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_Pp3c22_7490 Pp3c22_7490	Chr22	4671126	4673466	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_Pp3c22_7490V3.1 Pp3c22_7490V3.1 PAC:32904755	High	No	868		Get ORF Coding potential... Type: noncoding Potential: -0.712 Folding energies... MFEI: -26.287 AMFE: -0.627 GC content %: 41.935
Ppatens_Pp3c22_7490V3.2 Pp3c22_7490V3.2 PAC:32904756	High	No	647		Get ORF Coding potential... Type: noncoding Potential: -0.631 Folding energies... MFEI: -28.408 AMFE: -0.647 GC content %: 43.895
Ppatens_Pp3c22_7490V3.3 Pp3c22_7490V3.3 PAC:32904757	High	No	1058		Get ORF Coding potential... Type: noncoding Potential: -0.761 Folding energies... MFEI: -25.180 AMFE: -0.710 GC content %: 35.444
Ppatens_Pp3c22_7490V3.4 Pp3c22_7490V3.4 PAC:32904758	High	No	1322		Get ORF Coding potential... Type: noncoding Potential: -0.810 Folding energies... MFEI: -25.590 AMFE: -0.698 GC content %: 36.687

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_Pp3c22_7490V3.4	RepBase (RepeatMasker)	2014-01-31	Helitron-4N1_SMo
Ppatens_Pp3c22_7490V3.3	RepBase (RepeatMasker)	2014-01-31	Helitron-4N1_SMo

Gene models

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