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_Pp3c3_2650 Pp3c3_2650	Chr03	1528801	1529471	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_Pp3c3_2650V3.1 Pp3c3_2650V3.1 PAC:32942307	High	No	303		Get ORF Coding potential... Type: noncoding Potential: -0.755 Folding energies... MFEI: -25.248 AMFE: -0.659 GC content %: 38.284
Ppatens_Pp3c3_2650V3.2 Pp3c3_2650V3.2 PAC:32942308	High	No	671		Get ORF Coding potential... Type: noncoding Potential: -0.879 Folding energies... MFEI: -24.009 AMFE: -0.668 GC content %: 35.917

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_Pp3c3_2650V3.2	RepBase (RepeatMasker)	2014-01-31	HELITRON7_OS

Gene models

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