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_HORVU7Hr1G044150 [ HORVU7Hr1G044150]	chr7H	136407722	136410802	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_HORVU7Hr1G044150.4 HORVU7Hr1G044150.4	High	No	475	OG0193265		Get ORF Coding potential... Type: noncoding Potential: -0.949 Folding energies... MFEI: -37.874 AMFE: -0.647 GC content %: 58.526
Hvulgare_HORVU7Hr1G044150.5 HORVU7Hr1G044150.5	Low	No	1767	OG0049009		Get ORF Coding potential... Type: noncoding Potential: -1.268 Folding energies... MFEI: -33.220 AMFE: -0.654 GC content %: 50.821
Hvulgare_HORVU7Hr1G044150.6 HORVU7Hr1G044150.6	High	No	601	OG0049010		Get ORF Coding potential... Type: noncoding Potential: -1.110 Folding energies... MFEI: -34.692 AMFE: -0.546 GC content %: 63.561

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_HORVU7Hr1G044150.5	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm; DNA/PIF-Harbinger; LTR/Copia

Gene models

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