GreeNC

Gene information

This table contains information about coordinates, assembly and annotation regarding the lncRNA-transcribing gene. In details, it shows whether this this gene transcribes any protein-coding transcript.

Gene alias / name	Chrom.	Start	End	Assembly	Species	Details
Ghirsutum_Gohir.A05G226600 [ Gohir.A05G226600]	A05	23059062	23060077	v2.1	Gossypium hirsutum (Phytozome 13)	Coding? No

Transcript features

This table shows how a lncRNA has been classified (high/low confidence) or whether it has been classified as pre-miRNA (go to FAQ for classification criteria). Besides, it displays the lncRNA length and sequence as well as information about the ORF, the coding potential calculated by the Coding Potential Calculator (CPC), and the folding energies calculated by RNAfold.

Transcript alias / name	Confidence	Pre-miRNA	Length	Orthologous group	Sequence	Details
Ghirsutum_Gohir.A05G226600.1 Gohir.A05G226600.1	High	No	580	OG0007538		Get ORF Coding potential... Type: noncoding Potential: -0.226 Folding energies... MFEI: -26.690 AMFE: -0.676 GC content %: 39.483
Ghirsutum_Gohir.A05G226600.2 Gohir.A05G226600.2	Low	No	519	OG0174077		Get ORF Coding potential... Type: noncoding Potential: -0.195 Folding energies... MFEI: -26.628 AMFE: -0.652 GC content %: 40.848

Matches to external databases

The lncRNAs from GreeNC have been analysed against the following databases: SwissProt, miRBase, Rfam, RepBase (RepeatMasker), NONCODE, and lncRNAdb. This table displays any association with these databases.

Transcript alias	Database	Version	Hit	Evalue
Ghirsutum_Gohir.A05G226600.2	RepBase (RepeatMasker)	2014-01-31	LTR/Copia

Gene models

Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).