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_HORVU2Hr1G000770 [ HORVU2Hr1G000770]	chr2H	1674782	1719647	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_HORVU2Hr1G000770.1 HORVU2Hr1G000770.1	Low	No	826	OG0037466		Get ORF Coding potential... Type: noncoding Potential: -1.186 Folding energies... MFEI: -28.487 AMFE: -0.613 GC content %: 46.489
Hvulgare_HORVU2Hr1G000770.2 HORVU2Hr1G000770.2	High	No	708	OG0037467		Get ORF Coding potential... Type: noncoding Potential: -1.147 Folding energies... MFEI: -26.935 AMFE: -0.600 GC content %: 44.915
Hvulgare_HORVU2Hr1G000770.3 HORVU2Hr1G000770.3	High	No	285	OG0012190		Get ORF Coding potential... Type: noncoding Potential: -0.468 Folding energies... MFEI: -33.193 AMFE: -0.662 GC content %: 50.175
Hvulgare_HORVU2Hr1G000770.31 HORVU2Hr1G000770.31	High	No	439	OG0037468		Get ORF Coding potential... Type: noncoding Potential: -1.036 Folding energies... MFEI: -25.809 AMFE: -0.558 GC content %: 46.241
Hvulgare_HORVU2Hr1G000770.32 HORVU2Hr1G000770.32	High	No	1051	OG0037469		Get ORF Coding potential... Type: noncoding Potential: -1.147 Folding energies... MFEI: -32.664 AMFE: -0.720 GC content %: 45.385
Hvulgare_HORVU2Hr1G000770.33 HORVU2Hr1G000770.33	High	No	880	OG0037470		Get ORF Coding potential... Type: noncoding Potential: -1.092 Folding energies... MFEI: -33.102 AMFE: -0.712 GC content %: 46.477

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_HORVU2Hr1G000770.1	RepBase (RepeatMasker)	2014-01-31	SINE; Unknown

Gene models

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