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_HORVU5Hr1G009880 [ HORVU5Hr1G009880]	chr5H	24736672	24740236	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_HORVU5Hr1G009880.5 HORVU5Hr1G009880.5	Low	No	2816	OG0044344		Get ORF Coding potential... Type: noncoding Potential: -0.683 Folding energies... MFEI: -28.015 AMFE: -0.681 GC content %: 41.158
Hvulgare_HORVU5Hr1G009880.7 HORVU5Hr1G009880.7	Low	No	1104	OG0044345		Get ORF Coding potential... Type: noncoding Potential: -0.522 Folding energies... MFEI: -31.929 AMFE: -0.683 GC content %: 46.739

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_HORVU5Hr1G009880.7	SwissProt	2021-04-01	C0HIA3	1.94e-10
Hvulgare_HORVU5Hr1G009880.5	RepBase (RepeatMasker)	2014-01-31	LTR/Pao
Hvulgare_HORVU5Hr1G009880.7	RepBase (RepeatMasker)	2014-01-31	LTR/Pao
Hvulgare_HORVU5Hr1G009880.5	SwissProt	2021-04-01	C0HIA3	4.0e-6

Gene models

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