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
Onivara_ONIVA11G23120 [ ONIVA11G23120]	11	24199681	24208686	v1	Oryza nivara (Ensembl Plants 51)	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
Onivara_ONIVA11G23120.1 ONIVA11G23120.1	High	No	887	OG0262335		Get ORF Coding potential... Type: noncoding Potential: -1.570 Folding energies... MFEI: -22.773 AMFE: -0.579 GC content %: 39.346
Onivara_ONIVA11G23120.2 ONIVA11G23120.2	Low	No	1919	OG0021052		Get ORF Coding potential... Type: noncoding Potential: -0.522 Folding energies... MFEI: -28.338 AMFE: -0.642 GC content %: 44.138
Onivara_ONIVA11G23120.3 ONIVA11G23120.3	Low	No	2334	OG0021052		Get ORF Coding potential... Type: noncoding Potential: -0.523 Folding energies... MFEI: -28.209 AMFE: -0.644 GC content %: 43.830

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
Onivara_ONIVA11G23120.2	SwissProt	2021-04-01	P0C5B3	1.82e-18
Onivara_ONIVA11G23120.3	SwissProt	2021-04-01	P0C5B3	2.23e-18

Gene models

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