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_HORVU2Hr1G053160 [ HORVU2Hr1G053160]	chr2H	322513047	322516571	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_HORVU2Hr1G053160.1 HORVU2Hr1G053160.1	Low	No	1082	OG0012330		Get ORF Coding potential... Type: noncoding Potential: -1.128 Folding energies... MFEI: -35.268 AMFE: -0.645 GC content %: 54.713
Hvulgare_HORVU2Hr1G053160.2 HORVU2Hr1G053160.2	Low	No	1060	OG0012330		Get ORF Coding potential... Type: noncoding Potential: -1.153 Folding energies... MFEI: -35.821 AMFE: -0.654 GC content %: 54.811
Hvulgare_HORVU2Hr1G053160.3 HORVU2Hr1G053160.3	High	No	341	OG0012331		Get ORF Coding potential... Type: noncoding Potential: -1.044 Folding energies... MFEI: -24.516 AMFE: -0.589 GC content %: 41.642
Hvulgare_HORVU2Hr1G053160.4 HORVU2Hr1G053160.4	High	No	707	OG0012331		Get ORF Coding potential... Type: noncoding Potential: -1.123 Folding energies... MFEI: -30.085 AMFE: -0.648 GC content %: 46.393
Hvulgare_HORVU2Hr1G053160.5 HORVU2Hr1G053160.5	High	No	594	OG0038656		Get ORF Coding potential... Type: noncoding Potential: -1.107 Folding energies... MFEI: -33.704 AMFE: -0.654 GC content %: 51.515
Hvulgare_HORVU2Hr1G053160.6 HORVU2Hr1G053160.6	Low	No	2482	OG0038657		Get ORF Coding potential... Type: noncoding Potential: -1.244 Folding energies... MFEI: -29.214 AMFE: -0.628 GC content %: 46.495

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_HORVU2Hr1G053160.1	SwissProt	2021-04-01	Q0DGS1	4.95e-5
Hvulgare_HORVU2Hr1G053160.2	SwissProt	2021-04-01	Q0DGS1	6.3e-5
Hvulgare_HORVU2Hr1G053160.6	SwissProt	2021-04-01	Q0DGS1	1.9e-4

Gene models

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