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.1G038400 Seita.1G038400	scaffold_1	3785806	3788192	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.1G038400.1 Seita.1G038400.1 PAC:32696781	Low	Yes	2174		Get ORF Coding potential... Type: noncoding Potential: -1.242 Folding energies... MFEI: -32.015 AMFE: -0.714 GC content %: 44.848
Sitalica_Seita.1G038400.2 Seita.1G038400.2 PAC:32696782	Low	Yes	2116		Get ORF Coding potential... Type: noncoding Potential: -1.264 Folding energies... MFEI: -31.961 AMFE: -0.716 GC content %: 44.660

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.1G038400.2	RepBase (RepeatMasker)	2014-01-31	STOWAWAY1_SB
Sitalica_Seita.1G038400.1	Rfam	11.0	MIR1122	9.9e-6
Sitalica_Seita.1G038400.2	Rfam	11.0	MIR1122	9.7e-6
Sitalica_Seita.1G038400.1	RepBase (RepeatMasker)	2014-01-31	STOWAWAY1_SB

Gene models

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