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_PGSC0003DMG401028118 PGSC0003DMG401028118	chr10	49482045	49486363	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_PGSC0003DMT400072252 PGSC0003DMT400072252 PAC:24410790	Low	No	3358		Get ORF Coding potential... Type: noncoding Potential: -0.296 Folding energies... MFEI: -25.739 AMFE: -0.707 GC content %: 36.420

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_PGSC0003DMT400072252	SwissProt	2015-06-01	P50846	4.0e-10
Stuberosum_PGSC0003DMT400072252	RepBase (RepeatMasker)	2014-01-31	Copia28-VV_I-int

Gene models

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