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.J02206 Brara.J02206	A10	16648422	16649859	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.J02206.1 Brara.J02206.1 PAC:30612362	Low	No	1103		Get ORF Coding potential... Type: noncoding Potential: -1.053 Folding energies... MFEI: -20.925 AMFE: -0.603 GC content %: 34.723
BrapaFPsc_Brara.J02206.2 Brara.J02206.2 PAC:30612361	Low	No	1043		Get ORF Coding potential... Type: noncoding Potential: -1.045 Folding energies... MFEI: -20.920 AMFE: -0.608 GC content %: 34.420

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.J02206.1	RepBase (RepeatMasker)	2014-01-31	Helitron-1_EPa
BrapaFPsc_Brara.J02206.2	RepBase (RepeatMasker)	2014-01-31	Helitron-1_EPa

Gene models

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