Human Gene PODXL (uc003vqw.4)
  Description: Homo sapiens podocalyxin-like (PODXL), transcript variant 1, mRNA.
RefSeq Summary (NM_001018111): This gene encodes a member of the sialomucin protein family. The encoded protein was originally identified as an important component of glomerular podocytes. Podocytes are highly differentiated epithelial cells with interdigitating foot processes covering the outer aspect of the glomerular basement membrane. Other biological activities of the encoded protein include: binding in a membrane protein complex with Na+/H+ exchanger regulatory factor to intracellular cytoskeletal elements, playing a role in hematopoetic cell differentiation, and being expressed in vascular endothelium cells and binding to L-selectin. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr7:131,185,021-131,241,376 Size: 56,356 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr7:131,189,070-131,241,118 Size: 52,049 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:131,185,021-131,241,376)mRNA (may differ from genome)Protein (558 aa)
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MGIneXtProtOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PODXL_HUMAN
DESCRIPTION: RecName: Full=Podocalyxin; AltName: Full=GCTM-2 antigen; AltName: Full=Gp200; AltName: Full=Podocalyxin-like protein 1; Short=PC; Short=PCLP-1; Flags: Precursor;
FUNCTION: Involved in the regulation of both adhesion and cell morphology and cancer progression. Function as an anti-adhesive molecule that maintains an open filtration pathway between neighboring foot processes in the podocyte by charge repulsion. Acts as a pro-adhesive molecule, enhancing the adherence of cells to immobilized ligands, increasing the rate of migration and cell- cell contacts in an integrin-dependent manner. Induces the formation of apical actin-dependent microvilli. Involved in the formation of a preapical plasma membrane subdomain to set up inital epithelial polarization and the apical lumen formation during renal tubulogenesis. Plays a role in cancer development and aggressiveness by inducing cell migration and invasion through its interaction with the actin-binding protein EZR. Affects EZR- dependent signaling events, leading to increased activities of the MAPK and PI3K pathways in cancer cells.
SUBUNIT: Monomer; when associated with the membrane raft. Oligomer; when integrated in the apical membrane. Interacts (via the C-terminal PDZ-binding motif DTHL) with SLC9A3R1 (via the PDZ domains); the interaction is not detected in glomerular epithelium cells, take place early in the secretory pathway and is necessary for its apical membrane sorting. Found in a complex with EZR, PODXL and SLC9A3R2. Associates with the actin cytoskeleton through complex formation with EZR and SLC9A3R2. Interacts (via the C- terminal PDZ-binding motif DTHL) with SLC9A3R2 (via the PDZ 1 domain); interaction is detected in glomerular epithelium cells (By similarity). Interacts with EZR.
SUBCELLULAR LOCATION: Apical cell membrane. Cell projection, lamellipodium. Cell projection, filopodium. Cell projection, ruffle. Cell projection, microvillus (By similarity). Membrane raft (By similarity). Membrane; Single-pass type I membrane protein (Potential). Note=In single attached epithelial cells is restricted to a preapical pole on the free plasma membrane whereas other apical and basolateral proteins are not yet polarized. Colocalizes with SLC9A3R2 at the apical plasma membrane during epithelial polarization. Colocalizes with SLC9A3R1 at the trans- Golgi network (transiently) and at the apical plasma membrane. Its association with the membrane raft is transient. Colocalizes with actin filaments, EZR and SLC9A3R1 in a punctate pattern at the apical cell surface where microvilli form. Colocalizes with EZR and SLC9A3R2 at the apical cell membrane of glomerular epithelium cells (By similarity). Forms granular, punctuated pattern, forming patches, preferentially adopting a polar distribution, located on the migrating poles of the cell or forming clusters along the terminal ends of filipodia establishing contact with the endothelial cells. Colocalizes with the submembrane actin of lamellipodia, particularly associated with ruffles. Colocalizes with vinculin at protrusions of cells. Colocalizes with ITGB1. Colocalizes with PARD3, PRKCI, EXOC5, OCLN, RAB11A and RAB8A in apical membrane initiation sites (AMIS) during the generation of apical surface and luminogenesis (By similarity).
TISSUE SPECIFICITY: Glomerular epithelium cell (podocyte).
DOMAIN: Both the O-glycan-rich domain of the extracellular domain and the C-terminus PDZ-binding motif (DTHL) in the cytoplasmic tail harbor an apical sorting signal. The cytoplasmic domain is necessary for the apical membrane targeting and renal tubulogenesis. The cytoplasmic C-terminus PDZ-binding motif (DTHL) is essential for interaction with SLC9A3R1 and for targeting SLC9A3R1 to the apical cell membrane. The extracellular domain is necessary for microvillus formation (By similarity). The large highly anionic extracellular domain allows to maintain open filtration pathways between neighboring podocyte foot processes.
PTM: N- and O-linked glycosylated. Sialoglycoprotein (By similarity).
SIMILARITY: Belongs to the podocalyxin family.

