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_5AL_EF49DF1E8 Traes_5AL_EF49DF1E8	ta_iwgsc_5al_v1_765999	18	3103	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_5AL_EF49DF1E8.2 Traes_5AL_EF49DF1E8.2 PAC:32007712	Low	No	2698		Get ORF Coding potential... Type: noncoding Potential: -0.197 Folding energies... MFEI: -24.396 AMFE: -0.643 GC content %: 37.917
Taestivum_Traes_5AL_EF49DF1E8.3 Traes_5AL_EF49DF1E8.3 PAC:32007714	Low	No	2138		Get ORF Coding potential... Type: noncoding Potential: -0.147 Folding energies... MFEI: -24.294 AMFE: -0.646 GC content %: 37.605
Taestivum_Traes_5AL_EF49DF1E8.4 Traes_5AL_EF49DF1E8.4 PAC:32007713	High	No	2365		Get ORF Coding potential... Type: noncoding Potential: -1.266 Folding energies... MFEI: -23.383 AMFE: -0.651 GC content %: 35.941
Taestivum_Traes_5AL_EF49DF1E8.5 Traes_5AL_EF49DF1E8.5 PAC:32007716	Low	No	2590		Get ORF Coding potential... Type: noncoding Potential: -0.024 Folding energies... MFEI: -24.409 AMFE: -0.648 GC content %: 37.683
Taestivum_Traes_5AL_EF49DF1E8.6 Traes_5AL_EF49DF1E8.6 PAC:32007715	Low	No	2371		Get ORF Coding potential... Type: noncoding Potential: -0.508 Folding energies... MFEI: -24.011 AMFE: -0.640 GC content %: 37.537
Taestivum_Traes_5AL_EF49DF1E8.7 Traes_5AL_EF49DF1E8.7 PAC:32007718	Low	No	2426		Get ORF Coding potential... Type: noncoding Potential: -0.162 Folding energies... MFEI: -24.522 AMFE: -0.651 GC content %: 37.675

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_5AL_EF49DF1E8.5	RepBase (RepeatMasker)	2014-01-31	Gypsy-30_GM-I
Taestivum_Traes_5AL_EF49DF1E8.6	RepBase (RepeatMasker)	2014-01-31	Gypsy-30_GM-I
Taestivum_Traes_5AL_EF49DF1E8.2	RepBase (RepeatMasker)	2014-01-31	Gypsy-30_GM-I

Gene models

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