Human Gene PSD4 (uc002tjg.3) Description and Page Index
  Description: Homo sapiens pleckstrin and Sec7 domain containing 4 (PSD4), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr2:113,954,772-113,960,677 Size: 5,906 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr2:113,955,369-113,958,992 Size: 3,624 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:113,954,772-113,960,677)mRNA (may differ from genome)Protein (222 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIPubMedStanford SOURCE
UniProtKB

-  Comments and Description Text from UniProtKB
  ID: B4DFU9_HUMAN
DESCRIPTION: SubName: Full=cDNA FLJ55963, highly similar to Homo sapiens pleckstrin and Sec7 domain containing 4 (PSD4), mRNA;
SIMILARITY: Contains 1 PH domain.

-  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: 20.51 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 196.06 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 -214.30597-0.359 Picture PostScript Text
3' UTR -748.991685-0.445 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
IPR001605 - PH_dom-spectrin-type
IPR011993 - PH_like_dom
IPR001849 - Pleckstrin_homology

Pfam Domains:
PF00169 - PH domain
PF15410 - Pleckstrin homology domain

SCOP Domains:
50729 - PH domain-like

ModBase Predicted Comparative 3D Structure on B4DFU9
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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005543 phospholipid binding


-  Descriptions from all associated GenBank mRNAs
  AK290045 - Homo sapiens cDNA FLJ76048 complete cds, highly similar to Homo sapiens pleckstrin and Sec7 domain containing 4 (PSD4), mRNA.
AB208798 - Homo sapiens mRNA for Pleckstrin and Sec7 domain containing 4 variant protein.
BC035307 - Homo sapiens pleckstrin and Sec7 domain containing 4, mRNA (cDNA clone MGC:17283 IMAGE:4339380), complete cds.
BC073151 - Homo sapiens pleckstrin and Sec7 domain containing 4, mRNA (cDNA clone MGC:87975 IMAGE:5757431), complete cds.
U63127 - Human SEC7 homolog Tic (TIC) mRNA, complete cds.
AJ459781 - Homo sapiens mRNA for ADP-ribosylation factor guanine nucleotide-exchange factor 6 (EFA6B gene).
KJ902355 - Synthetic construct Homo sapiens clone ccsbBroadEn_11749 PSD4 gene, encodes complete protein.
EU176621 - Synthetic construct Homo sapiens clone IMAGE:100011414; FLH178126.01L; RZPDo839A07254D pleckstrin and Sec7 domain containing 4 (PSD4) gene, encodes complete protein.
AK023421 - Homo sapiens cDNA FLJ13359 fis, clone PLACE1000081, highly similar to Homo sapiens pleckstrin and Sec7 domain containing 4 (PSD4), mRNA.
AK094598 - Homo sapiens cDNA FLJ37279 fis, clone BRAMY2012880, highly similar to Human SEC7 homolog Tic (TIC) mRNA.
AK294268 - Homo sapiens cDNA FLJ55963 complete cds, highly similar to Homo sapiens pleckstrin and Sec7 domain containing 4 (PSD4), mRNA.
AK093556 - Homo sapiens cDNA FLJ36237 fis, clone THYMU2001381, highly similar to Human SEC7 homolog Tic (TIC) mRNA.
AX748199 - Sequence 1724 from Patent EP1308459.
JD468146 - Sequence 449170 from Patent EP1572962.
JD169929 - Sequence 150953 from Patent EP1572962.
JD248192 - Sequence 229216 from Patent EP1572962.
JD207092 - Sequence 188116 from Patent EP1572962.
JD464484 - Sequence 445508 from Patent EP1572962.
JD155025 - Sequence 136049 from Patent EP1572962.
JD350456 - Sequence 331480 from Patent EP1572962.
JD416994 - Sequence 398018 from Patent EP1572962.
JD221589 - Sequence 202613 from Patent EP1572962.
JD397383 - Sequence 378407 from Patent EP1572962.
JD276520 - Sequence 257544 from Patent EP1572962.
JD317469 - Sequence 298493 from Patent EP1572962.
JD323489 - Sequence 304513 from Patent EP1572962.
DL492489 - Novel nucleic acids.
DL490959 - Novel nucleic acids.
JD103860 - Sequence 84884 from Patent EP1572962.
JD211468 - Sequence 192492 from Patent EP1572962.
JD418018 - Sequence 399042 from Patent EP1572962.
JD300377 - Sequence 281401 from Patent EP1572962.
JD376268 - Sequence 357292 from Patent EP1572962.
JD201941 - Sequence 182965 from Patent EP1572962.
JD441860 - Sequence 422884 from Patent EP1572962.
JD320512 - Sequence 301536 from Patent EP1572962.
JD071395 - Sequence 52419 from Patent EP1572962.
JD338351 - Sequence 319375 from Patent EP1572962.
JD237466 - Sequence 218490 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04144 - Endocytosis

-  Other Names for This Gene
  Alternate Gene Symbols: AK094598, B4DFU9, B4DFU9_HUMAN
UCSC ID: uc002tjg.3
RefSeq Accession: NM_012455
Protein: B4DFU9

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK094598.1
exon count: 4CDS single in 3' UTR: no RNA size: 2763
ORF size: 669CDS single in intron: no Alignment % ID: 99.86
txCdsPredict score: 1140.00frame 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: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 552# 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.