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_2AS_8D645C4F5 Traes_2AS_8D645C4F5	ta_iwgsc_2as_v1_4444564	16	2998	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_2AS_8D645C4F5.1 Traes_2AS_8D645C4F5.1 PAC:31900032	Low	No	532		Get ORF Coding potential... Type: noncoding Potential: -0.877 Folding energies... MFEI: -24.436 AMFE: -0.619 GC content %: 39.474
Taestivum_Traes_2AS_8D645C4F5.2 Traes_2AS_8D645C4F5.2 PAC:31900031	Low	No	2708		Get ORF Coding potential... Type: noncoding Potential: -0.802 Folding energies... MFEI: -32.145 AMFE: -0.687 GC content %: 46.824
Taestivum_Traes_2AS_8D645C4F5.3 Traes_2AS_8D645C4F5.3 PAC:31900030	High	No	1758		Get ORF Coding potential... Type: noncoding Potential: -0.755 Folding energies... MFEI: -28.191 AMFE: -0.652 GC content %: 43.231

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_2AS_8D645C4F5.1	RepBase (RepeatMasker)	2014-01-31	Tourist1f_SB
Taestivum_Traes_2AS_8D645C4F5.2	RepBase (RepeatMasker)	2014-01-31	Gypsy-81_ZM-I

Gene models

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