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_4DL_2CC7963CE Traes_4DL_2CC7963CE	ta_iwgsc_4dl_v3_14460995	6345	10781	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_4DL_2CC7963CE.4 Traes_4DL_2CC7963CE.4 PAC:31899605	High	No	337		Get ORF Coding potential... Type: noncoding Potential: -0.251 Folding energies... MFEI: -33.769 AMFE: -0.662 GC content %: 51.039
Taestivum_Traes_4DL_2CC7963CE.5 Traes_4DL_2CC7963CE.5 PAC:31899604	Low	No	478		Get ORF Coding potential... Type: noncoding Potential: -0.377 Folding energies... MFEI: -26.360 AMFE: -0.692 GC content %: 38.075

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_4DL_2CC7963CE.5	RepBase (RepeatMasker)	2014-01-31	STOWAWAY14_SB

Gene models

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