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
Gmax_Glyma.02G099600 Glyma.02G099600	Chr02	9366239	9369181	Phytozome	Wm82.a2.v1	Glycine_max	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
Gmax_Glyma.02G099600.1 Glyma.02G099600.1 PAC:30507421	Low	No	844		Get ORF Coding potential... Type: noncoding Potential: -1.172 Folding energies... MFEI: -19.419 AMFE: -0.530 GC content %: 36.611
Gmax_Glyma.02G099600.2 Glyma.02G099600.2 PAC:30507422	High	No	605		Get ORF Coding potential... Type: noncoding Potential: -1.263 Folding energies... MFEI: -18.099 AMFE: -0.517 GC content %: 35.041
Gmax_Glyma.02G099600.3 Glyma.02G099600.3 PAC:30507420	Low	No	759		Get ORF Coding potential... Type: noncoding Potential: -1.159 Folding energies... MFEI: -19.987 AMFE: -0.540 GC content %: 37.022

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
Gmax_Glyma.02G099600.3	RepBase (RepeatMasker)	2014-01-31	Gypsy-155_ZM-I
Gmax_Glyma.02G099600.1	RepBase (RepeatMasker)	2014-01-31	Gypsy-155_ZM-I

Gene models

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