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_3DL_D8504A5BF Traes_3DL_D8504A5BF	ta_iwgsc_3dl_v1_6951081	1	1618	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_3DL_D8504A5BF.7 Traes_3DL_D8504A5BF.7 PAC:31770898	Low	No	813		Get ORF Coding potential... Type: noncoding Potential: -0.833 Folding energies... MFEI: -29.533 AMFE: -0.692 GC content %: 42.681
Taestivum_Traes_3DL_D8504A5BF.8 Traes_3DL_D8504A5BF.8 PAC:31770899	Low	No	670		Get ORF Coding potential... Type: noncoding Potential: -0.810 Folding energies... MFEI: -27.448 AMFE: -0.662 GC content %: 41.493

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_3DL_D8504A5BF.7	RepBase (RepeatMasker)	2014-01-31	STOWAWAY41_OS
Taestivum_Traes_3DL_D8504A5BF.8	RepBase (RepeatMasker)	2014-01-31	STOWAWAY41_OS

Gene models

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