILARITY: Contains 1 ETS DNA-binding domain.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SPDEF
CDC HuGE Published Literature: SPDEF
Positive Disease Associations: Cholesterol , Cholesterol, HDL , Waist Circumference
Related Studies:
  1. Cholesterol
    Tanya M Teslovich et al. Nature 2010, Biological, clinical and population relevance of 95 loci for blood lipids., Nature. [PubMed 20686565]
  2. Cholesterol, HDL
    Tanya M Teslovich et al. Nature 2010, Biological, clinical and population relevance of 95 loci for blood lipids., Nature. [PubMed 20686565]
  3. Waist Circumference
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SPDEF
Diseases sorted by gene-association score: prostate cancer (3)

-  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: 97.44 RPKM in Prostate
Total median expression: 241.77 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 -189.90434-0.438 Picture PostScript Text
3' UTR -219.52472-0.465 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
IPR000418 - Ets
IPR003118 - Pointed_dom
IPR013761 - SAM/pointed
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00178 - Ets-domain
PF02198 - Sterile alpha motif (SAM)/Pointed domain

SCOP Domains:
46785 - "Winged helix" DNA-binding domain
47769 - SAM/Pointed domain

ModBase Predicted Comparative 3D Structure on F5H778
FrontTopSide
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 orthologGenome BrowserNo orthologGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGD FlyBaseWormBase 
 Protein Sequence Protein SequenceProtein Sequence 
 Alignment AlignmentAlignment 

-  Descriptions from all associated GenBank mRNAs
  AB031549 - Homo sapiens PSE mRNA for prostate ets, complete cds.
BC021299 - Homo sapiens SAM pointed domain containing ets transcription factor, mRNA (cDNA clone MGC:29592 IMAGE:4546860), complete cds.
AF071538 - Homo sapiens Ets transcription factor PDEF (PDEF) mRNA, complete cds.
JD385956 - Sequence 366980 from Patent EP1572962.
JD518489 - Sequence 499513 from Patent EP1572962.
JD420301 - Sequence 401325 from Patent EP1572962.
AK301543 - Homo sapiens cDNA FLJ59217 complete cds, highly similar to SAM pointed domain-containing Ets transcription factor.
JD218339 - Sequence 199363 from Patent EP1572962.
JD471250 - Sequence 452274 from Patent EP1572962.
JD398396 - Sequence 379420 from Patent EP1572962.
JD323442 - Sequence 304466 from Patent EP1572962.
JD218754 - Sequence 199778 from Patent EP1572962.
JD192682 - Sequence 173706 from Patent EP1572962.
JD259300 - Sequence 240324 from Patent EP1572962.
JD418770 - Sequence 399794 from Patent EP1572962.
JD477155 - Sequence 458179 from Patent EP1572962.
EU832677 - Synthetic construct Homo sapiens clone HAIB:100067706; DKFZo008H1231 SAM pointed domain containing ets transcription factor protein (SPDEF) gene, encodes complete protein.
EU832757 - Synthetic construct Homo sapiens clone HAIB:100067786; DKFZo004H1232 SAM pointed domain containing ets transcription factor protein (SPDEF) gene, encodes complete protein.
KJ893461 - Synthetic construct Homo sapiens clone ccsbBroadEn_02855 SPDEF gene, encodes complete protein.
EU446697 - Synthetic construct Homo sapiens clone IMAGE:100070359; IMAGE:100011906; FLH257237.01L SAM pointed domain containing ets transcription factor (SPDEF) gene, encodes complete protein.
AB527466 - Synthetic construct DNA, clone: pF1KB7661, Homo sapiens SPDEF gene for SAM pointed domain containing ets transcription factor, without stop codon, in Flexi system.
CU676914 - Synthetic construct Homo sapiens gateway clone IMAGE:100018132 5' read SPDEF mRNA.
JD039887 - Sequence 20911 from Patent EP1572962.
JD134390 - Sequence 115414 from Patent EP1572962.
JD134389 - Sequence 115413 from Patent EP1572962.
JD266087 - Sequence 247111 from Patent EP1572962.
JD383156 - Sequence 364180 from Patent EP1572962.
JD403079 - Sequence 384103 from Patent EP1572962.
JD450191 - Sequence 431215 from Patent EP1572962.
JD338052 - Sequence 319076 from Patent EP1572962.
JD385028 - Sequence 366052 from Patent EP1572962.
JD114927 - Sequence 95951 from Patent EP1572962.
JD358089 - Sequence 339113 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: F5H778, F5H778_HUMAN, NM_001252294, NP_001239223
UCSC ID: uc011dsq.2
RefSeq Accession: NM_001252294
Protein: F5H778 CCDS: CCDS4794.1, CCDS59013.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001252294.1
exon count: 5CDS single in 3' UTR: no RNA size: 1866
ORF size: 960CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1892.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.