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_HORVU1Hr1G066520 [ HORVU1Hr1G066520]	chr1H	472951480	472953979	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_HORVU1Hr1G066520.1 HORVU1Hr1G066520.1	Low	Yes	1245	OG0036907		Get ORF Coding potential... Type: noncoding Potential: -1.315 Folding energies... MFEI: -25.984 AMFE: -0.673 GC content %: 38.635
Hvulgare_HORVU1Hr1G066520.2 HORVU1Hr1G066520.2	High	No	1500	OG0036908		Get ORF Coding potential... Type: noncoding Potential: -0.881 Folding energies... MFEI: -32.527 AMFE: -0.667 GC content %: 48.800
Hvulgare_HORVU1Hr1G066520.3 HORVU1Hr1G066520.3	High	No	257	OG0000612		Get ORF Coding potential... Type: noncoding Potential: -0.921 Folding energies... MFEI: -52.802 AMFE: -0.710 GC content %: 74.319

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_HORVU1Hr1G066520.1	Rfam	14.6	MIR1122	5.1e-8

Gene models

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