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_6AS_5BFFF5CCF Traes_6AS_5BFFF5CCF	ta_iwgsc_6as_v1_4426752	614	1357	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_6AS_5BFFF5CCF.1 Traes_6AS_5BFFF5CCF.1 PAC:31796294	Low	No	339		Get ORF Coding potential... Type: noncoding Potential: -0.994 Folding energies... MFEI: -26.608 AMFE: -0.590 GC content %: 45.133
Taestivum_Traes_6AS_5BFFF5CCF.3 Traes_6AS_5BFFF5CCF.3 PAC:31796296	Low	No	288		Get ORF Coding potential... Type: noncoding Potential: -0.898 Folding energies... MFEI: -27.535 AMFE: -0.601 GC content %: 45.833

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_6AS_5BFFF5CCF.1	RepBase (RepeatMasker)	2014-01-31	LINE1-38_SBi
Taestivum_Traes_6AS_5BFFF5CCF.3	RepBase (RepeatMasker)	2014-01-31	L1-8_SBi

Gene models

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