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_GSVIVG01003264001 GSVIVG01003264001	chrUn	8553856	8554247	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_GSVIVT01003264001 GSVIVT01003264001 PAC:17818393	Low	Yes	314		Get ORF Coding potential... Type: noncoding Potential: -0.610 Folding energies... MFEI: -23.025 AMFE: -0.593 GC content %: 38.854

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_GSVIVT01003264001	Rfam	11.0	mir-598	6.2e-5
Vvinifera_GSVIVT01003264001	RepBase (RepeatMasker)	2014-01-31	(ATG)n

Gene models

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