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_HORVU2Hr1G087730 [ HORVU2Hr1G087730]	chr2H	629896988	629903015	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_HORVU2Hr1G087730.1 HORVU2Hr1G087730.1	High	No	921	OG0012399		Get ORF Coding potential... Type: noncoding Potential: -0.817 Folding energies... MFEI: -39.240 AMFE: -0.710 GC content %: 55.266
Hvulgare_HORVU2Hr1G087730.2 HORVU2Hr1G087730.2	Low	No	499	OG0039375		Get ORF Coding potential... Type: noncoding Potential: -1.217 Folding energies... MFEI: -34.970 AMFE: -0.690 GC content %: 50.701
Hvulgare_HORVU2Hr1G087730.3 HORVU2Hr1G087730.3	High	No	771	OG0012399		Get ORF Coding potential... Type: noncoding Potential: -0.602 Folding energies... MFEI: -39.741 AMFE: -0.696 GC content %: 57.069
Hvulgare_HORVU2Hr1G087730.5 HORVU2Hr1G087730.5	Low	No	778	OG0039376		Get ORF Coding potential... Type: noncoding Potential: -0.786 Folding energies... MFEI: -40.694 AMFE: -0.713 GC content %: 57.069

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_HORVU2Hr1G087730.5	SwissProt	2021-04-01	Q9SRY4	1.18e-4
Hvulgare_HORVU2Hr1G087730.2	SwissProt	2021-04-01	Q9SRY4	4.69e-6

Gene models

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