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_1AS_0B93DEE0B Traes_1AS_0B93DEE0B	ta_iwgsc_1as_v1_1494400	4	2774	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_1AS_0B93DEE0B.3 Traes_1AS_0B93DEE0B.3 PAC:31798717	High	No	643		Get ORF Coding potential... Type: noncoding Potential: -1.203 Folding energies... MFEI: -31.928 AMFE: -0.650 GC content %: 49.145
Taestivum_Traes_1AS_0B93DEE0B.5 Traes_1AS_0B93DEE0B.5 PAC:31798719	Low	No	1085		Get ORF Coding potential... Type: noncoding Potential: -1.028 Folding energies... MFEI: -25.650 AMFE: -0.671 GC content %: 38.249

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_1AS_0B93DEE0B.5	RepBase (RepeatMasker)	2014-01-31	SINE2-1_TAe

Gene models

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