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_6DL_7D596276D Traes_6DL_7D596276D	ta_iwgsc_6dl_v1_3269464	1095	18930	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_6DL_7D596276D.14 Traes_6DL_7D596276D.14 PAC:31884685	High	No	1062		Get ORF Coding potential... Type: noncoding Potential: -0.815 Folding energies... MFEI: -25.791 AMFE: -0.630 GC content %: 40.960
Taestivum_Traes_6DL_7D596276D.15 Traes_6DL_7D596276D.15 PAC:31884686	Low	No	1116		Get ORF Coding potential... Type: noncoding Potential: -1.062 Folding energies... MFEI: -25.600 AMFE: -0.657 GC content %: 38.978
Taestivum_Traes_6DL_7D596276D.16 Traes_6DL_7D596276D.16 PAC:31884687	High	No	881		Get ORF Coding potential... Type: noncoding Potential: -0.809 Folding energies... MFEI: -26.016 AMFE: -0.628 GC content %: 41.430
Taestivum_Traes_6DL_7D596276D.17 Traes_6DL_7D596276D.17 PAC:31884688	High	No	832		Get ORF Coding potential... Type: noncoding Potential: -1.318 Folding energies... MFEI: -25.096 AMFE: -0.625 GC content %: 40.144
Taestivum_Traes_6DL_7D596276D.18 Traes_6DL_7D596276D.18 PAC:31884689	High	No	665		Get ORF Coding potential... Type: noncoding Potential: -1.305 Folding energies... MFEI: -25.023 AMFE: -0.610 GC content %: 41.053
Taestivum_Traes_6DL_7D596276D.19 Traes_6DL_7D596276D.19 PAC:31884690	High	No	591		Get ORF Coding potential... Type: noncoding Potential: -1.297 Folding energies... MFEI: -23.807 AMFE: -0.596 GC content %: 39.932

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_6DL_7D596276D.15	RepBase (RepeatMasker)	2014-01-31	Copia-11_BD-LTR

Gene models

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