Panther Database: how to find start and end position of a Panther ID?

Question

[Chat-ra]

Hello everyone!

I’ve downloaded a file from the Ensembl Biomart here : https://www.ensembl.org/biomart/martview/4cab87e631cda01b9def14f09cc2021f

The chosen database is: “Ensembl Genes 95” and the chosen dataset is “Human Genes (GRCh38.p12)” The chosen attributes are:

• Gene stable ID
• Transcript stable ID
• Protein stable ID
• hmmpanther ID
• hmmpanther start
• hmmpanther end

I’ve access to a start and end position for each Panther ID, same goes with Intepro when I download the last release (protein2ipr.dat.gz) https://www.ebi.ac.uk/interpro/download.html.

My problem is that I can’t seem to find this information in the files provided by Panther DB (http://pantherdb.org/downloads/index.jsp)

Is someone knows where I can find information about the start and end position for a Panther ID?

Thank you for any suggestions!!!

[lieven.sterck]

Are you looking to find the start/stop of where the panther domains map on the protein or which part of the panther domain has been mapped to the protein?

[Chat-ra]

I'm looking to find the start/stop of where the panther domains map on the protein

[lieven.sterck]

Did you not mention you have that?

What am I overlooking?

[Chat-ra]

I would like to retrieve this information from the Panther database and not a another source in order to assure the validity of the information. I'm sorry if it wasn't clear!

[lieven.sterck]

The pantherDB does not work like that. It assigns genes to families from which then HMM are build that can be used to screen 'new' sequences. So a sequence is either part of the certain pantherID or not (== the assignment is always on a complete gene basis).

For a certain pantherID you can look up though which genes are assigned to it. eg. PTHR18929

[Chat-ra]

Okey thank you for your help !