Can some known person explain to me the class code of NONCODE database?

Question

[tiago211287]

The NONCODE v4 (http://www.noncode.org/) has a file named mouse_rna.cc and contain the following data:

NONCODE_ID         Antisense,"Exonic","Sense No Exonic","Linc"
NONMMUT000001      1
NONMMUT000009      100
NONMMUT000027      1000
NONMMUT000472      1010
NONMMUT000965      1100

What does this mean?

Answer 1

[h.mon]

The codes represent NONCODE gene class codes. The classes are, well, "Antisense","Exonic","Sense No Exonic","Linc" (Long intergenic non-coding). You should write all digits, i.e, 0001 instead of 1, because 0001 means it is not antisense, not exonic, not sense no exonic, but yes it is linc. The classes are not (completely) mutually exclusive, so you can have a 1100 code, for example.

[tiago211287]

Ok, thank you for your answer, but how can a noncode be for example 1010, antisense and sense no exonic at same time? sense and antisense.

P.S: and, yes, the excel erases the 000 from the 0001 that's what I did not see before.

[h.mon]

If you want to (blindly) believe in a guess, I would say one possible explanation is nested genes - but this is just a guess. However, you can easily check for yourself: find some 1010 codes, grab their sequence, and blast or browse an annotated genome on IGV, for example.