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_Pp3c13_18410 Pp3c13_18410	Chr13	13100483	13102262	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_Pp3c13_18410V3.1 Pp3c13_18410V3.1 PAC:32931699	High	No	231		Get ORF Coding potential... Type: noncoding Potential: -1.493 Folding energies... MFEI: -25.628 AMFE: -0.592 GC content %: 43.290
Ppatens_Pp3c13_18410V3.2 Pp3c13_18410V3.2 PAC:32931700	High	No	1597		Get ORF Coding potential... Type: noncoding Potential: -1.378 Folding energies... MFEI: -24.358 AMFE: -0.597 GC content %: 40.827

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_Pp3c13_18410V3.1	RepBase (RepeatMasker)	2014-01-31	Copia-40_Pru-I
Ppatens_Pp3c13_18410V3.2	RepBase (RepeatMasker)	2014-01-31	Copia-40_Pru-I

Gene models

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