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_Pp3c12_3980 Pp3c12_3980	Chr12	3023283	3025082	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_Pp3c12_3980V3.1 Pp3c12_3980V3.1 PAC:32974357	High	No	1529		Get ORF Coding potential... Type: noncoding Potential: -1.109 Folding energies... MFEI: -28.339 AMFE: -0.657 GC content %: 43.165
Ppatens_Pp3c12_3980V3.2 Pp3c12_3980V3.2 PAC:32974358	High	No	278		Get ORF Coding potential... Type: noncoding Potential: -0.952 Folding energies... MFEI: -24.245 AMFE: -0.562 GC content %: 43.165

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_Pp3c12_3980V3.1	RepBase (RepeatMasker)	2014-01-31	MARINER2_MT

Gene models

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