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_HORVU4Hr1G074800 [ HORVU4Hr1G074800]	chr4H	595765001	595767436	r1	Hordeum vulgare (Phytozome 13)	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	Orthologous group	Sequence	Details
Hvulgare_HORVU4Hr1G074800.1 HORVU4Hr1G074800.1	Low	No	860	OG0043922		Get ORF Coding potential... Type: noncoding Potential: -0.848 Folding energies... MFEI: -32.442 AMFE: -0.611 GC content %: 53.140
Hvulgare_HORVU4Hr1G074800.2 HORVU4Hr1G074800.2	High	No	262	OG0043923		Get ORF Coding potential... Type: noncoding Potential: -0.693 Folding energies... MFEI: -30.229 AMFE: -0.614 GC content %: 49.237

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_HORVU4Hr1G074800.1	RepBase (RepeatMasker)	2014-01-31	DNA/TcMar-Stowaway

Gene models

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