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
Mtruncatula_MTR_2g090355 [ MTR_2g090355]	2	38456023	38459201	v4	Medicago truncatula (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
Mtruncatula_KEH39129 KEH39129	Low	No	1681	OG0051871		Get ORF Coding potential... Type: noncoding Potential: -1.097 Folding energies... MFEI: -22.302 AMFE: -0.629 GC content %: 35.455
Mtruncatula_KEH39130 KEH39130	Low	No	607	OG0051871		Get ORF Coding potential... Type: noncoding Potential: -0.917 Folding energies... MFEI: -22.471 AMFE: -0.650 GC content %: 34.596

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
Mtruncatula_KEH39129	SwissProt	2021-04-01	Q9FLB0	3.79e-10
Mtruncatula_KEH39130	SwissProt	2021-04-01	P54765	1.19e-5

Gene models

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