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_PGSC0003DMG400003621 PGSC0003DMG400003621	chr02	61817957	61825476	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_PGSC0003DMT400009319 PGSC0003DMT400009319 PAC:24427005	Low	No	2504		Get ORF Coding potential... Type: noncoding Potential: -0.977 Folding energies... MFEI: -19.828 AMFE: -0.555 GC content %: 35.703
Stuberosum_PGSC0003DMT400009320 PGSC0003DMT400009320 PAC:24427006	Low	No	1585		Get ORF Coding potential... Type: noncoding Potential: -0.911 Folding energies... MFEI: -18.587 AMFE: -0.526 GC content %: 35.331

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_PGSC0003DMT400009319	SwissProt	2015-06-01	O82663	2.0e-27
Stuberosum_PGSC0003DMT400009320	SwissProt	2015-06-01	O82663	1.0e-27
Stuberosum_PGSC0003DMT400009319	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).