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_Pp3c22_7340 Pp3c22_7340	Chr22	4582630	4584421	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_Pp3c22_7340V3.1 Pp3c22_7340V3.1 PAC:32905017	High	No	1317		Get ORF Coding potential... Type: noncoding Potential: -0.962 Folding energies... MFEI: -32.658 AMFE: -0.676 GC content %: 48.292
Ppatens_Pp3c22_7340V3.2 Pp3c22_7340V3.2 PAC:32905018	High	No	1593		Get ORF Coding potential... Type: noncoding Potential: -0.703 Folding energies... MFEI: -31.764 AMFE: -0.682 GC content %: 46.579
Ppatens_Pp3c22_7340V3.3 Pp3c22_7340V3.3 PAC:32905019	High	No	854		Get ORF Coding potential... Type: noncoding Potential: -1.174 Folding energies... MFEI: -33.267 AMFE: -0.644 GC content %: 51.639

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_Pp3c22_7340V3.1	RepBase (RepeatMasker)	2014-01-31	RTEX-1_CR
Ppatens_Pp3c22_7340V3.2	RepBase (RepeatMasker)	2014-01-31	RTEX-1_CR

Gene models

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