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
Ppatens_Pp3c23_12840 Pp3c23_12840	Chr23	8626233	8630950	Phytozome	v3.3	Physcomitrella_patens	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
Ppatens_Pp3c23_12840V3.1 Pp3c23_12840V3.1 PAC:32948759	High	No	1958		Get ORF Coding potential... Type: noncoding Potential: -1.337 Folding energies... MFEI: -29.775 AMFE: -0.667 GC content %: 44.637
Ppatens_Pp3c23_12840V3.2 Pp3c23_12840V3.2 PAC:32948760	High	No	3537		Get ORF Coding potential... Type: noncoding Potential: -1.135 Folding energies... MFEI: -30.455 AMFE: -0.677 GC content %: 44.982

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
Ppatens_Pp3c23_12840V3.2	RepBase (RepeatMasker)	2014-01-31	ATLINE1_6

Gene models

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