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_1AL_0BEF6CF7C Traes_1AL_0BEF6CF7C	ta_iwgsc_1al_v2_3975271	246	673	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_1AL_0BEF6CF7C.1 Traes_1AL_0BEF6CF7C.1 PAC:31937849	Low	No	288		Get ORF Coding potential... Type: noncoding Potential: -0.466 Folding energies... MFEI: -22.014 AMFE: -0.593 GC content %: 37.153
Taestivum_Traes_1AL_0BEF6CF7C.2 Traes_1AL_0BEF6CF7C.2 PAC:31937848	Low	No	288		Get ORF Coding potential... Type: noncoding Potential: -0.471 Folding energies... MFEI: -21.111 AMFE: -0.574 GC content %: 36.806

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_1AL_0BEF6CF7C.1	RepBase (RepeatMasker)	2014-01-31	hAT2_SB
Taestivum_Traes_1AL_0BEF6CF7C.2	RepBase (RepeatMasker)	2014-01-31	hAT2_SB

Gene models

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