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_Pp3c5_4160 Pp3c5_4160	Chr05	2820785	2823336	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_Pp3c5_4160V3.1 Pp3c5_4160V3.1 PAC:32954665	Low	No	2323		Get ORF Coding potential... Type: noncoding Potential: -0.572 Folding energies... MFEI: -30.280 AMFE: -0.674 GC content %: 44.942
Ppatens_Pp3c5_4160V3.2 Pp3c5_4160V3.2 PAC:32954666	High	No	843		Get ORF Coding potential... Type: noncoding Potential: -1.354 Folding energies... MFEI: -30.071 AMFE: -0.650 GC content %: 46.263

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_Pp3c5_4160V3.1	SwissProt	2015-06-01	Q944H2	3.0e-6

Gene models

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