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	Assembly	Species	Details
Stuberosum_PGSC0003DMG400000014 [ PGSC0003DMG400000014]	ST4.03ch01	71644624	71648549	v4.03	Solanum tuberosum (Phytozome 13)	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	Orthologous group	Sequence	Details
Stuberosum_PGSC0003DMT400000047 PGSC0003DMT400000047	Low	No	228	OG0332467		Get ORF Coding potential... Type: noncoding Potential: -0.454 Folding energies... MFEI: -26.754 AMFE: -0.678 GC content %: 39.474
Stuberosum_PGSC0003DMT400000048 PGSC0003DMT400000048	Low	No	330	OG0332468		Get ORF Coding potential... Type: noncoding Potential: -0.291 Folding energies... MFEI: -25.091 AMFE: -0.623 GC content %: 40.303

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_PGSC0003DMT400000047	SwissProt	2021-04-01	Q9LKJ1	1.29e-18
Stuberosum_PGSC0003DMT400000048	SwissProt	2021-04-01	Q9LKJ1	2.51e-29

Gene models

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