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_PGSC0003DMG400003634 PGSC0003DMG400003634	chr02	61569810	61575349	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_PGSC0003DMT400009346 PGSC0003DMT400009346 PAC:24426908	Low	No	837		Get ORF Coding potential... Type: noncoding Potential: -1.268 Folding energies... MFEI: -21.493 AMFE: -0.575 GC content %: 37.395
Stuberosum_PGSC0003DMT400009347 PGSC0003DMT400009347 PAC:24426909	Low	No	1413		Get ORF Coding potential... Type: noncoding Potential: -1.305 Folding energies... MFEI: -20.498 AMFE: -0.567 GC content %: 36.164

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_PGSC0003DMT400009346	SwissProt	2015-06-01	O82793	3.0e-8
Stuberosum_PGSC0003DMT400009347	SwissProt	2015-06-01	O82793	2.0e-8
Stuberosum_PGSC0003DMT400009346	RepBase (RepeatMasker)	2014-01-31	GYPSODE1_LTR
Stuberosum_PGSC0003DMT400009347	RepBase (RepeatMasker)	2014-01-31	GYPSODE1_LTR

Gene models

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