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_80FC35AD0 Traes_1AL_80FC35AD0	ta_iwgsc_1al_v2_3320744	1	415	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_80FC35AD0.1 Traes_1AL_80FC35AD0.1 PAC:31869065	Low	No	286		Get ORF Coding potential... Type: noncoding Potential: -1.037 Folding energies... MFEI: -27.762 AMFE: -0.616 GC content %: 45.105
Taestivum_Traes_1AL_80FC35AD0.2 Traes_1AL_80FC35AD0.2 PAC:31869066	Low	No	240		Get ORF Coding potential... Type: noncoding Potential: -0.924 Folding energies... MFEI: -25.167 AMFE: -0.604 GC content %: 41.667

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_80FC35AD0.1	RepBase (RepeatMasker)	2014-01-31	HARB-4A_SBi
Taestivum_Traes_1AL_80FC35AD0.2	RepBase (RepeatMasker)	2014-01-31	HARB-4A_SBi

Gene models

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