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_1AL_9092735FA Traes_1AL_9092735FA	ta_iwgsc_1al_v2_3925625	293	3912	Phytozome	v2.2	Triticum_aestivum	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
Taestivum_Traes_1AL_9092735FA.1 Traes_1AL_9092735FA.1 PAC:31893849	High	No	946		Get ORF Coding potential... Type: noncoding Potential: -1.001 Folding energies... MFEI: -28.858 AMFE: -0.625 GC content %: 46.195
Taestivum_Traes_1AL_9092735FA.2 Traes_1AL_9092735FA.2 PAC:31893846	Low	No	799		Get ORF Coding potential... Type: noncoding Potential: -1.161 Folding energies... MFEI: -30.651 AMFE: -0.706 GC content %: 43.429
Taestivum_Traes_1AL_9092735FA.3 Traes_1AL_9092735FA.3 PAC:31893847	High	No	676		Get ORF Coding potential... Type: noncoding Potential: -1.273 Folding energies... MFEI: -30.902 AMFE: -0.627 GC content %: 49.260
Taestivum_Traes_1AL_9092735FA.4 Traes_1AL_9092735FA.4 PAC:31893848	High	No	747		Get ORF Coding potential... Type: noncoding Potential: -0.962 Folding energies... MFEI: -28.086 AMFE: -0.605 GC content %: 46.452
Taestivum_Traes_1AL_9092735FA.5 Traes_1AL_9092735FA.5 PAC:31893850	High	No	847		Get ORF Coding potential... Type: noncoding Potential: -1.042 Folding energies... MFEI: -28.442 AMFE: -0.639 GC content %: 44.510
Taestivum_Traes_1AL_9092735FA.6 Traes_1AL_9092735FA.6 PAC:31893845	Low	No	1156		Get ORF Coding potential... Type: noncoding Potential: -0.999 Folding energies... MFEI: -30.848 AMFE: -0.708 GC content %: 43.599

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_1AL_9092735FA.2	RepBase (RepeatMasker)	2014-01-31	LINE1-8_OS
Taestivum_Traes_1AL_9092735FA.6	RepBase (RepeatMasker)	2014-01-31	LINE1-8_OS

Gene models

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