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	Assembly	Species	Details
Bstacei_Brast06G076800 [ Brast06G076800]	Chr06	4669625	4671368	v1.1	Brachypodium stacei (Phytozome 13)	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	Orthologous group	Sequence	Details
Bstacei_Brast06G076800.1 Brast06G076800.1	High	No	1254	OG0017148		Get ORF Coding potential... Type: noncoding Potential: -0.766 Folding energies... MFEI: -23.150 AMFE: -0.471 GC content %: 49.203
Bstacei_Brast06G076800.2 Brast06G076800.2	Low	Yes	1016	OG0017148		Get ORF Coding potential... Type: noncoding Potential: -0.741 Folding energies... MFEI: -22.851 AMFE: -0.435 GC content %: 52.559
Bstacei_Brast06G076800.3 Brast06G076800.3	High	No	929	OG0017148		Get ORF Coding potential... Type: noncoding Potential: -0.732 Folding energies... MFEI: -21.784 AMFE: -0.406 GC content %: 53.714

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
Bstacei_Brast06G076800.2	Rfam	14.6	mir-205	0.0087

Gene models

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