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_3AL_4C4A0BCD8 Traes_3AL_4C4A0BCD8	ta_iwgsc_3al_v1_4448101	65	2248	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_3AL_4C4A0BCD8.1 Traes_3AL_4C4A0BCD8.1 PAC:31761568	Low	No	709		Get ORF Coding potential... Type: noncoding Potential: -0.673 Folding energies... MFEI: -25.444 AMFE: -0.591 GC content %: 43.018
Taestivum_Traes_3AL_4C4A0BCD8.3 Traes_3AL_4C4A0BCD8.3 PAC:31761569	High	No	640		Get ORF Coding potential... Type: noncoding Potential: -1.207 Folding energies... MFEI: -24.391 AMFE: -0.640 GC content %: 38.125

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_3AL_4C4A0BCD8.1	RepBase (RepeatMasker)	2014-01-31	ATMU8

Gene models

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