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_HORVU0Hr1G000740 [ HORVU0Hr1G000740]	chrUn	4739459	4740267	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_HORVU0Hr1G000740.1 HORVU0Hr1G000740.1	Low	No	239	OG0035147		Get ORF Coding potential... Type: noncoding Potential: -1.144 Folding energies... MFEI: -25.649 AMFE: -0.613 GC content %: 41.841
Hvulgare_HORVU0Hr1G000740.2 HORVU0Hr1G000740.2	Low	No	599	OG0035148		Get ORF Coding potential... Type: noncoding Potential: -0.682 Folding energies... MFEI: -25.192 AMFE: -0.634 GC content %: 39.733

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_HORVU0Hr1G000740.1	SwissProt	2021-04-01	Q17QR8	1.15e-4
Hvulgare_HORVU0Hr1G000740.1	RepBase (RepeatMasker)	2014-01-31	DNA/PIF-Harbinger
Hvulgare_HORVU0Hr1G000740.2	RepBase (RepeatMasker)	2014-01-31	DNA/PIF-Harbinger

Gene models

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