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_5591A4421 Traes_3AL_5591A4421	ta_iwgsc_3al_v1_4403736	1683	3448	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_3AL_5591A4421.1 Traes_3AL_5591A4421.1 PAC:31990684	Low	No	846		Get ORF Coding potential... Type: noncoding Potential: -0.206 Folding energies... MFEI: -27.825 AMFE: -0.645 GC content %: 43.144
Taestivum_Traes_3AL_5591A4421.2 Traes_3AL_5591A4421.2 PAC:31990683	Low	No	1264		Get ORF Coding potential... Type: noncoding Potential: -0.159 Folding energies... MFEI: -26.788 AMFE: -0.668 GC content %: 40.111
Taestivum_Traes_3AL_5591A4421.3 Traes_3AL_5591A4421.3 PAC:31990682	Low	No	1021		Get ORF Coding potential... Type: noncoding Potential: -0.235 Folding energies... MFEI: -27.708 AMFE: -0.647 GC content %: 42.801

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_5591A4421.2	RepBase (RepeatMasker)	2014-01-31	ATHOS_HV

Gene models

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