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_HORVU6Hr1G033160 [ HORVU6Hr1G033160]	chr6H	149856196	149868725	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_HORVU6Hr1G033160.23 HORVU6Hr1G033160.23	Low	No	215	OG0004164		Get ORF Coding potential... Type: noncoding Potential: -0.775 Folding energies... MFEI: -35.070 AMFE: -0.567 GC content %: 61.860
Hvulgare_HORVU6Hr1G033160.24 HORVU6Hr1G033160.24	Low	No	603	OG0004164		Get ORF Coding potential... Type: noncoding Potential: -1.297 Folding energies... MFEI: -25.290 AMFE: -0.703 GC content %: 35.987
Hvulgare_HORVU6Hr1G033160.26 HORVU6Hr1G033160.26	High	No	229	OG0047021		Get ORF Coding potential... Type: noncoding Potential: -1.237 Folding energies... MFEI: -17.598 AMFE: -0.480 GC content %: 36.681
Hvulgare_HORVU6Hr1G033160.30 HORVU6Hr1G033160.30	High	No	537	OG0047022		Get ORF Coding potential... Type: noncoding Potential: -0.888 Folding energies... MFEI: -28.231 AMFE: -0.689 GC content %: 40.968
Hvulgare_HORVU6Hr1G033160.31 HORVU6Hr1G033160.31	High	No	854	OG0047023		Get ORF Coding potential... Type: noncoding Potential: -1.275 Folding energies... MFEI: -25.644 AMFE: -0.545 GC content %: 47.073

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_HORVU6Hr1G033160.23	SwissProt	2021-04-01	P27522	1.46e-10
Hvulgare_HORVU6Hr1G033160.24	SwissProt	2021-04-01	Q99LJ8	1.02e-6

Gene models

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