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_HORVU0Hr1G009060 [ HORVU0Hr1G009060]	chrUn	53877033	53884998	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_HORVU0Hr1G009060.1 HORVU0Hr1G009060.1	High	No	587	OG0035276		Get ORF Coding potential... Type: noncoding Potential: -0.619 Folding energies... MFEI: -34.549 AMFE: -0.531 GC content %: 65.077
Hvulgare_HORVU0Hr1G009060.10 HORVU0Hr1G009060.10	High	No	508	OG0035277		Get ORF Coding potential... Type: noncoding Potential: -0.953 Folding energies... MFEI: -28.445 AMFE: -0.587 GC content %: 48.425
Hvulgare_HORVU0Hr1G009060.7 HORVU0Hr1G009060.7	Low	No	671	OG0035278		Get ORF Coding potential... Type: noncoding Potential: -0.739 Folding energies... MFEI: -29.165 AMFE: -0.598 GC content %: 48.733
Hvulgare_HORVU0Hr1G009060.8 HORVU0Hr1G009060.8	Low	No	585	OG0035279		Get ORF Coding potential... Type: noncoding Potential: -1.050 Folding energies... MFEI: -28.615 AMFE: -0.596 GC content %: 48.034
Hvulgare_HORVU0Hr1G009060.9 HORVU0Hr1G009060.9	Low	No	580	OG0035280		Get ORF Coding potential... Type: noncoding Potential: -0.698 Folding energies... MFEI: -28.138 AMFE: -0.591 GC content %: 47.586

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_HORVU0Hr1G009060.8	SwissProt	2021-04-01	Q59695	1.26e-4
Hvulgare_HORVU0Hr1G009060.9	SwissProt	2021-04-01	Q52532	4.7e-6
Hvulgare_HORVU0Hr1G009060.7	SwissProt	2021-04-01	Q52532	5.46e-6

Gene models

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