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_Pp3c20_13100 Pp3c20_13100	Chr20	8573591	8577227	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_Pp3c20_13100V3.1 Pp3c20_13100V3.1 PAC:32946661	High	No	2439		Get ORF Coding potential... Type: noncoding Potential: -1.213 Folding energies... MFEI: -22.829 AMFE: -0.724 GC content %: 31.529
Ppatens_Pp3c20_13100V3.2 Pp3c20_13100V3.2 PAC:32946662	High	No	3249		Get ORF Coding potential... Type: noncoding Potential: -1.240 Folding energies... MFEI: -23.783 AMFE: -0.701 GC content %: 33.949
Ppatens_Pp3c20_13100V3.3 Pp3c20_13100V3.3 PAC:32946663	High	No	3275		Get ORF Coding potential... Type: noncoding Potential: -1.251 Folding energies... MFEI: -23.863 AMFE: -0.702 GC content %: 33.985
Ppatens_Pp3c20_13100V3.4 Pp3c20_13100V3.4 PAC:32946664	High	No	1469		Get ORF Coding potential... Type: noncoding Potential: -1.164 Folding energies... MFEI: -24.860 AMFE: -0.674 GC content %: 36.896
Ppatens_Pp3c20_13100V3.5 Pp3c20_13100V3.5 PAC:32946665	High	No	1696		Get ORF Coding potential... Type: noncoding Potential: -1.184 Folding energies... MFEI: -26.250 AMFE: -0.638 GC content %: 41.156

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_Pp3c20_13100V3.1	RepBase (RepeatMasker)	2014-01-31	MuDR-6_GM
Ppatens_Pp3c20_13100V3.2	RepBase (RepeatMasker)	2014-01-31	MuDR-6_GM
Ppatens_Pp3c20_13100V3.3	RepBase (RepeatMasker)	2014-01-31	MuDR-6_GM

Gene models

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