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_Pp3c14_13450 Pp3c14_13450	Chr14	8573678	8574286	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_Pp3c14_13450V3.1 Pp3c14_13450V3.1 PAC:32961671	Low	No	366		Get ORF Coding potential... Type: noncoding Potential: -0.618 Folding energies... MFEI: -16.557 AMFE: -0.638 GC content %: 25.956
Ppatens_Pp3c14_13450V3.2 Pp3c14_13450V3.2 PAC:32961672	Low	No	360		Get ORF Coding potential... Type: noncoding Potential: -0.622 Folding energies... MFEI: -16.556 AMFE: -0.634 GC content %: 26.111

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_Pp3c14_13450V3.1	RepBase (RepeatMasker)	2014-01-31	Copia-64_VV-I
Ppatens_Pp3c14_13450V3.2	RepBase (RepeatMasker)	2014-01-31	Copia-64_VV-I
Ppatens_Pp3c14_13450V3.1	SwissProt	2015-06-01	P10978	3.0e-6
Ppatens_Pp3c14_13450V3.2	SwissProt	2015-06-01	P10978	1.0e-4

Gene models

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