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_PGSC0003DMG400028366 [ PGSC0003DMG400028366]	ST4.03ch05	639134	640509	v4.03	Solanum tuberosum (Phytozome 13)	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	Orthologous group	Sequence	Details
Stuberosum_PGSC0003DMT400072909 PGSC0003DMT400072909	Low	No	339	OG0059295		Get ORF Coding potential... Type: noncoding Potential: -0.534 Folding energies... MFEI: -29.381 AMFE: -0.586 GC content %: 50.147
Stuberosum_PGSC0003DMT400072910 PGSC0003DMT400072910	Low	No	339	OG0059295		Get ORF Coding potential... Type: noncoding Potential: -0.534 Folding energies... MFEI: -29.381 AMFE: -0.586 GC content %: 50.147

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_PGSC0003DMT400072909	SwissProt	2021-04-01	B3H4F1	3.63e-24
Stuberosum_PGSC0003DMT400072910	SwissProt	2021-04-01	B3H4F1	3.63e-24

Gene models

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