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.2299s0001 Kalax.2299s0001	scaffold_2299	66	1672	Phytozome		[[Species:|]]"Species:" cannot be used as a page name in this wiki.	Coding? Yes

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.2299s0001.2 Kalax.2299s0001.2 PAC:32540682	High	No	440		Get ORF Coding potential... Type: noncoding Potential: -0.499 Folding energies... MFEI: -27.136 AMFE: -0.594 GC content %: 45.682
Klaxiflora_Kalax.2299s0001.3 Kalax.2299s0001.3 PAC:32540681	Low	No	706		Get ORF Coding potential... Type: noncoding Potential: -0.835 Folding energies... MFEI: -26.062 AMFE: -0.634 GC content %: 41.076
Klaxiflora_Kalax.2299s0001.4 Kalax.2299s0001.4 PAC:32540683	High	No	670		Get ORF Coding potential... Type: noncoding Potential: -0.742 Folding energies... MFEI: -26.060 AMFE: -0.630 GC content %: 41.343

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.2299s0001.3	SwissProt	2015-06-01	Q9UHR6	6.0e-9

Gene models

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