Human Gene DEAF1 (uc001lqq.1) Description and Page Index
  Description: Homo sapiens DEAF1 transcription factor (DEAF1), mRNA.
RefSeq Summary (NM_021008): This gene encodes a zinc finger domain-containing protein that functions as a regulator of transcription. The encoded proteins binds to its own promoter as well as to that of several target genes. Activity of this protein is important in the regulation of embryonic development. Mutations in this gene have been found in individuals with autosomal dominant cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014].
Transcript (Including UTRs)
   Position: hg19 chr11:644,225-695,740 Size: 51,516 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr11:644,550-695,047 Size: 50,498 Coding Exon Count: 12 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:644,225-695,740)mRNA (may differ from genome)Protein (565 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: DEAF1_HUMAN
DESCRIPTION: RecName: Full=Deformed epidermal autoregulatory factor 1 homolog; AltName: Full=Nuclear DEAF-1-related transcriptional regulator; Short=NUDR; AltName: Full=Suppressin; AltName: Full=Zinc finger MYND domain-containing protein 5;
FUNCTION: Transcription factor that binds to sequence with multiple copies of 5'-TTC[CG]G-3' present in its own promoter and that of the HNRPA2B1 gene. Down-regulates transcription of these genes. Binds to the retinoic acid response element (RARE) 5'- AGGGTTCACCGAAAGTTCA-3'. Activates the proenkephalin gene independently of promoter binding, probably through protein- protein interaction. When secreted, behaves as an inhibitor of cell proliferation, by arresting cells in the G0 or G1 phase. Required for neural tube closure and skeletal patterning. Regulates epithelial cell proliferation and side-branching in the mammary gland. Controls the expression of peripheral tissue antigens in pancreatic lymph nodes. Isoform 1 displays greater transcriptional activity than isoform 4. Isoform 4 may inhibit transcriptional activity of isoform 1 by interacting with isoform 1 and retaining it in the cytoplasm.
SUBUNIT: Homodimer (Probable). Isoform 1 and isoform 4 may form a heterodimer. Binds to LMO4 (via its C-terminus), LMO2 and CLIM2 (By similarity). May interact with the corepressor NCOR.
INTERACTION: P42771:CDKN2A; NbExp=2; IntAct=EBI-718185, EBI-375053; P49840:GSK3A; NbExp=2; IntAct=EBI-718185, EBI-1044067; P49841:GSK3B; NbExp=2; IntAct=EBI-718185, EBI-373586;
SUBCELLULAR LOCATION: Isoform 1: Nucleus. Cytoplasm. Note=Cytoplasmic in non-mucinous colorectal carcinoma. When expressed alone, localized almost exclusively in the nucleus but, when expressed with isoform 4, nuclear expression decreases to 32% and cytoplasmic expression increases by 270%.
SUBCELLULAR LOCATION: Isoform 2: Secreted. Note=Secreted in some cell types.
SUBCELLULAR LOCATION: Isoform 3: Secreted. Note=Secreted in some cell types.
SUBCELLULAR LOCATION: Isoform 4: Cytoplasm. Nucleus. Note=When expressed alone, localizes mainly in the cytoplasm but, when expressed with isoform 1, nuclear localization is enhanced.
TISSUE SPECIFICITY: Expressed in various tissues and cells such as in peripheral mononuclear cells and hormone-secreting pituitary cells. Expression in pancreatic lymph nodes of patients with type 1 diabetes is 20 times higher than in healthy controls.
MISCELLANEOUS: Defective DEAF1 could confer a growth advantage to the mutated cells influencing the development and progression of neoplasia, e.g. in the case of colorectal carcinomas. Subcellular location in colorectal carcinomas (cytoplasmic or nuclear) is a prognostic factor that identifies a subgroup of patients with reduced survival. In addition, changes in the subcellular location correlates with the proliferative status of the cells.
SIMILARITY: Contains 1 MYND-type zinc finger.
SIMILARITY: Contains 1 SAND domain.
CAUTION: This protein was first known as suppressin (characterized in bovine neuroendocrine and immune cells). However, according to PubMed:9773984, it is uncertain whether it corresponds really to the suppressin also described in Ref.4. DEAF1 has been described as a nuclear dimeric protein and suppressin as a secreted monomeric protein.

