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
BrapaFPsc_Brara.A01668 Brara.A01668	A01	9332350	9333271	Phytozome		[[Species:|]]"Species:" cannot be used as a page name in this wiki.	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
BrapaFPsc_Brara.A01668.1 Brara.A01668.1 PAC:30638545	Low	No	716		Get ORF Coding potential... Type: noncoding Potential: -0.430 Folding energies... MFEI: -25.880 AMFE: -0.635 GC content %: 40.782
BrapaFPsc_Brara.A01668.2 Brara.A01668.2 PAC:30638546	Low	No	709		Get ORF Coding potential... Type: noncoding Potential: -0.427 Folding energies... MFEI: -26.135 AMFE: -0.637 GC content %: 41.044

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
BrapaFPsc_Brara.A01668.1	SwissProt	2015-06-01	Q08747	1.0e-8
BrapaFPsc_Brara.A01668.2	SwissProt	2015-06-01	Q08747	5.0e-9

Gene models

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