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_Pp3c2_5150 Pp3c2_5150	Chr02	3463834	3466064	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_Pp3c2_5150V3.1 Pp3c2_5150V3.1 PAC:32936494	High	No	1083		Get ORF Coding potential... Type: noncoding Potential: -1.260 Folding energies... MFEI: -30.157 AMFE: -0.624 GC content %: 48.292
Ppatens_Pp3c2_5150V3.2 Pp3c2_5150V3.2 PAC:32936492	High	No	273		Get ORF Coding potential... Type: noncoding Potential: -1.173 Folding energies... MFEI: -19.597 AMFE: -0.425 GC content %: 46.154
Ppatens_Pp3c2_5150V3.3 Pp3c2_5150V3.3 PAC:32936493	High	No	1874		Get ORF Coding potential... Type: noncoding Potential: -1.108 Folding energies... MFEI: -27.508 AMFE: -0.623 GC content %: 44.184

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_Pp3c2_5150V3.1	RepBase (RepeatMasker)	2014-01-31	Gypsy-12_PPa-I
Ppatens_Pp3c2_5150V3.3	RepBase (RepeatMasker)	2014-01-31	Gypsy-12_PPa-I

Gene models

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