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
Stuberosum_PGSC0003DMG400014737 PGSC0003DMG400014737	chr01	5951882	5954110	Phytozome	v3.4	Solanum_tuberosum	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
Stuberosum_PGSC0003DMT400038210 PGSC0003DMT400038210 PAC:24423347	High	No	835		Get ORF Coding potential... Type: noncoding Potential: -1.293 Folding energies... MFEI: -22.647 AMFE: -0.641 GC content %: 35.329
Stuberosum_PGSC0003DMT400038212 PGSC0003DMT400038212 PAC:24423348	Low	No	2229		Get ORF Coding potential... Type: noncoding Potential: -1.253 Folding energies... MFEI: -22.607 AMFE: -0.678 GC content %: 33.333

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
Stuberosum_PGSC0003DMT400038212	RepBase (RepeatMasker)	2014-01-31	HarbN_I

Gene models

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