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.1G133100 Seita.1G133100	scaffold_1	12694129	12699287	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.1G133100.1 Seita.1G133100.1 PAC:32696139	Low	No	4287		Get ORF Coding potential... Type: noncoding Potential: -1.097 Folding energies... MFEI: -27.908 AMFE: -0.676 GC content %: 41.288
Sitalica_Seita.1G133100.2 Seita.1G133100.2 PAC:32696140	Low	No	4104		Get ORF Coding potential... Type: noncoding Potential: -1.096 Folding energies... MFEI: -28.124 AMFE: -0.677 GC content %: 41.569

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.1G133100.1	RepBase (RepeatMasker)	2014-01-31	Copia-13_SB-I
Sitalica_Seita.1G133100.2	RepBase (RepeatMasker)	2014-01-31	Copia-13_SB-I

Gene models

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