Human Gene PSD (ENST00000020673.6) from GENCODE V44
  Description: Homo sapiens pleckstrin and Sec7 domain containing (PSD), transcript variant 1, mRNA. (from RefSeq NM_002779)
RefSeq Summary (NM_002779): This gene encodes a Plekstrin homology and SEC7 domains-containing protein that functions as a guanine nucleotide exchange factor. The encoded protein regulates signal transduction by activating ADP-ribosylation factor 6. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012].
Gencode Transcript: ENST00000020673.6
Gencode Gene: ENSG00000059915.17
Transcript (Including UTRs)
   Position: hg38 chr10:102,402,619-102,418,785 Size: 16,167 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg38 chr10:102,403,200-102,417,038 Size: 13,839 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:102,402,619-102,418,785)mRNA (may differ from genome)Protein (1024 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PSD1_HUMAN
DESCRIPTION: RecName: Full=PH and SEC7 domain-containing protein 1; AltName: Full=Exchange factor for ARF6; AltName: Full=Pleckstrin homology and SEC7 domain-containing protein 1;
FUNCTION: Guanine nucleotide exchange factor for ARF6. Induces cytoskeletal remodeling (By similarity).
SUBUNIT: Interacts with ACTN1 (By similarity).
SUBCELLULAR LOCATION: Cell membrane (By similarity). Cell projection, ruffle (By similarity).
TISSUE SPECIFICITY: Isoform 2 is expressed in the brain.
SIMILARITY: Belongs to the PSD family.
SIMILARITY: Contains 1 PH domain.
SIMILARITY: Contains 1 SEC7 domain.
SEQUENCE CAUTION: Sequence=BAC23107.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: PSD
Diseases sorted by gene-association score: branch retinal artery occlusion (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 154.62 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 1319.47 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 -51.40168-0.306 Picture PostScript Text
3' UTR -280.60581-0.483 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
IPR000904 - Sec7
IPR023394 - SEC7_alpha_orthog

Pfam Domains:
PF00169 - PH domain
PF01369 - Sec7 domain

ModBase Predicted Comparative 3D Structure on A5PKW4
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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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004871 signal transducer activity
GO:0005085 guanyl-nucleotide exchange factor activity
GO:0005086 ARF guanyl-nucleotide exchange factor activity
GO:0005515 protein binding
GO:0005543 phospholipid binding

Biological Process:
GO:0007165 signal transduction
GO:0031175 neuron projection development
GO:0032012 regulation of ARF protein signal transduction

Cellular Component:
GO:0005886 plasma membrane
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0032154 cleavage furrow
GO:0032587 ruffle membrane
GO:0042995 cell projection
GO:0043197 dendritic spine
GO:0098999 extrinsic component of postsynaptic endosome membrane


-  Descriptions from all associated GenBank mRNAs
  X99688 - H.sapiens mRNA from TYL gene.
LF211355 - JP 2014500723-A/18858: Polycomb-Associated Non-Coding RNAs.
MA446932 - JP 2018138019-A/18858: Polycomb-Associated Non-Coding RNAs.
BC037332 - Homo sapiens cDNA clone IMAGE:5264357, containing frame-shift errors.
AB095931 - Homo sapiens mRNA for KIAA2011 protein.
BC039259 - Homo sapiens pleckstrin and Sec7 domain containing, mRNA (cDNA clone IMAGE:5312040), partial cds.
BC142643 - Homo sapiens pleckstrin and Sec7 domain containing, mRNA (cDNA clone MGC:164849 IMAGE:40147927), complete cds.
BC142689 - Homo sapiens pleckstrin and Sec7 domain containing, mRNA (cDNA clone MGC:165002 IMAGE:40148656), complete cds.
JD395994 - Sequence 377018 from Patent EP1572962.
JD216930 - Sequence 197954 from Patent EP1572962.
JD251594 - Sequence 232618 from Patent EP1572962.
JD222580 - Sequence 203604 from Patent EP1572962.
LF345862 - JP 2014500723-A/153365: Polycomb-Associated Non-Coding RNAs.
MA581439 - JP 2018138019-A/153365: Polycomb-Associated Non-Coding RNAs.
JD432080 - Sequence 413104 from Patent EP1572962.
JD111141 - Sequence 92165 from Patent EP1572962.
JD209143 - Sequence 190167 from Patent EP1572962.
JD530436 - Sequence 511460 from Patent EP1572962.
JD322381 - Sequence 303405 from Patent EP1572962.
JD466393 - Sequence 447417 from Patent EP1572962.
JD498664 - Sequence 479688 from Patent EP1572962.
JD393129 - Sequence 374153 from Patent EP1572962.
AB463176 - Synthetic construct DNA, clone: pF1KA2011, Homo sapiens PSD gene for pleckstrin and Sec7 domain containing, without stop codon, in Flexi system.
CU691700 - Synthetic construct Homo sapiens gateway clone IMAGE:100022706 5' read PSD mRNA.
LF345870 - JP 2014500723-A/153373: Polycomb-Associated Non-Coding RNAs.
MA581447 - JP 2018138019-A/153373: Polycomb-Associated Non-Coding RNAs.
JD256368 - Sequence 237392 from Patent EP1572962.
JD406449 - Sequence 387473 from Patent EP1572962.
JD389548 - Sequence 370572 from Patent EP1572962.
AF452641 - Homo sapiens tissue-type brain hypothetical protein mRNA, complete cds.
JD387560 - Sequence 368584 from Patent EP1572962.
JD383657 - Sequence 364681 from Patent EP1572962.
JD387559 - Sequence 368583 from Patent EP1572962.
JD054431 - Sequence 35455 from Patent EP1572962.
JD395934 - Sequence 376958 from Patent EP1572962.
JD413173 - Sequence 394197 from Patent EP1572962.
LF212797 - JP 2014500723-A/20300: Polycomb-Associated Non-Coding RNAs.
MA448374 - JP 2018138019-A/20300: Polycomb-Associated Non-Coding RNAs.
JD150646 - Sequence 131670 from Patent EP1572962.
JD525871 - Sequence 506895 from Patent EP1572962.

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

-  Other Names for This Gene
  Alternate Gene Symbols: A5PKW4, B1AKX7, D3DR87, EFA6, ENST00000020673.1, ENST00000020673.2, ENST00000020673.3, ENST00000020673.4, ENST00000020673.5, KIAA2011, NM_002779, PSD1, PSD1_HUMAN, Q15673, Q8IVG0, TYL, uc001kvg.1, uc001kvg.2, uc001kvg.3, uc001kvg.4
UCSC ID: ENST00000020673.6
RefSeq Accession: NM_002779
Protein: A5PKW4 (aka PSD1_HUMAN)
CCDS: CCDS31272.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.