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
Bstricta_Bostr.13083s0056 Bostr.13083s0056	Scaffold13083	649931	654990	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
Bstricta_Bostr.13083s0056.1 Bostr.13083s0056.1 PAC:30664285	Low	No	1775		Get ORF Coding potential... Type: noncoding Potential: -1.035 Folding energies... MFEI: -26.541 AMFE: -0.587 GC content %: 45.239
Bstricta_Bostr.13083s0056.2 Bostr.13083s0056.2 PAC:30664284	Low	No	1689		Get ORF Coding potential... Type: noncoding Potential: -1.027 Folding energies... MFEI: -26.477 AMFE: -0.580 GC content %: 45.648

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
Bstricta_Bostr.13083s0056.2	RepBase (RepeatMasker)	2014-01-31	Gypsy-21_BRa-I
Bstricta_Bostr.13083s0056.1	RepBase (RepeatMasker)	2014-01-31	Gypsy-21_BRa-I

Gene models

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