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
Egrandis_Eucgr.F03809 Eucgr.F03809	Chr06	48803887	48806752	Phytozome	v2.0	Eucalyptus_grandis	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
Egrandis_Eucgr.F03809.1 Eucgr.F03809.1 PAC:32056343	Low	No	2546		Get ORF Coding potential... Type: noncoding Potential: -1.092 Folding energies... MFEI: -26.791 AMFE: -0.699 GC content %: 38.335
Egrandis_Eucgr.F03809.2 Eucgr.F03809.2 PAC:32056344	Low	No	2540		Get ORF Coding potential... Type: noncoding Potential: -1.092 Folding energies... MFEI: -26.673 AMFE: -0.697 GC content %: 38.268

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
Egrandis_Eucgr.F03809.1	SwissProt	2015-06-01	Q9SCV9	4.0e-13
Egrandis_Eucgr.F03809.2	SwissProt	2015-06-01	Q9SCV9	1.0e-12
Egrandis_Eucgr.F03809.1	RepBase (RepeatMasker)	2014-01-31	Copia-46_ZM-I
Egrandis_Eucgr.F03809.2	RepBase (RepeatMasker)	2014-01-31	Copia-46_ZM-I

Gene models

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