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_HORVU1Hr1G040260 [ HORVU1Hr1G040260]	chr1H	284574939	284575781	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_HORVU1Hr1G040260.1 HORVU1Hr1G040260.1	Low	No	234	OG0005697		Get ORF Coding potential... Type: noncoding Potential: -0.910 Folding energies... MFEI: -30.214 AMFE: -0.540 GC content %: 55.983
Hvulgare_HORVU1Hr1G040260.2 HORVU1Hr1G040260.2	Low	No	356	OG0012082		Get ORF Coding potential... Type: noncoding Potential: -1.346 Folding energies... MFEI: -32.191 AMFE: -0.551 GC content %: 58.427

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_HORVU1Hr1G040260.1	RepBase (RepeatMasker)	2014-01-31	LINE/L1
Hvulgare_HORVU1Hr1G040260.2	RepBase (RepeatMasker)	2014-01-31	LINE/L1
Hvulgare_HORVU1Hr1G040260.2	SwissProt	2021-04-01	P0C2F6	5.31e-4

Gene models

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