what is the meaning of var.N in the TF name?

[cnzq...@gmail.com]

Hi, Dear All,

I have a question about the TF name.

For example. For TFAP2A, we can see three TF names for this TF, TFAP2A(var.1), TFAP2A(var.2), and TFAP2A(var.3). what is the meaning of var.N in the TF name?

Best,

QZ

[Oriol Fornés]

Hi,

Some transcription factors are able to recognize and bind to multiple consensus sequences.

For instance, members of the AP-1 family of transcription factors, such as JUN, recognize two different consensus sequences: TRE (5'-TGAG/CTCA-3') and CRE (5'-TGAGCTCA-3') (https://pubmed.ncbi.nlm.nih.gov/11988758/).

In JASPAR, the profile representing the binding of JUN to CRE sequences is given my the matrix MA0488.1, while the binding of JUN to TRE sequences is given by MA0489.1. The var.N account for these different consensus sequences.

In your specific example, TFAP2A recognizes the motif GCCN3/4GGC (https://pubmed.ncbi.nlm.nih.gov/16420676/). This means that it can accept any 3 or 4 nucleotides between the consensus palindrome GCC GGC.

Hope this helps.

[cnzq...@gmail.com]

Hi, 

It is very helpful. Understand now. Thank you very much for your explanation. But I have another question about the TF name like that "ARNT::HIF1A". Does it mean that the TF ARNT and HIF1A recognize the same consensus sequences?

Thanks & Best,

[Anthony Mathelier]

Hello,

When you have the :: sign, it means that the profile refers to a heterodimer. In your example, the profile corresponds to a dimer between ARNT and HIF1A.

Best

AM

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[cnzq...@gmail.com]

Hi,

Get it now. Thank you very much for your explanation.

Thanks & Best,

QZ

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