Human Gene DEF6 (ENST00000316637.7_5) from GENCODE V47lift37
  Description: DEF6 guanine nucleotide exchange factor (from RefSeq NM_022047.4)
Gencode Transcript: ENST00000316637.7_5
Gencode Gene: ENSG00000023892.12_8
Transcript (Including UTRs)
   Position: hg19 chr6:35,265,595-35,289,548 Size: 23,954 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr6:35,265,634-35,289,187 Size: 23,554 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:35,265,595-35,289,548)mRNA (may differ from genome)Protein (631 aa)
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HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DEFI6_HUMAN
DESCRIPTION: RecName: Full=Differentially expressed in FDCP 6 homolog; Short=DEF-6; AltName: Full=IRF4-binding protein;
FUNCTION: Phosphatidylinositol 3,4,5-trisphosphate-dependent guanine nucleotide exchange factor (GEF) which plays a role in the activation of Rho GTPases RAC1, RhoA and CDC42. Can regulate cell morphology in cooperation with activated RAC1. Plays a role in Th2 (T helper cells) development and/or activation, perhaps by interfering with ZAP70 signaling (By similarity).
SUBUNIT: Interacts with ZAP70 (By similarity). Interacts with IRF4, activated RAC1 and F-actin. Both the phosphorylated and non- phosphorylated forms bind phosphatidylinositol 3,4,5-trisphosphate (PtdInsP3).
SUBCELLULAR LOCATION: Cytoplasm. Cell membrane. Nucleus. Note=Recruited to the plasma membrane upon binding phosphatidylinositol 3,4,5-trisphosphate.
TISSUE SPECIFICITY: Broadly expressed in the immune system and can be detected in T and B-cells.
DOMAIN: The PH domain is essential for phosphatidylinositol 3,4,5- trisphosphate binding.
PTM: Tyrosine-phosphorylated by tyrosine-protein kinase LCK in response to T-cell activation.
SIMILARITY: Contains 1 PH domain.

-  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


-  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: 60.18 RPKM in Whole Blood
Total median expression: 401.22 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 -16.4039-0.421 Picture PostScript Text
3' UTR -132.40361-0.367 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
IPR011993 - PH_like_dom
IPR001849 - Pleckstrin_homology

Pfam Domains:
PF00169 - PH domain

SCOP Domains:
47473 - EF-hand
50729 - PH domain-like

ModBase Predicted Comparative 3D Structure on Q9H4E7
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030175 filopodium
GO:0042995 cell projection
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK093613 - Homo sapiens cDNA FLJ36294 fis, clone THYMU2004123, highly similar to Homo sapiens differentially expressed in FDCP 6 homolog (mouse) (DEF6), mRNA.
AY241694 - Homo sapiens IRF4-binding protein (IBP) mRNA, complete cds.
AK314756 - Homo sapiens cDNA, FLJ95623, highly similar to Homo sapiens differentially expressed in FDCP 6 homolog (mouse) (DEF6), mRNA.
BC017504 - Homo sapiens differentially expressed in FDCP 6 homolog (mouse), mRNA (cDNA clone IMAGE:4864393).
AB527549 - Synthetic construct DNA, clone: pF1KB6134, Homo sapiens DEF6 gene for differentially expressed in FDCP 6 homolog, without stop codon, in Flexi system.
BC168373 - Synthetic construct Homo sapiens clone IMAGE:100068269, MGC:195886 differentially expressed in FDCP 6 homolog (mouse) (DEF6) mRNA, encodes complete protein.
KJ902530 - Synthetic construct Homo sapiens clone ccsbBroadEn_11924 DEF6 gene, encodes complete protein.
AJ276095 - Homo sapiens mRNA for putative recombinase (def-6 gene).
BC007702 - Homo sapiens differentially expressed in FDCP 6 homolog (mouse), mRNA (cDNA clone IMAGE:3956940), partial cds.
JD075620 - Sequence 56644 from Patent EP1572962.
AL110182 - Homo sapiens mRNA; cDNA DKFZp566A201 (from clone DKFZp566A201).
JD517001 - Sequence 498025 from Patent EP1572962.
JD562027 - Sequence 543051 from Patent EP1572962.
JD528769 - Sequence 509793 from Patent EP1572962.
JD240633 - Sequence 221657 from Patent EP1572962.
JD210049 - Sequence 191073 from Patent EP1572962.
JD075778 - Sequence 56802 from Patent EP1572962.
JD468181 - Sequence 449205 from Patent EP1572962.
JD435074 - Sequence 416098 from Patent EP1572962.
JD371429 - Sequence 352453 from Patent EP1572962.
JD103216 - Sequence 84240 from Patent EP1572962.
JD551603 - Sequence 532627 from Patent EP1572962.
JD121007 - Sequence 102031 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: DEFI6_HUMAN, ENST00000316637.1, ENST00000316637.2, ENST00000316637.3, ENST00000316637.4, ENST00000316637.5, ENST00000316637.6, IBP, NM_022047, Q86VF4, Q9H4E7, uc317qbm.1, uc317qbm.2
UCSC ID: ENST00000316637.7_5
RefSeq Accession: NM_022047.4
Protein: Q9H4E7 (aka DEFI6_HUMAN)

-  Gene Model Information
  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.