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_HORVU2Hr1G105100 [ HORVU2Hr1G105100]	chr2H	705662379	705663632	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_HORVU2Hr1G105100.1 HORVU2Hr1G105100.1	High	No	601	OG0012433		Get ORF Coding potential... Type: noncoding Potential: -1.164 Folding energies... MFEI: -34.958 AMFE: -0.684 GC content %: 51.082
Hvulgare_HORVU2Hr1G105100.2 HORVU2Hr1G105100.2	Low	No	753	OG0012433		Get ORF Coding potential... Type: noncoding Potential: -0.561 Folding energies... MFEI: -39.270 AMFE: -0.732 GC content %: 53.652
Hvulgare_HORVU2Hr1G105100.3 HORVU2Hr1G105100.3	Low	No	324	OG0192566		Get ORF Coding potential... Type: noncoding Potential: -0.361 Folding energies... MFEI: -31.944 AMFE: -0.655 GC content %: 48.765
Hvulgare_HORVU2Hr1G105100.4 HORVU2Hr1G105100.4	Low	No	308	OG0039777		Get ORF Coding potential... Type: noncoding Potential: -0.844 Folding energies... MFEI: -21.558 AMFE: -0.604 GC content %: 35.714
Hvulgare_HORVU2Hr1G105100.5 HORVU2Hr1G105100.5	High	No	281	OG0039778		Get ORF Coding potential... Type: noncoding Potential: -1.106 Folding energies... MFEI: -25.907 AMFE: -0.428 GC content %: 60.498

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_HORVU2Hr1G105100.2	SwissProt	2021-04-01	Q9FGQ9	1.1e-6
Hvulgare_HORVU2Hr1G105100.3	SwissProt	2021-04-01	Q9FGQ9	2.18e-8
Hvulgare_HORVU2Hr1G105100.4	SwissProt	2021-04-01	Q9FGQ9	1.85e-8

Gene models

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