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_HORVU5Hr1G067470 [ HORVU5Hr1G067470]	chr5H	512980649	512987218	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_HORVU5Hr1G067470.11 HORVU5Hr1G067470.11	High	No	359	OG0003319		Get ORF Coding potential... Type: noncoding Potential: -0.920 Folding energies... MFEI: -33.621 AMFE: -0.619 GC content %: 54.318
Hvulgare_HORVU5Hr1G067470.2 HORVU5Hr1G067470.2	Low	No	3330	OG0045415		Get ORF Coding potential... Type: noncoding Potential: -1.038 Folding energies... MFEI: -27.622 AMFE: -0.636 GC content %: 43.453
Hvulgare_HORVU5Hr1G067470.4 HORVU5Hr1G067470.4	Low	No	1612	OG0003319		Get ORF Coding potential... Type: noncoding Potential: -1.165 Folding energies... MFEI: -30.019 AMFE: -0.638 GC content %: 47.022
Hvulgare_HORVU5Hr1G067470.6 HORVU5Hr1G067470.6	High	No	844	OG0003319		Get ORF Coding potential... Type: noncoding Potential: -1.123 Folding energies... MFEI: -33.318 AMFE: -0.606 GC content %: 54.976

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_HORVU5Hr1G067470.2	RepBase (RepeatMasker)	2014-01-31	DNA/TcMar-Stowaway; SINE/tRNA
Hvulgare_HORVU5Hr1G067470.4	RepBase (RepeatMasker)	2014-01-31	DNA/TcMar-Stowaway; SINE/tRNA

Gene models

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