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_2DS_3628E237B Traes_2DS_3628E237B	ta_iwgsc_2ds_v1_5384561	5647	8303	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_2DS_3628E237B.1 Traes_2DS_3628E237B.1 PAC:31856486	Low	No	216		Get ORF Coding potential... Type: noncoding Potential: -1.105 Folding energies... MFEI: -32.685 AMFE: -0.609 GC content %: 53.704
Taestivum_Traes_2DS_3628E237B.2 Traes_2DS_3628E237B.2 PAC:31856485	Low	No	1358		Get ORF Coding potential... Type: noncoding Potential: -0.349 Folding energies... MFEI: -30.302 AMFE: -0.667 GC content %: 45.434

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_2DS_3628E237B.2	RepBase (RepeatMasker)	2014-01-31	LINE1-4_SBi
Taestivum_Traes_2DS_3628E237B.1	RepBase (RepeatMasker)	2014-01-31	LINE1-2_ZM

Gene models

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