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_5AL_736B24453 Traes_5AL_736B24453	ta_iwgsc_5al_v1_2689311	3614	3982	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_5AL_736B24453.1 Traes_5AL_736B24453.1 PAC:31760929	Low	No	294		Get ORF Coding potential... Type: noncoding Potential: -0.927 Folding energies... MFEI: -25.816 AMFE: -0.584 GC content %: 44.218
Taestivum_Traes_5AL_736B24453.2 Traes_5AL_736B24453.2 PAC:31760930	Low	No	288		Get ORF Coding potential... Type: noncoding Potential: -0.890 Folding energies... MFEI: -29.653 AMFE: -0.637 GC content %: 46.528

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_5AL_736B24453.2	RepBase (RepeatMasker)	2014-01-31	LINE1-34_SBi
Taestivum_Traes_5AL_736B24453.1	RepBase (RepeatMasker)	2014-01-31	LINE1-34_SBi

Gene models

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