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_GSVIVG01000064001 GSVIVG01000064001	chr14	3185338	3186328	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_GSVIVT01000064001 GSVIVT01000064001 PAC:17816678	Low	No	679		Get ORF Coding potential... Type: noncoding Potential: -0.988 Folding energies... MFEI: -26.745 AMFE: -0.624 GC content %: 42.857

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_GSVIVT01000064001	SwissProt	2015-06-01	Q9FIC6	2.0e-7

Gene models

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