-  MalaCards Disease Associations
  MalaCards Gene Search: DEAF1
Diseases sorted by gene-association score: mental retardation, autosomal dominant 24* (1330), dyskinesia, seizures, and intellectual developmental disorder* (1319), autosomal dominant non-syndromic intellectual disability* (124), smith-magenis syndrome* (9), intellectual disability (2)
* = Manually curated disease association

-  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: 63.84 RPKM in Brain - Anterior cingulate cortex (BA24)
Total median expression: 883.49 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 -371.90693-0.537 Picture PostScript Text
3' UTR -122.50325-0.377 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
IPR000770 - SAND_dom
IPR010919 - SAND_dom-like
IPR024119 - TF_DEAF-1
IPR002893 - Znf_MYND

Pfam Domains:
PF01342 - SAND domain
PF01753 - MYND finger

SCOP Domains:
63763 - SAND domain-like

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

2JW6
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on O75398
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 BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001662 behavioral fear response
GO:0001843 neural tube closure
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007281 germ cell development
GO:0007399 nervous system development
GO:0008542 visual learning
GO:0009653 anatomical structure morphogenesis
GO:0033599 regulation of mammary gland epithelial cell proliferation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0048706 embryonic skeletal system development

Cellular Component:
GO:0001650 fibrillar center
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005667 transcription factor complex
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AB209831 - Homo sapiens mRNA for suppressin variant protein.
AF007165 - Homo sapiens suppressin (spn) mRNA, complete cds.
AF049459 - Homo sapiens nuclear DEAF-1 related transcriptional regulator protein mRNA, complete cds.
BC042135 - Homo sapiens cDNA clone IMAGE:5804787, containing frame-shift errors.
BC053322 - Homo sapiens deformed epidermal autoregulatory factor 1 (Drosophila), mRNA (cDNA clone MGC:59746 IMAGE:6584290), complete cds.
AF049460 - Homo sapiens nuclear DEAF-1 related transcriptional regulator protein 8 mRNA, complete cds.
AK289873 - Homo sapiens cDNA FLJ77017 complete cds, highly similar to Homo sapiens rectosigmoid colon primary adenocarcinoma suppressin mRNA, allele 1.
AK291383 - Homo sapiens cDNA FLJ77139 complete cds, highly similar to Homo sapiens deformed epidermal autoregulatory factor 1 (DEAF1), mRNA.
AF068896 - Homo sapiens normal colorectal epithelium suppressin mRNA, complete cds.
AF068897 - Homo sapiens normal colorectal epithelium/colorectal adenocarcinoma suppressin mRNA, complete cds.
AF068892 - Homo sapiens Duke's type B colon adenocarcinoma truncated suppressin mRNA, complete cds.
AF068893 - Homo sapiens Duke's type B colon adenocarcinoma suppressin mRNA, complete cds.
AF068894 - Homo sapiens rectosigmoid colon primary adenocarcinoma suppressin mRNA, allele 1, complete cds.
AF068895 - Homo sapiens rectosigmoid colon primary adenocarcinoma suppressin mRNA, allele 2, complete cds.
EU831436 - Synthetic construct Homo sapiens clone HAIB:100066465; DKFZo008C1217 deformed epidermal autoregulatory factor 1 (Drosophila) protein (DEAF1) gene, encodes complete protein.
FJ985253 - Homo sapiens deformed epidermal autoregulatory factor 1 variant (DEAF1) mRNA, complete cds, alternatively spliced.
EU831528 - Synthetic construct Homo sapiens clone HAIB:100066557; DKFZo004C1218 deformed epidermal autoregulatory factor 1 (Drosophila) protein (DEAF1) gene, encodes complete protein.
AB489172 - Synthetic construct DNA, clone: pF1KB8135, Homo sapiens DEAF1 gene for deformed epidermal autoregulatory factor 1, without stop codon, in Flexi system.
JD136789 - Sequence 117813 from Patent EP1572962.
JD282935 - Sequence 263959 from Patent EP1572962.
JD390657 - Sequence 371681 from Patent EP1572962.
JD196423 - Sequence 177447 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K1F8, A8K5R8, C7T5V5, DEAF1_HUMAN, NM_021008, NP_066288, O15152, O75398, O75399, O75510, O75511, O75512, O75513, Q9UET1, SPN, ZMYND5
UCSC ID: uc001lqq.1
RefSeq Accession: NM_021008
Protein: O75398 (aka DEAF1_HUMAN or DEAF_HUMAN)
CCDS: CCDS31327.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_021008.2
exon count: 12CDS single in 3' UTR: no RNA size: 2737
ORF size: 1698CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2870.00frame shift in genome: no % Coverage: 99.23
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.