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
Sitalica_Seita.9G309300 Seita.9G309300	scaffold_9	35724334	35728532	Phytozome	v2.2	Setaria_italica	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
Sitalica_Seita.9G309300.1 Seita.9G309300.1 PAC:32687430	Low	No	2382		Get ORF Coding potential... Type: noncoding Potential: -0.956 Folding energies... MFEI: -30.185 AMFE: -0.673 GC content %: 44.836
Sitalica_Seita.9G309300.2 Seita.9G309300.2 PAC:32687433	Low	No	2300		Get ORF Coding potential... Type: noncoding Potential: -1.088 Folding energies... MFEI: -30.087 AMFE: -0.672 GC content %: 44.783
Sitalica_Seita.9G309300.3 Seita.9G309300.3 PAC:32687431	High	No	863		Get ORF Coding potential... Type: noncoding Potential: -0.860 Folding energies... MFEI: -34.728 AMFE: -0.627 GC content %: 55.388
Sitalica_Seita.9G309300.4 Seita.9G309300.4 PAC:32687432	High	No	734		Get ORF Coding potential... Type: noncoding Potential: -0.840 Folding energies... MFEI: -34.087 AMFE: -0.629 GC content %: 54.223

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
Sitalica_Seita.9G309300.2	RepBase (RepeatMasker)	2014-01-31	Helitron-4_ZM
Sitalica_Seita.9G309300.1	RepBase (RepeatMasker)	2014-01-31	Helitron-4_ZM

Gene models

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