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_HORVU5Hr1G023140 [ HORVU5Hr1G023140]	chr5H	120874424	120882275	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_HORVU5Hr1G023140.19 HORVU5Hr1G023140.19	High	No	810	OG0044621		Get ORF Coding potential... Type: noncoding Potential: -1.084 Folding energies... MFEI: -27.333 AMFE: -0.657 GC content %: 41.605
Hvulgare_HORVU5Hr1G023140.20 HORVU5Hr1G023140.20	High	No	1026	OG0044622		Get ORF Coding potential... Type: noncoding Potential: -1.136 Folding energies... MFEI: -25.146 AMFE: -0.647 GC content %: 38.889
Hvulgare_HORVU5Hr1G023140.6 HORVU5Hr1G023140.6	Low	No	504	OG0044623		Get ORF Coding potential... Type: noncoding Potential: -0.170 Folding energies... MFEI: -27.837 AMFE: -0.635 GC content %: 43.849
Hvulgare_HORVU5Hr1G023140.7 HORVU5Hr1G023140.7	Low	No	557	OG0044624		Get ORF Coding potential... Type: noncoding Potential: -0.116 Folding energies... MFEI: -29.210 AMFE: -0.631 GC content %: 46.320

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_HORVU5Hr1G023140.6	SwissProt	2021-04-01	O04834	7.5e-15
Hvulgare_HORVU5Hr1G023140.7	SwissProt	2021-04-01	O04834	4.8e-26

Gene models

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