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_PGSC0003DMG400008073 PGSC0003DMG400008073	chr11	38153277	38155532	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_PGSC0003DMT400020855 PGSC0003DMT400020855 PAC:24409070	Low	No	2255		Get ORF Coding potential... Type: noncoding Potential: -1.343 Folding energies... MFEI: -19.064 AMFE: -0.734 GC content %: 25.987
Stuberosum_PGSC0003DMT400020856 PGSC0003DMT400020856 PAC:24409071	High	No	338		Get ORF Coding potential... Type: noncoding Potential: -0.939 Folding energies... MFEI: -19.112 AMFE: -0.593 GC content %: 32.249

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_PGSC0003DMT400020855	RepBase (RepeatMasker)	2014-01-31	DNA-TA-2_STu

Gene models

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