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
Alyrata_AL1G49310 [ AL1G49310]	scaffold_1	16563669	16567959	v2.1	Arabidopsis lyrata (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
Alyrata_AL1G49310.t1 AL1G49310.t1	Low	No	828	OG0027068		Get ORF Coding potential... Type: noncoding Potential: -1.178 Folding energies... MFEI: -29.167 AMFE: -0.660 GC content %: 44.203
Alyrata_AL1G49310.t2 AL1G49310.t2	Low	Yes	2056	OG0027068		Get ORF Coding potential... Type: noncoding Potential: -0.966 Folding energies... MFEI: -26.999 AMFE: -0.690 GC content %: 39.154

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
Alyrata_AL1G49310.t1	SwissProt	2021-04-01	Q8LFN2	2.08e-5
Alyrata_AL1G49310.t2	SwissProt	2021-04-01	Q9M9S4	3.54e-6
Alyrata_AL1G49310.t2	Rfam	14.6	MIR167_1	6.6e-9
Alyrata_AL1G49310.t2	RepBase (RepeatMasker)	2014-01-31	LTR/Gypsy

Gene models

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