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
Athaliana_AT3G05035 AT3G05035	Chr3	1398717	1399887	v11	Arabidopsis thaliana (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
Athaliana_AT3G05035.1 AT3G05035.1	Low	No	403	OG0065857		Get ORF Coding potential... Type: noncoding Potential: -0.841 Folding energies... MFEI: -27.692 AMFE: -0.660 GC content %: 41.935
Athaliana_AT3G05035.2 AT3G05035.2	High	No	574	OG0024042		Get ORF Coding potential... Type: noncoding Potential: -0.745 Folding energies... MFEI: -23.589 AMFE: -0.657 GC content %: 35.889
Athaliana_AT3G05035.3 AT3G05035.3	High	No	573	OG0024042		Get ORF Coding potential... Type: noncoding Potential: -0.745 Folding energies... MFEI: -24.031 AMFE: -0.662 GC content %: 36.300

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
Athaliana_AT3G05035.1	SwissProt	2021-04-01	Q0WP44	5.73e-5

Gene models

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