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_1DS_9D0A687D5 Traes_1DS_9D0A687D5	ta_iwgsc_1ds_v1_1896439	1726	8005	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_1DS_9D0A687D5.3 Traes_1DS_9D0A687D5.3 PAC:31916507	Low	No	1526		Get ORF Coding potential... Type: noncoding Potential: -0.667 Folding energies... MFEI: -26.468 AMFE: -0.645 GC content %: 41.022
Taestivum_Traes_1DS_9D0A687D5.4 Traes_1DS_9D0A687D5.4 PAC:31916509	High	No	388		Get ORF Coding potential... Type: noncoding Potential: -0.820 Folding energies... MFEI: -23.119 AMFE: -0.561 GC content %: 41.237
Taestivum_Traes_1DS_9D0A687D5.5 Traes_1DS_9D0A687D5.5 PAC:31916508	High	No	543		Get ORF Coding potential... Type: noncoding Potential: -0.911 Folding energies... MFEI: -24.843 AMFE: -0.616 GC content %: 40.331
Taestivum_Traes_1DS_9D0A687D5.6 Traes_1DS_9D0A687D5.6 PAC:31916510	High	No	544		Get ORF Coding potential... Type: noncoding Potential: -1.186 Folding energies... MFEI: -25.588 AMFE: -0.568 GC content %: 45.037

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_1DS_9D0A687D5.3	RepBase (RepeatMasker)	2014-01-31	LINE1-53_SBi

Gene models

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