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
Pvirgatum_Pavir.5KG258000 [ Pavir.5KG258000]	Chr05K	19326545	19328762	v5.1	Panicum virgatum (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
Pvirgatum_Pavir.5KG258000.1 Pavir.5KG258000.1	High	No	879	OG0056036		Get ORF Coding potential... Type: noncoding Potential: -0.490 Folding energies... MFEI: -35.404 AMFE: -0.627 GC content %: 56.428
Pvirgatum_Pavir.5KG258000.2 Pavir.5KG258000.2	Low	Yes	1389	OG0056036		Get ORF Coding potential... Type: noncoding Potential: -0.707 Folding energies... MFEI: -34.636 AMFE: -0.691 GC content %: 50.108

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
Pvirgatum_Pavir.5KG258000.2	Rfam	14.6	mir-338	2.6e-4
Pvirgatum_Pavir.5KG258000.2	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm

Gene models

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