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_2AL_0D5516974 Traes_2AL_0D5516974	ta_iwgsc_2al_v1_6396950	7	3303	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_2AL_0D5516974.3 Traes_2AL_0D5516974.3 PAC:31941426	High	No	715		Get ORF Coding potential... Type: noncoding Potential: -0.665 Folding energies... MFEI: -27.594 AMFE: -0.636 GC content %: 43.357
Taestivum_Traes_2AL_0D5516974.4 Traes_2AL_0D5516974.4 PAC:31941427	Low	No	949		Get ORF Coding potential... Type: noncoding Potential: -0.965 Folding energies... MFEI: -28.061 AMFE: -0.658 GC content %: 42.677
Taestivum_Traes_2AL_0D5516974.5 Traes_2AL_0D5516974.5 PAC:31941428	High	No	642		Get ORF Coding potential... Type: noncoding Potential: -1.052 Folding energies... MFEI: -31.386 AMFE: -0.601 GC content %: 52.181

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_2AL_0D5516974.4	RepBase (RepeatMasker)	2014-01-31	EWAY1_TM-LTR

Gene models

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