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.30275s0186 Bostr.30275s0186	Scaffold30275	1152620	1155584	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.30275s0186.1 Bostr.30275s0186.1 PAC:30665416	High	No	349		Get ORF Coding potential... Type: noncoding Potential: -1.031 Folding energies... MFEI: -26.132 AMFE: -0.512 GC content %: 51.003
Bstricta_Bostr.30275s0186.2 Bostr.30275s0186.2 PAC:30665417	Low	No	1918		Get ORF Coding potential... Type: noncoding Potential: -1.193 Folding energies... MFEI: -25.016 AMFE: -0.621 GC content %: 40.302

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.30275s0186.2	SwissProt	2015-06-01	Q3EAZ3	2.0e-8

Gene models

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