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_HORVU4Hr1G058050 [ HORVU4Hr1G058050]	chr4H	485396736	485400225	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_HORVU4Hr1G058050.2 HORVU4Hr1G058050.2	Low	No	2874	OG0004752		Get ORF Coding potential... Type: noncoding Potential: -0.095 Folding energies... MFEI: -28.633 AMFE: -0.695 GC content %: 41.197
Hvulgare_HORVU4Hr1G058050.3 HORVU4Hr1G058050.3	Low	No	2392	OG0004752		Get ORF Coding potential... Type: noncoding Potential: -0.076 Folding energies... MFEI: -29.624 AMFE: -0.689 GC content %: 42.977

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_HORVU4Hr1G058050.2	RepBase (RepeatMasker)	2014-01-31	LTR/Gypsy
Hvulgare_HORVU4Hr1G058050.3	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).