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.001G338500 Potri.001G338500	Chr01	34215563	34216936	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.001G338500.1 Potri.001G338500.1 PAC:27043919	Low	No	544		Get ORF Coding potential... Type: noncoding Potential: -0.623 Folding energies... MFEI: -26.415 AMFE: -0.611 GC content %: 43.199
Ptrichocarpa_Potri.001G338500.2 Potri.001G338500.2 PAC:27043920	Low	No	735		Get ORF Coding potential... Type: noncoding Potential: -0.799 Folding energies... MFEI: -23.184 AMFE: -0.546 GC content %: 42.449

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.001G338500.1	SwissProt	2015-06-01	Q8GYN5	2.0e-6
Ptrichocarpa_Potri.001G338500.2	SwissProt	2015-06-01	Q8GYN5	6.0e-6

Gene models

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