-  Primer design for this transcript
 

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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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PODXL
CDC HuGE Published Literature: PODXL
Positive Disease Associations: monocyte chemoattractant protein 1 (66-77)
Related Studies:
  1. monocyte chemoattractant protein 1 (66-77)
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: PODXL
Diseases sorted by gene-association score: parkinson disease, juvenile, type 2* (175), embryonal carcinoma (12), acute proliferative glomerulonephritis (5), kidney hypertrophy (5)
* = 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: 72.06 RPKM in Kidney - Cortex
Total median expression: 716.14 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -122.40258-0.474 Picture PostScript Text
3' UTR -1433.214049-0.354 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
IPR013836 - CD34/Podocalyxin
IPR017403 - Podocalyxin-like_p1

Pfam Domains:
PF06365 - CD34/Podocalyxin family

ModBase Predicted Comparative 3D Structure on O00592
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007155 cell adhesion
GO:0007162 negative regulation of cell adhesion
GO:0016477 cell migration
GO:0022407 regulation of cell-cell adhesion
GO:0022408 negative regulation of cell-cell adhesion
GO:0030335 positive regulation of cell migration
GO:0032534 regulation of microvillus assembly
GO:0033634 positive regulation of cell-cell adhesion mediated by integrin
GO:0072015 glomerular visceral epithelial cell development
GO:0072175 epithelial tube formation

