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_D82F66A9D Traes_1AL_D82F66A9D	ta_iwgsc_1al_v2_3874114	1878	5370	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_1AL_D82F66A9D.5 Traes_1AL_D82F66A9D.5 PAC:31967866	Low	No	1262		Get ORF Coding potential... Type: noncoding Potential: -0.760 Folding energies... MFEI: -33.542 AMFE: -0.622 GC content %: 53.962
Taestivum_Traes_1AL_D82F66A9D.6 Traes_1AL_D82F66A9D.6 PAC:31967867	High	No	1201		Get ORF Coding potential... Type: noncoding Potential: -0.751 Folding energies... MFEI: -34.013 AMFE: -0.617 GC content %: 55.121
Taestivum_Traes_1AL_D82F66A9D.7 Traes_1AL_D82F66A9D.7 PAC:31967869	High	No	1441		Get ORF Coding potential... Type: noncoding Potential: -0.879 Folding energies... MFEI: -31.506 AMFE: -0.637 GC content %: 49.480
Taestivum_Traes_1AL_D82F66A9D.8 Traes_1AL_D82F66A9D.8 PAC:31967868	High	No	1564		Get ORF Coding potential... Type: noncoding Potential: -0.956 Folding energies... MFEI: -24.284 AMFE: -0.611 GC content %: 39.770
Taestivum_Traes_1AL_D82F66A9D.9 Traes_1AL_D82F66A9D.9 PAC:31967870	High	No	903		Get ORF Coding potential... Type: noncoding Potential: -0.855 Folding energies... MFEI: -34.053 AMFE: -0.595 GC content %: 57.254

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_D82F66A9D.5	RepBase (RepeatMasker)	2014-01-31	Copia-11_BD-I

Gene models

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