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_PGSC0003DMG401012435 PGSC0003DMG401012435	chr07	49015964	49017206	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_PGSC0003DMT400032377 PGSC0003DMT400032377 PAC:24417614	Low	No	487		Get ORF Coding potential... Type: noncoding Potential: -0.871 Folding energies... MFEI: -20.965 AMFE: -0.719 GC content %: 29.158
Stuberosum_PGSC0003DMT400032379 PGSC0003DMT400032379 PAC:24417615	Low	Yes	1243		Get ORF Coding potential... Type: noncoding Potential: -0.946 Folding energies... MFEI: -25.495 AMFE: -0.773 GC content %: 32.985

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_PGSC0003DMT400032379	Rfam	11.0	mir-315	3.9e-4
Stuberosum_PGSC0003DMT400032377	RepBase (RepeatMasker)	2014-01-31	MuDR-3_STu
Stuberosum_PGSC0003DMT400032379	RepBase (RepeatMasker)	2014-01-31	MuDR-3_STu

Gene models

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