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_HORVU2Hr1G028660 [ HORVU2Hr1G028660]	chr2H	97461300	97484755	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_HORVU2Hr1G028660.1 HORVU2Hr1G028660.1	Low	No	505	OG0038156		Get ORF Coding potential... Type: noncoding Potential: -0.129 Folding energies... MFEI: -28.000 AMFE: -0.582 GC content %: 48.119
Hvulgare_HORVU2Hr1G028660.2 HORVU2Hr1G028660.2	Low	Yes	1202	OG0038157		Get ORF Coding potential... Type: noncoding Potential: -0.329 Folding energies... MFEI: -26.065 AMFE: -0.634 GC content %: 41.098

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_HORVU2Hr1G028660.2	Rfam	14.6	MIR1122	0.0042
Hvulgare_HORVU2Hr1G028660.2	RepBase (RepeatMasker)	2014-01-31	DNA/TcMar-Stowaway
Hvulgare_HORVU2Hr1G028660.1	SwissProt	2021-04-01	P01053	3.19e-12
Hvulgare_HORVU2Hr1G028660.2	SwissProt	2021-04-01	P08626	4.11e-12

Gene models

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