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_7DL_854C069A1 Traes_7DL_854C069A1	ta_iwgsc_7dl_v1_3317045	1074	3384	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_7DL_854C069A1.2 Traes_7DL_854C069A1.2 PAC:31859497	Low	No	873		Get ORF Coding potential... Type: noncoding Potential: -0.389 Folding energies... MFEI: -26.861 AMFE: -0.603 GC content %: 44.559
Taestivum_Traes_7DL_854C069A1.3 Traes_7DL_854C069A1.3 PAC:31859499	Low	No	970		Get ORF Coding potential... Type: noncoding Potential: -0.474 Folding energies... MFEI: -28.072 AMFE: -0.630 GC content %: 44.536
Taestivum_Traes_7DL_854C069A1.4 Traes_7DL_854C069A1.4 PAC:31859498	Low	No	1181		Get ORF Coding potential... Type: noncoding Potential: -0.466 Folding energies... MFEI: -26.757 AMFE: -0.627 GC content %: 42.676

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_7DL_854C069A1.2	RepBase (RepeatMasker)	2014-01-31	Copia-79_ST-I
Taestivum_Traes_7DL_854C069A1.3	RepBase (RepeatMasker)	2014-01-31	Copia-79_ST-I
Taestivum_Traes_7DL_854C069A1.4	RepBase (RepeatMasker)	2014-01-31	Copia-79_ST-I

Gene models

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