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
Taestivum_Traes_2DL_FCB3D9B7E Traes_2DL_FCB3D9B7E	ta_iwgsc_2dl_v1_9908202	20	2105	Phytozome	v2.2	Triticum_aestivum	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	Sequence	Details
Taestivum_Traes_2DL_FCB3D9B7E.1 Traes_2DL_FCB3D9B7E.1 PAC:31913937	Low	No	522		Get ORF Coding potential... Type: noncoding Potential: -0.397 Folding energies... MFEI: -31.398 AMFE: -0.658 GC content %: 47.701
Taestivum_Traes_2DL_FCB3D9B7E.3 Traes_2DL_FCB3D9B7E.3 PAC:31913936	Low	No	867		Get ORF Coding potential... Type: noncoding Potential: -0.367 Folding energies... MFEI: -28.362 AMFE: -0.649 GC content %: 43.714
Taestivum_Traes_2DL_FCB3D9B7E.5 Traes_2DL_FCB3D9B7E.5 PAC:31913939	Low	Yes	1076		Get ORF Coding potential... Type: noncoding Potential: -0.908 Folding energies... MFEI: -28.067 AMFE: -0.674 GC content %: 41.636

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
Taestivum_Traes_2DL_FCB3D9B7E.5	Rfam	11.0	MIR1122	1.9e-7

Gene models

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