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_6BL_34565B900 Traes_6BL_34565B900	ta_iwgsc_6bl_v1_2590901	3	3846	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_6BL_34565B900.1 Traes_6BL_34565B900.1 PAC:32021745	High	No	944		Get ORF Coding potential... Type: noncoding Potential: -0.907 Folding energies... MFEI: -32.235 AMFE: -0.667 GC content %: 48.305
Taestivum_Traes_6BL_34565B900.2 Traes_6BL_34565B900.2 PAC:32021744	Low	No	1468		Get ORF Coding potential... Type: noncoding Potential: -0.810 Folding energies... MFEI: -30.668 AMFE: -0.668 GC content %: 45.913
Taestivum_Traes_6BL_34565B900.3 Traes_6BL_34565B900.3 PAC:32021746	Low	No	1281		Get ORF Coding potential... Type: noncoding Potential: -0.937 Folding energies... MFEI: -31.085 AMFE: -0.674 GC content %: 46.136
Taestivum_Traes_6BL_34565B900.4 Traes_6BL_34565B900.4 PAC:32021747	High	No	909		Get ORF Coding potential... Type: noncoding Potential: -0.873 Folding energies... MFEI: -25.897 AMFE: -0.682 GC content %: 37.954

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_6BL_34565B900.3	RepBase (RepeatMasker)	2014-01-31	LINE1-54_ZM
Taestivum_Traes_6BL_34565B900.2	RepBase (RepeatMasker)	2014-01-31	LINE1-54_ZM

Gene models

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