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	Source	Assembly	Species	Details
Mtruncatula_Medtr4g131150 Medtr4g131150	chr4	54704652	54706631	Phytozome	Mt4.0v1	Medicago_truncatula	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	Sequence	Details
Mtruncatula_Medtr4g131150.1 Medtr4g131150.1 PAC:31108639	High	No	857		Get ORF Coding potential... Type: noncoding Potential: -0.558 Folding energies... MFEI: -24.854 AMFE: -0.642 GC content %: 38.740
Mtruncatula_Medtr4g131150.2 Medtr4g131150.2 PAC:31108638	Low	No	1421		Get ORF Coding potential... Type: noncoding Potential: -0.651 Folding energies... MFEI: -24.272 AMFE: -0.652 GC content %: 37.227

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_Medtr4g131150.2	RepBase (RepeatMasker)	2014-01-31	Sat-1_CPa

Gene models

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