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.A01G068700 [ Gohir.A01G068700]	A01	8781422	8787705	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.A01G068700.2 Gohir.A01G068700.2	Low	Yes	1212	OG0004132		Get ORF Coding potential... Type: noncoding Potential: -0.804 Folding energies... MFEI: -27.888 AMFE: -0.724 GC content %: 38.531
Ghirsutum_Gohir.A01G068700.3 Gohir.A01G068700.3	High	No	1144	OG0004132		Get ORF Coding potential... Type: noncoding Potential: -0.919 Folding energies... MFEI: -28.357 AMFE: -0.739 GC content %: 38.374
Ghirsutum_Gohir.A01G068700.4 Gohir.A01G068700.4	High	No	1169	OG0004132		Get ORF Coding potential... Type: noncoding Potential: -0.921 Folding energies... MFEI: -27.759 AMFE: -0.729 GC content %: 38.067
Ghirsutum_Gohir.A01G068700.5 Gohir.A01G068700.5	Low	Yes	1187	OG0004132		Get ORF Coding potential... Type: noncoding Potential: -0.800 Folding energies... MFEI: -28.551 AMFE: -0.735 GC content %: 38.837
Ghirsutum_Gohir.A01G068700.6 Gohir.A01G068700.6	High	No	743	OG0004132		Get ORF Coding potential... Type: noncoding Potential: -0.876 Folding energies... MFEI: -23.674 AMFE: -0.659 GC content %: 35.935

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.A01G068700.2	Rfam	14.6	MIR821	1.3e-7
Ghirsutum_Gohir.A01G068700.5	Rfam	14.6	MIR821	1.3e-7

Gene models

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