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_HORVU5Hr1G011830 [ HORVU5Hr1G011830]	chr5H	32074880	32079137	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_HORVU5Hr1G011830.3 HORVU5Hr1G011830.3	Low	No	335	OG0000053		Get ORF Coding potential... Type: noncoding Potential: -0.983 Folding energies... MFEI: -22.448 AMFE: -0.530 GC content %: 42.388
Hvulgare_HORVU5Hr1G011830.4 HORVU5Hr1G011830.4	Low	No	326	OG0000053		Get ORF Coding potential... Type: noncoding Potential: -0.770 Folding energies... MFEI: -23.712 AMFE: -0.522 GC content %: 45.399

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_HORVU5Hr1G011830.3	SwissProt	2021-04-01	P07271	1.35e-9
Hvulgare_HORVU5Hr1G011830.4	SwissProt	2021-04-01	A6ZM04	7.3e-10
Hvulgare_HORVU5Hr1G011830.3	RepBase (RepeatMasker)	2014-01-31	RC/Helitron
Hvulgare_HORVU5Hr1G011830.4	RepBase (RepeatMasker)	2014-01-31	RC/Helitron

Gene models

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