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_6BS_DE7ED5F57 Traes_6BS_DE7ED5F57	ta_iwgsc_6bs_v1_3043960	104	628	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_6BS_DE7ED5F57.1 Traes_6BS_DE7ED5F57.1 PAC:31795470	Low	No	339		Get ORF Coding potential... Type: noncoding Potential: -0.766 Folding energies... MFEI: -29.764 AMFE: -0.534 GC content %: 55.752
Taestivum_Traes_6BS_DE7ED5F57.2 Traes_6BS_DE7ED5F57.2 PAC:31795469	Low	No	246		Get ORF Coding potential... Type: noncoding Potential: -1.139 Folding energies... MFEI: -34.390 AMFE: -0.631 GC content %: 54.472

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_6BS_DE7ED5F57.1	RepBase (RepeatMasker)	2014-01-31	LINE1-8_SBi
Taestivum_Traes_6BS_DE7ED5F57.2	RepBase (RepeatMasker)	2014-01-31	LINE-05_OS

Gene models

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