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_HORVU1Hr1G095310 [ HORVU1Hr1G095310]	chr1H	558024352	558026903	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_HORVU1Hr1G095310.1 HORVU1Hr1G095310.1	Low	No	1785	OG0037446		Get ORF Coding potential... Type: coding Potential: 0.015 Folding energies... MFEI: -26.768 AMFE: -0.556 GC content %: 48.123
Hvulgare_HORVU1Hr1G095310.2 HORVU1Hr1G095310.2	High	No	467	OG0005735		Get ORF Coding potential... Type: noncoding Potential: -1.067 Folding energies... MFEI: -27.837 AMFE: -0.578 GC content %: 48.180
Hvulgare_HORVU1Hr1G095310.3 HORVU1Hr1G095310.3	High	No	430	OG0005735		Get ORF Coding potential... Type: noncoding Potential: -1.048 Folding energies... MFEI: -27.674 AMFE: -0.567 GC content %: 48.837
Hvulgare_HORVU1Hr1G095310.4 HORVU1Hr1G095310.4	High	No	412	OG0012187		Get ORF Coding potential... Type: noncoding Potential: -1.038 Folding energies... MFEI: -26.675 AMFE: -0.533 GC content %: 50.000
Hvulgare_HORVU1Hr1G095310.5 HORVU1Hr1G095310.5	High	No	412	OG0012187		Get ORF Coding potential... Type: noncoding Potential: -1.038 Folding energies... MFEI: -26.650 AMFE: -0.533 GC content %: 50.000
Hvulgare_HORVU1Hr1G095310.6 HORVU1Hr1G095310.6	High	No	350	OG0005735		Get ORF Coding potential... Type: noncoding Potential: -0.997 Folding energies... MFEI: -28.657 AMFE: -0.554 GC content %: 51.714
Hvulgare_HORVU1Hr1G095310.8 HORVU1Hr1G095310.8	High	No	556	OG0037447		Get ORF Coding potential... Type: noncoding Potential: -0.730 Folding energies... MFEI: -36.799 AMFE: -0.637 GC content %: 57.734

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_HORVU1Hr1G095310.1	RepBase (RepeatMasker)	2014-01-31	LINE/RTE-X

Gene models

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