Clarification on JASPAR IDs MA0668.3 vs MA1993.2 for Neurod2

[Ambuj Kumar]

Dear JASPAR Team,

Thank you for your continued efforts in maintaining and improving such an invaluable resource for the research community.

I was reviewing the JASPAR database for transcription factor binding motifs related to Neurod2 and found two entries:

- MA0668.3
- MA1993.2

Both correspond to Neurod2 but appear to be from different species (MA0668.3 from Mus musculus, and earlier versions from Homo sapiens). In contrast, MA1993.2 is consistently labeled as Mus musculus. This led to the following questions:

1. What is the exact difference between MA0668.3 and MA1993.2?
2. Why does MA0668.3 still use the same base ID (MA0668) despite the shift in species from human to mouse?

I would appreciate any clarification on how JASPAR handles versioning and species-specific changes.

Best regards,
Ambuj Kumar 

[Anthony Mathelier]

Thanks for raising the issue, that is weird indeed. It looks like a glitch. We will investigate and will let you know.

Best
AM

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[Anthony Mathelier]

We have now investigated this and we provide two profiles for Neurod2 on purpose. Indeed, it has been established that Neurod2 can bind two different types of motifs. See from https://www.sciencedirect.com/science/article/pii/S1534580712000494?via%3Dihub: "We demonstrate that NEUROD2 and MYOD bind a shared CAGCTG E box motif and E box motifs specific for each factor: CAGGTG for MYOD and CAGATG for NEUROD2."

[Ambuj Kumar]

Thank you for your response and for clarifying that Neurod2 can bind two distinct motif types.

I still have a follow-up question:
Why does MA0668.3 continue to use the same base ID (MA0668) even though there appears to be a species shift from Homo sapiens (in earlier versions) to Mus musculus in the current one? 

Understanding how JASPAR handles species annotation and versioning in such cases would be very helpful. I would greatly appreciate any further insight on this as well.

Best regards,
Ambuj Kumar

[Anthony Mathelier]

The base ID is associated with a specific motif for a TF. JASPAR provides binding profiles per taxon, not species as orthologous TFs will bind the same motif. The species information corresponds to the origin of the data used to build the profile.

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Anthony

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