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_EBEE1E466 Traes_1AL_EBEE1E466	ta_iwgsc_1al_v2_3955288	14876	17294	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_1AL_EBEE1E466.3 Traes_1AL_EBEE1E466.3 PAC:31804360	Low	No	1806		Get ORF Coding potential... Type: noncoding Potential: -0.519 Folding energies... MFEI: -36.971 AMFE: -0.676 GC content %: 54.707
Taestivum_Traes_1AL_EBEE1E466.4 Traes_1AL_EBEE1E466.4 PAC:31804359	High	No	949		Get ORF Coding potential... Type: noncoding Potential: -0.082 Folding energies... MFEI: -34.679 AMFE: -0.590 GC content %: 58.799

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_EBEE1E466.3	RepBase (RepeatMasker)	2014-01-31	SABRINA_SC-int

Gene models

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