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_4DL_07C7ADEDF Traes_4DL_07C7ADEDF	ta_iwgsc_4dl_v3_14305135	8	3092	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_4DL_07C7ADEDF.4 Traes_4DL_07C7ADEDF.4 PAC:31910962	Low	No	853		Get ORF Coding potential... Type: noncoding Potential: -0.521 Folding energies... MFEI: -24.361 AMFE: -0.602 GC content %: 40.445
Taestivum_Traes_4DL_07C7ADEDF.5 Traes_4DL_07C7ADEDF.5 PAC:31910963	High	No	434		Get ORF Coding potential... Type: noncoding Potential: -0.874 Folding energies... MFEI: -21.290 AMFE: -0.592 GC content %: 35.945

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_4DL_07C7ADEDF.4	RepBase (RepeatMasker)	2014-01-31	TAM2_AM

Gene models

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