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_PGSC0003DMG401003620 PGSC0003DMG401003620	chr02	61832877	61836562	Phytozome	v3.4	Solanum_tuberosum	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
Stuberosum_PGSC0003DMT400009315 PGSC0003DMT400009315 PAC:24425036	Low	No	3458		Get ORF Coding potential... Type: noncoding Potential: -0.993 Folding energies... MFEI: -21.070 AMFE: -0.624 GC content %: 33.777
Stuberosum_PGSC0003DMT400009316 PGSC0003DMT400009316 PAC:24425035	Low	No	1276		Get ORF Coding potential... Type: noncoding Potential: -0.760 Folding energies... MFEI: -21.176 AMFE: -0.651 GC content %: 32.524

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_PGSC0003DMT400009315	SwissProt	2015-06-01	O64989	4.0e-18
Stuberosum_PGSC0003DMT400009316	SwissProt	2015-06-01	O64989	3.0e-4
Stuberosum_PGSC0003DMT400009315	RepBase (RepeatMasker)	2014-01-31	TS2

Gene models

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