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_HORVU2Hr1G068550 [ HORVU2Hr1G068550]	chr2H	482747346	482764546	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_HORVU2Hr1G068550.1 HORVU2Hr1G068550.1	Low	No	1248	OG0038913		Get ORF Coding potential... Type: noncoding Potential: -1.045 Folding energies... MFEI: -26.827 AMFE: -0.627 GC content %: 42.788
Hvulgare_HORVU2Hr1G068550.14 HORVU2Hr1G068550.14	Low	Yes	5511	OG0038914		Get ORF Coding potential... Type: noncoding Potential: -0.963 Folding energies... MFEI: -27.059 AMFE: -0.719 GC content %: 37.634

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_HORVU2Hr1G068550.1	SwissProt	2021-04-01	Q6NTR1	2.74e-7
Hvulgare_HORVU2Hr1G068550.14	Rfam	14.6	MIR1122	3.9e-13
Hvulgare_HORVU2Hr1G068550.14	RepBase (RepeatMasker)	2014-01-31	DNA/TcMar-Stowaway

Gene models

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