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_PGSC0003DMG400003625 PGSC0003DMG400003625	chr02	61763126	61766770	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_PGSC0003DMT400009327 PGSC0003DMT400009327 PAC:24427397	Low	No	531		Get ORF Coding potential... Type: noncoding Potential: -1.248 Folding energies... MFEI: -21.488 AMFE: -0.568 GC content %: 37.853
Stuberosum_PGSC0003DMT400009328 PGSC0003DMT400009328 PAC:24427396	Low	No	1997		Get ORF Coding potential... Type: noncoding Potential: -1.312 Folding energies... MFEI: -24.642 AMFE: -0.653 GC content %: 37.757

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_PGSC0003DMT400009327	RepBase (RepeatMasker)	2014-01-31	SINE2-1_STu
Stuberosum_PGSC0003DMT400009328	RepBase (RepeatMasker)	2014-01-31	SINE2-1_STu

Gene models

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