Human Gene PALS1 (ENST00000261681.9_6) from GENCODE V47lift37
  Description: protein associated with LIN7 1, MAGUK p55 family member, transcript variant 1 (from RefSeq NM_022474.4)
Gencode Transcript: ENST00000261681.9_6
Gencode Gene: ENSG00000072415.10_18
Transcript (Including UTRs)
   Position: hg19 chr14:67,708,152-67,802,778 Size: 94,627 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr14:67,745,888-67,799,673 Size: 53,786 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:67,708,152-67,802,778)mRNA (may differ from genome)Protein (675 aa)
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-  Comments and Description Text from UniProtKB
  ID: MPP5_HUMAN
DESCRIPTION: RecName: Full=MAGUK p55 subfamily member 5;
FUNCTION: May play a role in tight junctions biogenesis and in the establishment of cell polarity in epithelial cells. May modulate SC6A1/GAT1-mediated GABA uptake by stabilizing the transporter. Required for localization of EZR to the apical membrane of parietal cells and may play a role in the dynamic remodeling of the apical cytoskeleton (By similarity).
SUBUNIT: Interacts with CRB3, LIN7C and MPDZ. Interacts with INADL, PARD6B, SC6A1 and EZR (By similarity). Forms a complex with CRB1 and MPP4. Component of a complex whose core is composed of ARHGAP17, AMOT, MPP5/PALS1, INADL/PATJ and PARD3/PAR3. Heterodimer with MPP1. Interacts with MPP7.
SUBCELLULAR LOCATION: Cell membrane; Peripheral membrane protein. Endomembrane system; Peripheral membrane protein. Cell junction, tight junction. Note=Localized to the tight junctions of epithelial cells and a subset of intracellular vesicles. In the retina, detected at the outer limiting membrane (OLM), apical to the adherens junction (AJ), where it colocalizes with CRB1. Colocalizes with MPP1 in the retina at the outer limiting membrane (OLM). Localized to the Purkinje cell body and axon.
TISSUE SPECIFICITY: Expressed in the retina (at protein level).
DOMAIN: The L27 domain 1 functions in targeting to the tight junctions by binding to INADL (By similarity).
DOMAIN: The PDZ domain binds to the C-terminus of SC6A1 (By similarity).
SIMILARITY: Belongs to the MAGUK family.
SIMILARITY: Contains 1 guanylate kinase-like domain.
SIMILARITY: Contains 2 L27 domains.
SIMILARITY: Contains 1 PDZ (DHR) domain.
SIMILARITY: Contains 1 SH3 domain.
SEQUENCE CAUTION: Sequence=AAH53366.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=BAB14172.1; Type=Erroneous initiation;

-  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


+  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: 10.14 RPKM in Thyroid
Total median expression: 269.40 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 -94.90335-0.283 Picture PostScript Text
3' UTR -799.403105-0.257 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
IPR008144 - Guanylate_kin
IPR008145 - Guanylate_kin/L-typ_Ca_channel
IPR020590 - Guanylate_kinase_CS
IPR004172 - L27
IPR014775 - L27_C
IPR015145 - L27_N
IPR001478 - PDZ
IPR011511 - SH3_2
IPR001452 - SH3_domain

Pfam Domains:
PF00018 - SH3 domain
PF00595 - PDZ domain
PF00625 - Guanylate kinase
PF02828 - L27 domain
PF07653 - Variant SH3 domain
PF09060 - L27_N
PF17820 - PDZ domain

SCOP Domains:
101288 - L27 domain
50044 - SH3-domain
50156 - PDZ domain-like
52540 - P-loop containing nucleoside triphosphate hydrolases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1Y76 - NMR MuPIT 3UIT - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q8N3R9
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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
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
GO:0019904 protein domain specific binding

Biological Process:
GO:0002011 morphogenesis of an epithelial sheet
GO:0007009 plasma membrane organization
GO:0032287 peripheral nervous system myelin maintenance
GO:0032288 myelin assembly
GO:0035750 protein localization to myelin sheath abaxonal region
GO:0070830 bicellular tight junction assembly
GO:0072659 protein localization to plasma membrane
GO:0090162 establishment of epithelial cell polarity

