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_4BL_E3EC59A72 Traes_4BL_E3EC59A72	ta_iwgsc_4bl_v1_7040355	3605	10513	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_4BL_E3EC59A72.2 Traes_4BL_E3EC59A72.2 PAC:31967571	Low	No	1992		Get ORF Coding potential... Type: noncoding Potential: -1.257 Folding energies... MFEI: -22.967 AMFE: -0.638 GC content %: 35.994
Taestivum_Traes_4BL_E3EC59A72.3 Traes_4BL_E3EC59A72.3 PAC:31967572	High	No	719		Get ORF Coding potential... Type: noncoding Potential: -1.148 Folding energies... MFEI: -22.670 AMFE: -0.547 GC content %: 41.446
Taestivum_Traes_4BL_E3EC59A72.4 Traes_4BL_E3EC59A72.4 PAC:31967573	Low	No	926		Get ORF Coding potential... Type: noncoding Potential: -1.311 Folding energies... MFEI: -23.359 AMFE: -0.618 GC content %: 37.797

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_4BL_E3EC59A72.2	RepBase (RepeatMasker)	2014-01-31	ATHOS_TM
Taestivum_Traes_4BL_E3EC59A72.4	RepBase (RepeatMasker)	2014-01-31	EnSpm-1_TA

Gene models

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