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_4AL_8D6A610BE Traes_4AL_8D6A610BE	ta_iwgsc_4al_v2_7096467	1	7972	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_4AL_8D6A610BE.2 Traes_4AL_8D6A610BE.2 PAC:31776276	High	No	625		Get ORF Coding potential... Type: noncoding Potential: -0.296 Folding energies... MFEI: -27.296 AMFE: -0.592 GC content %: 46.080
Taestivum_Traes_4AL_8D6A610BE.4 Traes_4AL_8D6A610BE.4 PAC:31776277	High	No	1613		Get ORF Coding potential... Type: noncoding Potential: -0.362 Folding energies... MFEI: -27.706 AMFE: -0.643 GC content %: 43.087
Taestivum_Traes_4AL_8D6A610BE.6 Traes_4AL_8D6A610BE.6 PAC:31776280	High	No	1819		Get ORF Coding potential... Type: noncoding Potential: -0.372 Folding energies... MFEI: -26.938 AMFE: -0.635 GC content %: 42.441
Taestivum_Traes_4AL_8D6A610BE.7 Traes_4AL_8D6A610BE.7 PAC:31776281	High	No	348		Get ORF Coding potential... Type: noncoding Potential: -0.643 Folding energies... MFEI: -29.741 AMFE: -0.575 GC content %: 51.724
Taestivum_Traes_4AL_8D6A610BE.8 Traes_4AL_8D6A610BE.8 PAC:31776283	High	No	1594		Get ORF Coding potential... Type: noncoding Potential: -0.836 Folding energies... MFEI: -26.951 AMFE: -0.631 GC content %: 42.723
Taestivum_Traes_4AL_8D6A610BE.9 Traes_4AL_8D6A610BE.9 PAC:31776282	Low	No	2075		Get ORF Coding potential... Type: noncoding Potential: -0.885 Folding energies... MFEI: -26.665 AMFE: -0.664 GC content %: 40.145

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_4AL_8D6A610BE.9	RepBase (RepeatMasker)	2014-01-31	Copia-31_BD-I

Gene models

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