Human Gene SPOP (uc002ipf.3) Description and Page Index
  Description: Homo sapiens speckle-type POZ protein (SPOP), transcript variant 6, mRNA.
RefSeq Summary (NM_001007229): This gene encodes a protein that may modulate the transcriptional repression activities of death-associated protein 6 (DAXX), which interacts with histone deacetylase, core histones, and other histone-associated proteins. In mouse, the encoded protein binds to the putative leucine zipper domain of macroH2A1.2, a variant H2A histone that is enriched on inactivated X chromosomes. The BTB/POZ domain of this protein has been shown in other proteins to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes. Alternative splicing of this gene results in multiple transcript variants encoding the same protein. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr17:47,676,246-47,755,525 Size: 79,280 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr17:47,677,740-47,700,172 Size: 22,433 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:47,676,246-47,755,525)mRNA (may differ from genome)Protein (374 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
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neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SPOP_HUMAN
DESCRIPTION: RecName: Full=Speckle-type POZ protein; AltName: Full=HIB homolog 1; AltName: Full=Roadkill homolog 1;
FUNCTION: Inhibits IPF1/PDX1 transactivation of established target promoters, such as insulin, may be by recruiting a repressor complex (By similarity). In complex with CUL3, involved in ubiquitination of BMI1, H2AFY and DAXX, and probably also in ubiquitination and proteasomal degradation of Gli2 or Gli3.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Homodimer. Part of a complex consisting of BMI1, CUL3 and SPOP. Part of a complex consisting of H2AFY, CUL3 and SPOP. Part of a complex consisting of DAXX, CUL3 and SPOP. Interacts with H2AFY, IPF1/PDX1, BMI1 and DAXX. Interacts with CUL3.
INTERACTION: Q13618:CUL3; NbExp=2; IntAct=EBI-743549, EBI-456129; Q9UER7:DAXX; NbExp=5; IntAct=EBI-743549, EBI-77321; Q99836:MYD88; NbExp=6; IntAct=EBI-743549, EBI-447677; Q9Y6Q9:NCOA3; NbExp=6; IntAct=EBI-743549, EBI-81196;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Widely expressed.
DOMAIN: The MATH domain interacts with H2AFY and BMI1.
MISCELLANEOUS: Antigen recognized by serum from scleroderma patient.
SIMILARITY: Belongs to the Tdpoz family.
SIMILARITY: Contains 1 BTB (POZ) domain.
SIMILARITY: Contains 1 MATH domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SPOP
CDC HuGE Published Literature: SPOP
Positive Disease Associations: Heart Failure
Related Studies:
  1. Heart Failure
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 40.65 RPKM in Colon - Sigmoid
Total median expression: 759.77 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -136.90348-0.393 Picture PostScript Text
3' UTR -418.901494-0.280 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
IPR000210 - BTB/POZ-like
IPR011333 - BTB/POZ_fold
IPR013069 - BTB_POZ
IPR002083 - MATH
IPR008974 - TRAF-like
IPR013322 - TRAF-type

Pfam Domains:
PF00651 - BTB/POZ domain
PF00917 - MATH domain

SCOP Domains:
49599 - TRAF domain-like
54695 - POZ domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2CR2
- NMR MuPIT

3HQH
- X-ray MuPIT

3HQI
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
3HQL - X-ray MuPIT 3HQM - X-ray MuPIT 3HTM - X-ray MuPIT
3HU6 - X-ray MuPIT 3IVB - X-ray MuPIT 3IVQ - X-ray MuPIT
3IVV - X-ray MuPIT 4EOZ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O43791
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 orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001085 RNA polymerase II transcription factor binding
GO:0005515 protein binding
GO:0031625 ubiquitin protein ligase binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0016567 protein ubiquitination
GO:0030162 regulation of proteolysis
GO:0042593 glucose homeostasis
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity
GO:1902237 positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
GO:2000676 positive regulation of type B pancreatic cell apoptotic process

