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_HORVU1Hr1G015060 [ HORVU1Hr1G015060]	chr1H	42739685	42767912	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_HORVU1Hr1G015060.10 HORVU1Hr1G015060.10	Low	No	307	OG0035920		Get ORF Coding potential... Type: noncoding Potential: -0.976 Folding energies... MFEI: -25.016 AMFE: -0.565 GC content %: 44.300
Hvulgare_HORVU1Hr1G015060.8 HORVU1Hr1G015060.8	High	No	806	OG0035921		Get ORF Coding potential... Type: noncoding Potential: -1.431 Folding energies... MFEI: -25.670 AMFE: -0.543 GC content %: 47.270
Hvulgare_HORVU1Hr1G015060.9 HORVU1Hr1G015060.9	High	No	1415	OG0035922		Get ORF Coding potential... Type: noncoding Potential: -1.456 Folding energies... MFEI: -29.399 AMFE: -0.679 GC content %: 43.322

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_HORVU1Hr1G015060.10	RepBase (RepeatMasker)	2014-01-31	LTR/Gypsy

Gene models

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