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_6AL_31A70E50A Traes_6AL_31A70E50A	ta_iwgsc_6al_v1_5785983	3422	13367	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_6AL_31A70E50A.18 Traes_6AL_31A70E50A.18 PAC:31988128	Low	No	2973		Get ORF Coding potential... Type: noncoding Potential: -1.132 Folding energies... MFEI: -30.084 AMFE: -0.712 GC content %: 42.247
Taestivum_Traes_6AL_31A70E50A.25 Traes_6AL_31A70E50A.25 PAC:31988134	Low	No	3564		Get ORF Coding potential... Type: noncoding Potential: -0.994 Folding energies... MFEI: -27.674 AMFE: -0.690 GC content %: 40.095
Taestivum_Traes_6AL_31A70E50A.27 Traes_6AL_31A70E50A.27 PAC:31988137	Low	No	718		Get ORF Coding potential... Type: noncoding Potential: -1.257 Folding energies... MFEI: -27.270 AMFE: -0.806 GC content %: 33.844
Taestivum_Traes_6AL_31A70E50A.28 Traes_6AL_31A70E50A.28 PAC:31988138	High	No	911		Get ORF Coding potential... Type: noncoding Potential: -1.389 Folding energies... MFEI: -23.502 AMFE: -0.577 GC content %: 40.724

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_6AL_31A70E50A.27	RepBase (RepeatMasker)	2014-01-31	TYPEU4

Gene models

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