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.0016s0250 Kalax.0016s0250	scaffold_16	1804587	1810183	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.0016s0250.1 Kalax.0016s0250.1 PAC:32582076	Low	Yes	1557		Get ORF Coding potential... Type: noncoding Potential: -1.126 Folding energies... MFEI: -27.675 AMFE: -0.698 GC content %: 39.627
Klaxiflora_Kalax.0016s0250.2 Kalax.0016s0250.2 PAC:32582077	High	No	1445		Get ORF Coding potential... Type: noncoding Potential: -1.115 Folding energies... MFEI: -28.180 AMFE: -0.661 GC content %: 42.630

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.0016s0250.1	Rfam	11.0	MIR167_1	0.0036

Gene models

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