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_5BL_6343B4415 Traes_5BL_6343B4415	ta_iwgsc_5bl_v1_10783011	27	5491	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_5BL_6343B4415.6 Traes_5BL_6343B4415.6 PAC:32012161	High	No	560		Get ORF Coding potential... Type: noncoding Potential: -1.075 Folding energies... MFEI: -17.875 AMFE: -0.553 GC content %: 32.321
Taestivum_Traes_5BL_6343B4415.7 Traes_5BL_6343B4415.7 PAC:32012160	Low	No	2387		Get ORF Coding potential... Type: noncoding Potential: -1.137 Folding energies... MFEI: -24.554 AMFE: -0.677 GC content %: 36.280
Taestivum_Traes_5BL_6343B4415.8 Traes_5BL_6343B4415.8 PAC:32012162	High	No	497		Get ORF Coding potential... Type: noncoding Potential: -1.218 Folding energies... MFEI: -27.243 AMFE: -0.664 GC content %: 41.046

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_5BL_6343B4415.7	RepBase (RepeatMasker)	2014-01-31	tRNASAT-1_ZM

Gene models

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