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_HORVU1Hr1G006020 [ HORVU1Hr1G006020]	chr1H	13034781	13206635	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_HORVU1Hr1G006020.1 HORVU1Hr1G006020.1	Low	No	666	OG0012029		Get ORF Coding potential... Type: noncoding Potential: -0.944 Folding energies... MFEI: -25.240 AMFE: -0.630 GC content %: 40.090
Hvulgare_HORVU1Hr1G006020.10 HORVU1Hr1G006020.10	Low	No	491	OG0035768		Get ORF Coding potential... Type: noncoding Potential: -0.302 Folding energies... MFEI: -17.108 AMFE: -0.497 GC content %: 34.420
Hvulgare_HORVU1Hr1G006020.18 HORVU1Hr1G006020.18	Low	No	447	OG0035769		Get ORF Coding potential... Type: noncoding Potential: -1.183 Folding energies... MFEI: -21.745 AMFE: -0.568 GC content %: 38.255
Hvulgare_HORVU1Hr1G006020.2 HORVU1Hr1G006020.2	High	No	325	OG0012029		Get ORF Coding potential... Type: noncoding Potential: -1.117 Folding energies... MFEI: -27.108 AMFE: -0.608 GC content %: 44.615
Hvulgare_HORVU1Hr1G006020.3 HORVU1Hr1G006020.3	High	No	971	OG0035770		Get ORF Coding potential... Type: noncoding Potential: -1.231 Folding energies... MFEI: -24.799 AMFE: -0.649 GC content %: 38.208

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_HORVU1Hr1G006020.1	SwissProt	2021-04-01	Q6K4T4	2.14e-4
Hvulgare_HORVU1Hr1G006020.10	SwissProt	2021-04-01	Q6K4T4	3.59e-11
Hvulgare_HORVU1Hr1G006020.18	RepBase (RepeatMasker)	2014-01-31	LTR/Gypsy

Gene models

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