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.10040s0344 Bostr.10040s0344	Scaffold10040	3337610	3338424	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.10040s0344.1 Bostr.10040s0344.1 PAC:30670138	Low	No	633		Get ORF Coding potential... Type: noncoding Potential: -1.038 Folding energies... MFEI: -26.430 AMFE: -0.593 GC content %: 44.550
Bstricta_Bostr.10040s0344.2 Bostr.10040s0344.2 PAC:30670139	Low	No	627		Get ORF Coding potential... Type: noncoding Potential: -1.037 Folding energies... MFEI: -26.523 AMFE: -0.594 GC content %: 44.657

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.10040s0344.1	RepBase (RepeatMasker)	2014-01-31	MuDR-1_FV
Bstricta_Bostr.10040s0344.2	RepBase (RepeatMasker)	2014-01-31	MuDR-1_FV
Bstricta_Bostr.10040s0344.2	SwissProt	2015-06-01	Q54F15	6.0e-4

Gene models

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