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_PGSC0003DMG400002682 PGSC0003DMG400002682	chr09	8152959	8156135	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_PGSC0003DMT400006914 PGSC0003DMT400006914 PAC:24399837	High	No	279		Get ORF Coding potential... Type: noncoding Potential: -0.393 Folding energies... MFEI: -15.842 AMFE: -0.460 GC content %: 34.409
Stuberosum_PGSC0003DMT400006915 PGSC0003DMT400006915 PAC:24399836	Low	No	585		Get ORF Coding potential... Type: noncoding Potential: -0.345 Folding energies... MFEI: -15.915 AMFE: -0.571 GC content %: 27.863
Stuberosum_PGSC0003DMT400006916 PGSC0003DMT400006916 PAC:24399838	Low	No	993		Get ORF Coding potential... Type: noncoding Potential: -0.836 Folding energies... MFEI: -17.462 AMFE: -0.635 GC content %: 27.492

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_PGSC0003DMT400006915	SwissProt	2015-06-01	Q8LA14	7.0e-10
Stuberosum_PGSC0003DMT400006916	SwissProt	2015-06-01	Q8LA14	2.0e-7

Gene models

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