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	Source	Assembly	Species	Details
Klaxiflora_Kalax.0037s0120 Kalax.0037s0120	scaffold_37	995275	997428	Phytozome		[[Species:|]]"Species:" cannot be used as a page name in this wiki.	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	Sequence	Details
Klaxiflora_Kalax.0037s0120.1 Kalax.0037s0120.1 PAC:32533597	Low	No	1954		Get ORF Coding potential... Type: noncoding Potential: -1.276 Folding energies... MFEI: -24.529 AMFE: -0.706 GC content %: 34.749
Klaxiflora_Kalax.0037s0120.2 Kalax.0037s0120.2 PAC:32533598	High	No	1909		Get ORF Coding potential... Type: noncoding Potential: -1.275 Folding energies... MFEI: -24.568 AMFE: -0.712 GC content %: 34.521

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
Klaxiflora_Kalax.0037s0120.1	RepBase (RepeatMasker)	2014-01-31	Gypsy-36_GM-I

Gene models

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