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_AL3G27820 [ AL3G27820]	scaffold_3	6426597	6427361	v2.1	Arabidopsis lyrata (Phytozome 13)	Coding? Yes

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_AL3G27820.t1 AL3G27820.t1	Low	No	557	OG0089965		Get ORF Coding potential... Type: noncoding Potential: -0.085 Folding energies... MFEI: -22.406 AMFE: -0.567 GC content %: 39.497
Alyrata_AL3G27820.t3 AL3G27820.t3	Low	No	765	OG0089966		Get ORF Coding potential... Type: noncoding Potential: -0.111 Folding energies... MFEI: -22.288 AMFE: -0.578 GC content %: 38.562

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_AL3G27820.t3	SwissProt	2021-04-01	O22433	2.05e-15
Alyrata_AL3G27820.t1	RepBase (RepeatMasker)	2014-01-31	DNA/hAT-Tag1
Alyrata_AL3G27820.t3	RepBase (RepeatMasker)	2014-01-31	DNA/hAT-Tag1
Alyrata_AL3G27820.t1	SwissProt	2021-04-01	O22433	8.67e-14

Gene models

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