HELP:

To extract the information from database , go to search option and enter further parameters . Different parameters are:

• Type: There are 2 types of lncRNA i.e.
  • Genic : lncRNAs that overlap between a protein-coding transcript at one or more nucleotides.
  • Intergenic: lncRNAs that give rise to exclusively between two protein coding transcripts.

• Class code: Different types of class codes are :
  • j: Potentially novel isoform (fragment): at least one splice junction is shared with a reference transcript
  • u: Unknown, intergenic transcript.
  • x: Exonic overlap with reference on the opposite strand.
  • o: Generic exonic overlap with a reference transcript.
  • p: Possible polymerase run-on fragment (within 2K bases of a reference transcript).

• Direction: There are two types of diections viz., Sense and Antisense. Sense lncRNAs are transcribed from the sense strand of protein-coding genes, containing exons from protein-coding genes. Antisense RNA (asRNA), is a single stranded RNA that is complementary to a protein coding messenger RNA (mRNA) with which it hybridizes, and thereby blocks its translation into protein).

• Exon: Exons are coding sections of a protein RNA transcript, that are translated into protein.  In the cells of plants and animals, most gene sequences are broken up by one or more DNA sequences called introns. The parts of the gene sequence that are expressed in the protein are called exons.

• CPC Content (Coding Potential Calculator): To assess the protein-coding potential of a transcript based on six biologically meaningful sequence features CPC score is used. It  can discriminate coding from noncoding transcripts with high accuracy.