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_Pp3c16_6930 Pp3c16_6930	Chr16	4384666	4387996	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_Pp3c16_6930V3.1 Pp3c16_6930V3.1 PAC:32986589	High	No	1651		Get ORF Coding potential... Type: noncoding Potential: -1.161 Folding energies... MFEI: -26.933 AMFE: -0.660 GC content %: 40.824
Ppatens_Pp3c16_6930V3.2 Pp3c16_6930V3.2 PAC:32986590	High	No	2251		Get ORF Coding potential... Type: noncoding Potential: -1.066 Folding energies... MFEI: -29.110 AMFE: -0.650 GC content %: 44.780

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_Pp3c16_6930V3.2	RepBase (RepeatMasker)	2014-01-31	Gypsy-13_Mad-I
Ppatens_Pp3c16_6930V3.1	RepBase (RepeatMasker)	2014-01-31	Gypsy-13_Mad-I

Gene models

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