Cellular Component:
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0005913 cell-cell adherens junction
GO:0005923 bicellular tight junction
GO:0012505 endomembrane system
GO:0016020 membrane
GO:0030054 cell junction
GO:0032991 macromolecular complex
GO:0035749 myelin sheath adaxonal region
GO:0043219 lateral loop
GO:0043220 Schmidt-Lanterman incisure
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC095485 - Homo sapiens membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5), mRNA (cDNA clone MGC:111529 IMAGE:30520451), complete cds.
AK291240 - Homo sapiens cDNA FLJ77534 complete cds, highly similar to Homo sapiens membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5) (MPP5), mRNA.
AK098373 - Homo sapiens cDNA FLJ25507 fis, clone CBR05244, highly similar to Mus musculus PALS1 (Pals1) mRNA.
BC053366 - Homo sapiens membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5), mRNA (cDNA clone IMAGE:6142510), partial cds.
AL832326 - Homo sapiens mRNA; cDNA DKFZp451E015 (from clone DKFZp451E015); complete cds.
BC129933 - Homo sapiens membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5), mRNA (cDNA clone MGC:156154 IMAGE:40082250), complete cds.
AL832578 - Homo sapiens mRNA; cDNA DKFZp451E0516 (from clone DKFZp451E0516).
KJ894550 - Synthetic construct Homo sapiens clone ccsbBroadEn_03944 MPP5 gene, encodes complete protein.
AM392599 - Synthetic construct Homo sapiens clone IMAGE:100002331 for hypothetical protein (MPP5 gene).
AB385253 - Synthetic construct DNA, clone: pF1KB9500, Homo sapiens MPP5 gene for MAGUK p55 subfamily member 5, complete cds, without stop codon, in Flexi system.
AM392859 - Synthetic construct Homo sapiens clone IMAGE:100003081 for hypothetical protein (MPP5 gene).
AK022677 - Homo sapiens cDNA FLJ12615 fis, clone NT2RM4001629, weakly similar to MAGUK P55 SUBFAMILY MEMBER 3.
BC037966 - Homo sapiens membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5), mRNA (cDNA clone IMAGE:5764637), with apparent retained intron.
AK057160 - Homo sapiens cDNA FLJ32598 fis, clone STOMA1000013.
JD181909 - Sequence 162933 from Patent EP1572962.
JD224156 - Sequence 205180 from Patent EP1572962.
AL832936 - Homo sapiens mRNA; cDNA DKFZp666F1010 (from clone DKFZp666F1010).
JD527940 - Sequence 508964 from Patent EP1572962.
JD369840 - Sequence 350864 from Patent EP1572962.
JD091863 - Sequence 72887 from Patent EP1572962.
JD244851 - Sequence 225875 from Patent EP1572962.
JD453811 - Sequence 434835 from Patent EP1572962.
JD080053 - Sequence 61077 from Patent EP1572962.
JD341114 - Sequence 322138 from Patent EP1572962.
AF131764 - Homo sapiens clone 25032 mRNA sequence.
JD023737 - Sequence 4761 from Patent EP1572962.
JD031872 - Sequence 12896 from Patent EP1572962.

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

Protein Q8N3R9 (Reactome details) participates in the following event(s):

R-HSA-420661 Crumbs forms a ternary complex with Pals1 and PATJ at tight junctions
R-HSA-420029 Tight junction interactions
R-HSA-421270 Cell-cell junction organization
R-HSA-446728 Cell junction organization
R-HSA-1500931 Cell-Cell communication

-  Other Names for This Gene
  Alternate Gene Symbols: A1L380, ENST00000261681.1, ENST00000261681.2, ENST00000261681.3, ENST00000261681.4, ENST00000261681.5, ENST00000261681.6, ENST00000261681.7, ENST00000261681.8, MPP5 , NM_022474, PALS1 , PALS1_HUMAN, Q7Z631, Q86T98, Q8N3R9, Q8N7I5, Q9H9Q0, uc317gsl.1, uc317gsl.2
UCSC ID: ENST00000261681.9_6
RefSeq Accession: NM_022474.4
Protein: Q8N3R9 (aka MPP5_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.