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_F2C2109D4 Traes_1AL_F2C2109D4	ta_iwgsc_1al_v2_268345	3631	5804	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_1AL_F2C2109D4.1 Traes_1AL_F2C2109D4.1 PAC:31858425	High	No	675		Get ORF Coding potential... Type: noncoding Potential: -0.840 Folding energies... MFEI: -26.089 AMFE: -0.601 GC content %: 43.407
Taestivum_Traes_1AL_F2C2109D4.2 Traes_1AL_F2C2109D4.2 PAC:31858426	Low	No	927		Get ORF Coding potential... Type: noncoding Potential: -1.251 Folding energies... MFEI: -23.894 AMFE: -0.597 GC content %: 40.022

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_F2C2109D4.2	RepBase (RepeatMasker)	2014-01-31	DEIMOS_TM

Gene models

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