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.J00674 Eucgr.J00674	Chr10	7293038	7296303	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.J00674.2 Eucgr.J00674.2 PAC:32033447	Low	Yes	826		Get ORF Coding potential... Type: noncoding Potential: -0.235 Folding energies... MFEI: -33.366 AMFE: -0.714 GC content %: 46.731
Egrandis_Eucgr.J00674.3 Eucgr.J00674.3 PAC:32033448	Low	Yes	496		Get ORF Coding potential... Type: noncoding Potential: -0.500 Folding energies... MFEI: -33.891 AMFE: -0.721 GC content %: 46.976

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.J00674.2	Rfam	11.0	mir-316	5.1e-4
Egrandis_Eucgr.J00674.3	Rfam	11.0	mir-316	3.1e-4
Egrandis_Eucgr.J00674.2	RepBase (RepeatMasker)	2014-01-31	ATCopia59_I-int
Egrandis_Eucgr.J00674.3	RepBase (RepeatMasker)	2014-01-31	ATCopia59_I-int

Gene models

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