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.0068s0047 Kalax.0068s0047	scaffold_68	409585	416300	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.0068s0047.1 Kalax.0068s0047.1 PAC:32598194	Low	No	1147		Get ORF Coding potential... Type: noncoding Potential: -0.652 Folding energies... MFEI: -24.821 AMFE: -0.608 GC content %: 40.802
Klaxiflora_Kalax.0068s0047.2 Kalax.0068s0047.2 PAC:32598195	Low	No	494		Get ORF Coding potential... Type: noncoding Potential: -0.364 Folding energies... MFEI: -23.806 AMFE: -0.511 GC content %: 46.559

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.0068s0047.1	RepBase (RepeatMasker)	2014-01-31	Gypsy-27_ST-I
Klaxiflora_Kalax.0068s0047.1	SwissProt	2015-06-01	Q6ZLK0	1.0e-5
Klaxiflora_Kalax.0068s0047.2	SwissProt	2015-06-01	Q6ZLK0	1.0e-6

Gene models

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