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
Ptrichocarpa_Potri.001G198700 Potri.001G198700	Chr01	19221357	19225794	Phytozome	v3.0	Populus_trichocarpa	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
Ptrichocarpa_Potri.001G198700.1 Potri.001G198700.1 PAC:27048281	High	No	983		Get ORF Coding potential... Type: noncoding Potential: -0.687 Folding energies... MFEI: -26.796 AMFE: -0.638 GC content %: 42.014
Ptrichocarpa_Potri.001G198700.2 Potri.001G198700.2 PAC:27048286	Low	No	1137		Get ORF Coding potential... Type: noncoding Potential: -0.866 Folding energies... MFEI: -26.104 AMFE: -0.640 GC content %: 40.809
Ptrichocarpa_Potri.001G198700.3 Potri.001G198700.3 PAC:27048287	Low	No	1064		Get ORF Coding potential... Type: noncoding Potential: -0.777 Folding energies... MFEI: -25.949 AMFE: -0.638 GC content %: 40.695
Ptrichocarpa_Potri.001G198700.4 Potri.001G198700.4 PAC:27048282	High	No	960		Get ORF Coding potential... Type: noncoding Potential: -0.679 Folding energies... MFEI: -25.948 AMFE: -0.639 GC content %: 40.625
Ptrichocarpa_Potri.001G198700.5 Potri.001G198700.5 PAC:27048283	High	No	1116		Get ORF Coding potential... Type: noncoding Potential: -0.712 Folding energies... MFEI: -26.389 AMFE: -0.646 GC content %: 40.860
Ptrichocarpa_Potri.001G198700.6 Potri.001G198700.6 PAC:27048285	Low	No	564		Get ORF Coding potential... Type: noncoding Potential: -0.571 Folding energies... MFEI: -27.145 AMFE: -0.680 GC content %: 39.894
Ptrichocarpa_Potri.001G198700.7 Potri.001G198700.7 PAC:27048284	High	No	904		Get ORF Coding potential... Type: noncoding Potential: -0.665 Folding energies... MFEI: -26.692 AMFE: -0.656 GC content %: 40.708

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
Ptrichocarpa_Potri.001G198700.6	SwissProt	2015-06-01	Q8L9S1	9.0e-6
Ptrichocarpa_Potri.001G198700.2	SwissProt	2015-06-01	Q8L9S1	3.0e-5
Ptrichocarpa_Potri.001G198700.3	SwissProt	2015-06-01	Q8L9S1	5.0e-6

Gene models

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