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_24060 Pp3c2_24060	Chr02	16145923	16147452	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_24060V3.1 Pp3c2_24060V3.1 PAC:32936049	High	No	361		Get ORF Coding potential... Type: noncoding Potential: -1.013 Folding energies... MFEI: -30.222 AMFE: -0.649 GC content %: 46.537
Ppatens_Pp3c2_24060V3.2 Pp3c2_24060V3.2 PAC:32936051	High	No	893		Get ORF Coding potential... Type: noncoding Potential: -1.233 Folding energies... MFEI: -27.189 AMFE: -0.731 GC content %: 37.178
Ppatens_Pp3c2_24060V3.3 Pp3c2_24060V3.3 PAC:32936050	High	No	1269		Get ORF Coding potential... Type: noncoding Potential: -1.275 Folding energies... MFEI: -28.668 AMFE: -0.715 GC content %: 40.110

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_24060V3.2	RepBase (RepeatMasker)	2014-01-31	EnSpm6_SB
Ppatens_Pp3c2_24060V3.3	RepBase (RepeatMasker)	2014-01-31	EnSpm6_SB

Gene models

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