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_HORVU4Hr1G005450 [ HORVU4Hr1G005450]	chr4H	12279931	12284852	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_HORVU4Hr1G005450.10 HORVU4Hr1G005450.10	High	No	284	OG0005881		Get ORF Coding potential... Type: noncoding Potential: -1.453 Folding energies... MFEI: -25.775 AMFE: -0.555 GC content %: 46.479
Hvulgare_HORVU4Hr1G005450.6 HORVU4Hr1G005450.6	Low	No	598	OG0042592		Get ORF Coding potential... Type: noncoding Potential: -0.391 Folding energies... MFEI: -35.585 AMFE: -0.540 GC content %: 65.886
Hvulgare_HORVU4Hr1G005450.7 HORVU4Hr1G005450.7	Low	No	618	OG0005881		Get ORF Coding potential... Type: noncoding Potential: -0.316 Folding energies... MFEI: -32.508 AMFE: -0.512 GC content %: 63.430
Hvulgare_HORVU4Hr1G005450.8 HORVU4Hr1G005450.8	High	No	807	OG0042593		Get ORF Coding potential... Type: noncoding Potential: -0.452 Folding energies... MFEI: -31.685 AMFE: -0.543 GC content %: 58.364
Hvulgare_HORVU4Hr1G005450.9 HORVU4Hr1G005450.9	High	No	715	OG0005881		Get ORF Coding potential... Type: noncoding Potential: -0.860 Folding energies... MFEI: -29.287 AMFE: -0.523 GC content %: 55.944

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_HORVU4Hr1G005450.6	SwissProt	2021-04-01	Q9M015	4.79e-4
Hvulgare_HORVU4Hr1G005450.7	SwissProt	2021-04-01	Q9M015	3.26e-4

Gene models

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