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	Assembly	Species	Details
Hvulgare_HORVU6Hr1G088370 [ HORVU6Hr1G088370]	chr6H	566364689	566370699	r1	Hordeum vulgare (Phytozome 13)	Coding? Yes

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	Orthologous group	Sequence	Details
Hvulgare_HORVU6Hr1G088370.1 HORVU6Hr1G088370.1	Low	No	586	OG0048054		Get ORF Coding potential... Type: noncoding Potential: -1.085 Folding energies... MFEI: -25.922 AMFE: -0.467 GC content %: 55.461
Hvulgare_HORVU6Hr1G088370.3 HORVU6Hr1G088370.3	High	No	623	OG0193179		Get ORF Coding potential... Type: noncoding Potential: -0.787 Folding energies... MFEI: -31.108 AMFE: -0.609 GC content %: 51.043

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
Hvulgare_HORVU6Hr1G088370.1	RepBase (RepeatMasker)	2014-01-31	LTR/Gypsy

Gene models

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