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
Vvinifera_GSVIVG01038484001 GSVIVG01038484001	chr3	10217207	10217764	Phytozome	Genoscope.12X	Vitis_vinifera	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
Vvinifera_GSVIVT01038484001 GSVIVT01038484001 PAC:17842747	Low	No	380		Get ORF Coding potential... Type: noncoding Potential: -1.175 Folding energies... MFEI: -29.500 AMFE: -0.742 GC content %: 39.737

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
Vvinifera_GSVIVT01038484001	RepBase (RepeatMasker)	2014-01-31	MuDR-5_VV

Gene models

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