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_HORVU4Hr1G002300 [ HORVU4Hr1G002300]	chr4H	4205894	4208046	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_HORVU4Hr1G002300.1 HORVU4Hr1G002300.1	Low	No	635	OG0042513		Get ORF Coding potential... Type: noncoding Potential: -0.727 Folding energies... MFEI: -31.654 AMFE: -0.638 GC content %: 49.606
Hvulgare_HORVU4Hr1G002300.3 HORVU4Hr1G002300.3	Low	No	823	OG0042514		Get ORF Coding potential... Type: noncoding Potential: -0.800 Folding energies... MFEI: -29.162 AMFE: -0.632 GC content %: 46.173
Hvulgare_HORVU4Hr1G002300.4 HORVU4Hr1G002300.4	High	No	362	OG0192758		Get ORF Coding potential... Type: noncoding Potential: -0.812 Folding energies... MFEI: -29.365 AMFE: -0.572 GC content %: 51.381
Hvulgare_HORVU4Hr1G002300.5 HORVU4Hr1G002300.5	High	No	360	OG0042515		Get ORF Coding potential... Type: noncoding Potential: -0.582 Folding energies... MFEI: -29.500 AMFE: -0.577 GC content %: 51.111
Hvulgare_HORVU4Hr1G002300.6 HORVU4Hr1G002300.6	High	No	424	OG0192759		Get ORF Coding potential... Type: noncoding Potential: -0.823 Folding energies... MFEI: -26.509 AMFE: -0.579 GC content %: 45.755

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_HORVU4Hr1G002300.1	RepBase (RepeatMasker)	2014-01-31	LINE/L1
Hvulgare_HORVU4Hr1G002300.3	RepBase (RepeatMasker)	2014-01-31	LINE/L1

Gene models

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