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_PGSC0003DMG400029287 PGSC0003DMG400029287	chr12	64566580	64570376	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_PGSC0003DMT400075306 PGSC0003DMT400075306 PAC:24379075	Low	No	727		Get ORF Coding potential... Type: noncoding Potential: -0.926 Folding energies... MFEI: -20.303 AMFE: -0.586 GC content %: 34.663
Stuberosum_PGSC0003DMT400075310 PGSC0003DMT400075310 PAC:24379076	Low	No	1556		Get ORF Coding potential... Type: noncoding Potential: -1.091 Folding energies... MFEI: -24.158 AMFE: -0.637 GC content %: 37.918

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_PGSC0003DMT400075306	SwissProt	2015-06-01	Q2MIC5	2.0e-8
Stuberosum_PGSC0003DMT400075310	RepBase (RepeatMasker)	2014-01-31	SINE2-2_STu

Gene models

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