Cellular Component:
GO:0001726 ruffle
GO:0005615 extracellular space
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005815 microtubule organizing center
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005902 microvillus
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016324 apical plasma membrane
GO:0030027 lamellipodium
GO:0030175 filopodium
GO:0031528 microvillus membrane
GO:0036057 slit diaphragm
GO:0042995 cell projection
GO:0043231 intracellular membrane-bounded organelle
GO:0045121 membrane raft
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  KJ897352 - Synthetic construct Homo sapiens clone ccsbBroadEn_06746 PODXL gene, encodes complete protein.
BC042466 - Homo sapiens, Similar to podocalyxin-like, clone IMAGE:5172924, mRNA.
U97519 - Homo sapiens podocalyxin-like protein mRNA, complete cds.
AK055816 - Homo sapiens cDNA FLJ31254 fis, clone KIDNE2005526, highly similar to Homo sapiens podocalyxin-like protein mRNA.
AK223573 - Homo sapiens mRNA for podocalyxin-like precursor variant, clone: FCC129D02.
BC093730 - Homo sapiens podocalyxin-like, mRNA (cDNA clone MGC:120765 IMAGE:7939575), complete cds.
BC112035 - Homo sapiens podocalyxin-like, transcript variant 2, mRNA (cDNA clone MGC:138240 IMAGE:8327503), complete cds.
BC143318 - Homo sapiens podocalyxin-like, mRNA (cDNA clone MGC:176840 IMAGE:9051823), complete cds.
BX641124 - Homo sapiens mRNA; cDNA DKFZp686N11113 (from clone DKFZp686N11113).
JD470126 - Sequence 451150 from Patent EP1572962.
JD109782 - Sequence 90806 from Patent EP1572962.
JD360400 - Sequence 341424 from Patent EP1572962.
JD286133 - Sequence 267157 from Patent EP1572962.
JD091634 - Sequence 72658 from Patent EP1572962.
JD062069 - Sequence 43093 from Patent EP1572962.
JD212084 - Sequence 193108 from Patent EP1572962.
JD559128 - Sequence 540152 from Patent EP1572962.
JD197241 - Sequence 178265 from Patent EP1572962.
JD316668 - Sequence 297692 from Patent EP1572962.
JD459488 - Sequence 440512 from Patent EP1572962.
JD160068 - Sequence 141092 from Patent EP1572962.
JD338981 - Sequence 320005 from Patent EP1572962.
JD353428 - Sequence 334452 from Patent EP1572962.
JD198239 - Sequence 179263 from Patent EP1572962.
JD546923 - Sequence 527947 from Patent EP1572962.
JD420607 - Sequence 401631 from Patent EP1572962.
JD181002 - Sequence 162026 from Patent EP1572962.
JD145621 - Sequence 126645 from Patent EP1572962.
JD274485 - Sequence 255509 from Patent EP1572962.
JD193496 - Sequence 174520 from Patent EP1572962.
JD045135 - Sequence 26159 from Patent EP1572962.
JD361056 - Sequence 342080 from Patent EP1572962.
JD553517 - Sequence 534541 from Patent EP1572962.
JD081796 - Sequence 62820 from Patent EP1572962.
JD139315 - Sequence 120339 from Patent EP1572962.
JD219039 - Sequence 200063 from Patent EP1572962.
JD267254 - Sequence 248278 from Patent EP1572962.
JD131434 - Sequence 112458 from Patent EP1572962.
JD086665 - Sequence 67689 from Patent EP1572962.
JD077790 - Sequence 58814 from Patent EP1572962.
JD045723 - Sequence 26747 from Patent EP1572962.
JD112185 - Sequence 93209 from Patent EP1572962.
HZ473935 - WO 2016002844-A/49: ANTI-INVASIVE/ANTI-METASTATIC DRUG FOR PANCREATIC CANCER CELL.
JD108880 - Sequence 89904 from Patent EP1572962.
JD435185 - Sequence 416209 from Patent EP1572962.
JD045465 - Sequence 26489 from Patent EP1572962.
JD404829 - Sequence 385853 from Patent EP1572962.
JD202914 - Sequence 183938 from Patent EP1572962.
JD324274 - Sequence 305298 from Patent EP1572962.
JD082087 - Sequence 63111 from Patent EP1572962.
JD119937 - Sequence 100961 from Patent EP1572962.
JD434735 - Sequence 415759 from Patent EP1572962.
JD078954 - Sequence 59978 from Patent EP1572962.
JD252092 - Sequence 233116 from Patent EP1572962.
JD417341 - Sequence 398365 from Patent EP1572962.
JD304019 - Sequence 285043 from Patent EP1572962.
JD217863 - Sequence 198887 from Patent EP1572962.
JD038933 - Sequence 19957 from Patent EP1572962.
JD343970 - Sequence 324994 from Patent EP1572962.
JD549193 - Sequence 530217 from Patent EP1572962.
JD251803 - Sequence 232827 from Patent EP1572962.
JD248244 - Sequence 229268 from Patent EP1572962.
JD520002 - Sequence 501026 from Patent EP1572962.
JD463635 - Sequence 444659 from Patent EP1572962.
JD286504 - Sequence 267528 from Patent EP1572962.
JD483685 - Sequence 464709 from Patent EP1572962.
JD565489 - Sequence 546513 from Patent EP1572962.
JD409993 - Sequence 391017 from Patent EP1572962.
JD459379 - Sequence 440403 from Patent EP1572962.
HZ473936 - WO 2016002844-A/50: ANTI-INVASIVE/ANTI-METASTATIC DRUG FOR PANCREATIC CANCER CELL.
HZ473937 - WO 2016002844-A/51: ANTI-INVASIVE/ANTI-METASTATIC DRUG FOR PANCREATIC CANCER CELL.
JD441316 - Sequence 422340 from Patent EP1572962.
HZ473938 - WO 2016002844-A/52: ANTI-INVASIVE/ANTI-METASTATIC DRUG FOR PANCREATIC CANCER CELL.
LF212021 - JP 2014500723-A/19524: Polycomb-Associated Non-Coding RNAs.
LF213025 - JP 2014500723-A/20528: Polycomb-Associated Non-Coding RNAs.
JD187003 - Sequence 168027 from Patent EP1572962.
JD128468 - Sequence 109492 from Patent EP1572962.
JD458534 - Sequence 439558 from Patent EP1572962.
JD187226 - Sequence 168250 from Patent EP1572962.
JD187227 - Sequence 168251 from Patent EP1572962.
JD404652 - Sequence 385676 from Patent EP1572962.
JD458232 - Sequence 439256 from Patent EP1572962.
MA447598 - JP 2018138019-A/19524: Polycomb-Associated Non-Coding RNAs.
MA448602 - JP 2018138019-A/20528: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NHX8, NM_001018111, NP_001018121, O00592, PCLP, PCLP1, PODXL_HUMAN, Q52LZ7, Q53ER6
UCSC ID: uc003vqw.4
RefSeq Accession: NM_001018111
Protein: O00592 (aka PODXL_HUMAN)
CCDS: CCDS34755.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PODXL:
parkinson-overview (Parkinson Disease Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001018111.2
exon count: 9CDS single in 3' UTR: no RNA size: 6007
ORF size: 1677CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2702.00frame shift in genome: no % Coverage: 99.62
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.