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0016607 nuclear speck
GO:0019005 SCF ubiquitin ligase complex
GO:0031463 Cul3-RING ubiquitin ligase complex


-  Descriptions from all associated GenBank mRNAs
  AK293587 - Homo sapiens cDNA FLJ53827 complete cds, highly similar to Speckle-type POZ protein.
BC003385 - Homo sapiens speckle-type POZ protein, mRNA (cDNA clone MGC:5381 IMAGE:3445878), complete cds.
AK222589 - Homo sapiens mRNA for speckle-type POZ protein variant, clone: CAS04710.
BC001269 - Homo sapiens speckle-type POZ protein, mRNA (cDNA clone MGC:5068 IMAGE:3461565), complete cds.
AJ000644 - Homo sapiens mRNA for SPOP.
AK303268 - Homo sapiens cDNA FLJ51172 complete cds, highly similar to Speckle-type POZ protein.
AK300616 - Homo sapiens cDNA FLJ51096 complete cds, highly similar to Speckle-type POZ protein.
AK293045 - Homo sapiens cDNA FLJ78304 complete cds, highly similar to Homo sapiens speckle-type POZ protein (SPOP), transcript variant 2, mRNA.
AK316366 - Homo sapiens cDNA, FLJ79265 complete cds, highly similar to Speckle-type POZ protein.
AK312691 - Homo sapiens cDNA, FLJ93086, Homo sapiens speckle-type POZ protein (SPOP), mRNA.
AK123385 - Homo sapiens cDNA FLJ41391 fis, clone BRCAN2025349.
JD051238 - Sequence 32262 from Patent EP1572962.
JD486437 - Sequence 467461 from Patent EP1572962.
LF206218 - JP 2014500723-A/13721: Polycomb-Associated Non-Coding RNAs.
AM392588 - Synthetic construct Homo sapiens clone IMAGE:100002637 for hypothetical protein (SPOP gene).
AM392643 - Synthetic construct Homo sapiens clone IMAGE:100002903 for hypothetical protein (SPOP gene).
AM392731 - Synthetic construct Homo sapiens clone IMAGE:100002900 for hypothetical protein (SPOP gene).
AM393008 - Synthetic construct Homo sapiens clone IMAGE:100002904 for hypothetical protein (SPOP gene).
AM393567 - Synthetic construct Homo sapiens clone IMAGE:100002635 for hypothetical protein (SPOP gene).
AM393826 - Synthetic construct Homo sapiens clone IMAGE:100002636 for hypothetical protein (SPOP gene).
AB463281 - Synthetic construct DNA, clone: pF1KB8638, Homo sapiens SPOP gene for speckle-type POZ protein, without stop codon, in Flexi system.
DL491431 - Novel nucleic acids.
DL490053 - Novel nucleic acids.
JD429864 - Sequence 410888 from Patent EP1572962.
JD307276 - Sequence 288300 from Patent EP1572962.
MA441795 - JP 2018138019-A/13721: Polycomb-Associated Non-Coding RNAs.
JD467130 - Sequence 448154 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O43791 (Reactome details) participates in the following event(s):

R-HSA-5635855 phosphorylated GLI proteins bind SPOP:CUL3:RBX1
R-HSA-5635856 SPOP:CUL3:RBX1 ubiquitinates GLI2,3
R-HSA-5632684 Hedgehog 'on' state
R-HSA-5358351 Signaling by Hedgehog
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B2R6S3, D3DTW7, NM_001007229, NP_003554, O43791, Q53HJ1, SPOP_HUMAN
UCSC ID: uc002ipf.3
RefSeq Accession: NM_001007229
Protein: O43791 (aka SPOP_HUMAN)
CCDS: CCDS11551.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001007229.1
exon count: 11CDS single in 3' UTR: no RNA size: 2982
ORF size: 1125CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2304.00frame shift in genome: no % Coverage: 99.50
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.