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_Pp3c20_5790 Pp3c20_5790	Chr20	3553707	3555455	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_Pp3c20_5790V3.1 Pp3c20_5790V3.1 PAC:32946261	High	No	1749		Get ORF Coding potential... Type: noncoding Potential: -1.150 Folding energies... MFEI: -27.038 AMFE: -0.672 GC content %: 40.252
Ppatens_Pp3c20_5790V3.2 Pp3c20_5790V3.2 PAC:32946262	High	No	630		Get ORF Coding potential... Type: noncoding Potential: -0.897 Folding energies... MFEI: -36.968 AMFE: -0.669 GC content %: 55.238

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_Pp3c20_5790V3.1	RepBase (RepeatMasker)	2014-01-31	DNA-1N_PPa
Ppatens_Pp3c20_5790V3.2	RepBase (RepeatMasker)	2014-01-31	EnSpm1_SB

Gene models

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