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_5BS_3A28D084B Traes_5BS_3A28D084B	ta_iwgsc_5bs_v1_2246469	3734	12939	Phytozome	v2.2	Triticum_aestivum	Coding? No

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_5BS_3A28D084B.1 Traes_5BS_3A28D084B.1 PAC:31777991	High	No	858		Get ORF Coding potential... Type: noncoding Potential: -1.077 Folding energies... MFEI: -27.564 AMFE: -0.637 GC content %: 43.240
Taestivum_Traes_5BS_3A28D084B.2 Traes_5BS_3A28D084B.2 PAC:31777990	Low	No	1640		Get ORF Coding potential... Type: noncoding Potential: -1.154 Folding energies... MFEI: -30.183 AMFE: -0.656 GC content %: 46.037
Taestivum_Traes_5BS_3A28D084B.3 Traes_5BS_3A28D084B.3 PAC:31777992	High	No	987		Get ORF Coding potential... Type: noncoding Potential: -1.097 Folding energies... MFEI: -25.491 AMFE: -0.609 GC content %: 41.844
Taestivum_Traes_5BS_3A28D084B.4 Traes_5BS_3A28D084B.4 PAC:31777993	Low	No	1964		Get ORF Coding potential... Type: noncoding Potential: -1.168 Folding energies... MFEI: -29.313 AMFE: -0.663 GC content %: 44.196
Taestivum_Traes_5BS_3A28D084B.5 Traes_5BS_3A28D084B.5 PAC:31777994	Low	No	1813		Get ORF Coding potential... Type: noncoding Potential: -1.162 Folding energies... MFEI: -28.356 AMFE: -0.647 GC content %: 43.850

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_5BS_3A28D084B.4	RepBase (RepeatMasker)	2014-01-31	MuDR-15_GMa
Taestivum_Traes_5BS_3A28D084B.5	RepBase (RepeatMasker)	2014-01-31	MuDR-15_GMa
Taestivum_Traes_5BS_3A28D084B.2	RepBase (RepeatMasker)	2014-01-31	MuDR-15_GMa

Gene models

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