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_PGSC0003DMG400000442 PGSC0003DMG400000442	chr11	35903388	35909027	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_PGSC0003DMT400001177 PGSC0003DMT400001177 PAC:24408562	Low	No	5565		Get ORF Coding potential... Type: noncoding Potential: -1.213 Folding energies... MFEI: -24.873 AMFE: -0.678 GC content %: 36.694
Stuberosum_PGSC0003DMT400001178 PGSC0003DMT400001178 PAC:24408563	Low	No	5565		Get ORF Coding potential... Type: noncoding Potential: -1.213 Folding energies... MFEI: -24.873 AMFE: -0.678 GC content %: 36.694

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_PGSC0003DMT400001177	RepBase (RepeatMasker)	2014-01-31	RTE-2_STu
Stuberosum_PGSC0003DMT400001178	RepBase (RepeatMasker)	2014-01-31	RTE-2_STu

Gene models

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