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.0293s0004 Kalax.0293s0004	scaffold_293	39546	41985	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.0293s0004.1 Kalax.0293s0004.1 PAC:32550228	Low	No	2321		Get ORF Coding potential... Type: noncoding Potential: -0.857 Folding energies... MFEI: -24.468 AMFE: -0.666 GC content %: 36.751
Klaxiflora_Kalax.0293s0004.2 Kalax.0293s0004.2 PAC:32550229	Low	No	2242		Get ORF Coding potential... Type: noncoding Potential: -0.788 Folding energies... MFEI: -24.723 AMFE: -0.672 GC content %: 36.798

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.0293s0004.2	RepBase (RepeatMasker)	2014-01-31	Copia-30-I_VV
Klaxiflora_Kalax.0293s0004.1	RepBase (RepeatMasker)	2014-01-31	Copia-30-I_VV

Gene models

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