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_PGSC0003DMG400023973 PGSC0003DMG400023973	chr11	6603233	6608349	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_PGSC0003DMT400061582 PGSC0003DMT400061582 PAC:24408379	Low	No	2942		Get ORF Coding potential... Type: noncoding Potential: -0.035 Folding energies... MFEI: -24.194 AMFE: -0.672 GC content %: 36.030
Stuberosum_PGSC0003DMT400061583 PGSC0003DMT400061583 PAC:24408380	High	No	2070		Get ORF Coding potential... Type: noncoding Potential: -0.983 Folding energies... MFEI: -23.493 AMFE: -0.638 GC content %: 36.812
Stuberosum_PGSC0003DMT400061584 PGSC0003DMT400061584 PAC:24408377	High	No	878		Get ORF Coding potential... Type: noncoding Potential: -1.242 Folding energies... MFEI: -25.262 AMFE: -0.670 GC content %: 37.699

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_PGSC0003DMT400061582	SwissProt	2015-06-01	Q9CQF6	3.0e-10

Gene models

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