PTHR23315

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Questions that arose during PAINT curation

Questions for MOD curators

Phylogeny

  • Should the Dicty aardvark protein be in this family?

MF

Multiple organisms

  • Mouse, rat, worm, and fly: Can you make the "protein binding" annotations more specific?
  • All: Does Jup have DNA binding or transcription factor activity? Any annotations, positive or negative, would be very helpful.====Mouse====

Mouse

  • Mouse: Can you also make the Jup "protein binding" annotations more specific?
  • Mouse: Does PMID 16973135 justify annotation to GO:0019903 "protein phosphatase binding" for Ctnnb1 in addition to Jup? The abstract states, "Glutathione-S-transferase (GST) pulldown assays were used to show that RPTPrho interacts with several adherens junctional proteins in brain, including E-cadherin, N-cadherin, VE-cadherin (cadherin-5), desmoglein, alpha, beta [Ctnnb1] and gamma [Jup] catenin, p120(ctn) and alpha-actinin." Would GO:0042153 "RPTP-like protein binding" be a better term?

CC

Human

  • Human: The following GO terms are defined as containing beta-catenin. Should Ctnnb1 be annotated to them?
Reference GO term
PMID 9065401 GO:0070369 : beta-catenin-TCF7L2 complex
PMID 9065402 GO:0070369 : beta-catenin-TCF7L2 complex
PMID 16188939 GO:0034742 : APC-Axin-1-beta-catenin complex
PMID 16611247 GO:0034750 : Scrib-APC-beta-catenin complex
  • Human: The following GO terms are defined as containing gamma-catenin. Should Jup be annotated to them?
Reference GO term
PMID 14661054 GO:0071664 : catenin-TCF7L2 complex
PMID 14661054 GO:0071665 : gamma-catenin-TCF7L2 complex

Mouse

  • Mouse: Please verify any beta catenin annotations from MGI:3610682/PMID 16339037. I can't find the gene mentioned anywhere in the paper.
  • Mouse: Please check the GO:0045177 "apical part of cell" annotation from MGI:3037622/PMID 15037549, which states, "beta-catenin, f-actin, and myosin II-B localize predominantly to the apical–junctional complex in normal neuroepithelium (Fig. 6E–G)." Is there additional supporting evidence for the 45177 annotation? Note that GO:0043296 "apical junction complex" is not part of 45177.

Fly

  • Fly: Please check figure 4 of PMID 9657150 to verify the GO:0016324 "apical plasma membrane" annotation. Does the figure really show that armadillo is found in the apical region of the cell, or at apical junctions, which are not part of the apical region. The caption states, "In the larval eye disc, Arm is present at the apical junctions of all epithelial cells but concentrated at points of photoreceptor contact." Does the later statement "D-APC and Arm are both found apically within photoreceptor cells" actually refer to 16324 or is it shorthand for the junction?


BP

Mouse

  • Mouse Jup: Can you annotate to GO:0007016 "cytoskeletal anchoring at plasma membrane" based on PMID 18496566?
  • Mouse Ctnnb1: Instead of GO:0048593 "camera-type eye morphogenesis" would you prefer GO:0002089 "lens morphogenesis in camera-type eye" based on PMID 16102745, "The duality of beta-catenin function: a requirement in lens morphogenesis and signaling suppression of lens fate in periocular ectoderm"?
  • Mouse Ctnnb1: Is the GO:0045453 "bone resorption" annotation from PMID 15866165 correct, or is it the phenotype of a beta catenin knockout? See the section entitled "Low Bone Mass and High Bone Resorption in Mice Lacking ?-Catenin in Osteoblasts."


Questions for ontology curators

MF

  • GO:0042153 "RPTP-like protein binding" is not a child of GO:0019903 "protein phosphatase binding," presumably because the definition of 42153 does not require that the protein in question be a phosphatase but rather have "similar structure/function to receptor protein tyrosine phosphatases." So, how do you annotate binding to a protein that is like RPTP and is a known phosphatase?

CC

  • Please clarify the definition of GO:0030057 "desmosome." Does the desmosome include the associated intermediate filaments?