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_HORVU5Hr1G087920 [ HORVU5Hr1G087920]	chr5H	580102636	580103653	r1	Hordeum vulgare (Phytozome 13)	Coding? No

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_HORVU5Hr1G087920.1 HORVU5Hr1G087920.1	Low	No	1018	OG0013033		Get ORF Coding potential... Type: noncoding Potential: -0.542 Folding energies... MFEI: -32.426 AMFE: -0.718 GC content %: 45.187
Hvulgare_HORVU5Hr1G087920.2 HORVU5Hr1G087920.2	Low	No	935	OG0013033		Get ORF Coding potential... Type: noncoding Potential: -0.504 Folding energies... MFEI: -32.471 AMFE: -0.713 GC content %: 45.561

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_HORVU5Hr1G087920.1	SwissProt	2021-04-01	Q9C8E6	1.7e-11
Hvulgare_HORVU5Hr1G087920.2	SwissProt	2021-04-01	Q9C8E6	1.22e-11
Hvulgare_HORVU5Hr1G087920.1	RepBase (RepeatMasker)	2014-01-31	DNA/hAT-Tag1
Hvulgare_HORVU5Hr1G087920.2	RepBase (RepeatMasker)	2014-01-31	DNA/hAT-Tag1

Gene models

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