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_Pp3c13_4560 Pp3c13_4560	Chr13	2830532	2834007	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_Pp3c13_4560V3.1 Pp3c13_4560V3.1 PAC:32932207	Low	No	1488		Get ORF Coding potential... Type: noncoding Potential: -0.134 Folding energies... MFEI: -28.656 AMFE: -0.631 GC content %: 45.430
Ppatens_Pp3c13_4560V3.2 Pp3c13_4560V3.2 PAC:32932208	Low	No	3053		Get ORF Coding potential... Type: noncoding Potential: -0.233 Folding energies... MFEI: -28.726 AMFE: -0.650 GC content %: 44.219

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_Pp3c13_4560V3.1	SwissProt	2015-06-01	A9NKD9	9.0e-21
Ppatens_Pp3c13_4560V3.2	SwissProt	2015-06-01	A9NKD9	5.0e-20

Gene models

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