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_HORVU6Hr1G060870 [ HORVU6Hr1G060870]	chr6H	406806340	406810509	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_HORVU6Hr1G060870.10 HORVU6Hr1G060870.10	Low	No	595	OG0005979		Get ORF Coding potential... Type: noncoding Potential: -0.649 Folding energies... MFEI: -31.193 AMFE: -0.561 GC content %: 55.630
Hvulgare_HORVU6Hr1G060870.11 HORVU6Hr1G060870.11	High	No	863	OG0005979		Get ORF Coding potential... Type: noncoding Potential: -1.157 Folding energies... MFEI: -23.314 AMFE: -0.594 GC content %: 39.282
Hvulgare_HORVU6Hr1G060870.12 HORVU6Hr1G060870.12	High	No	400	OG0047486		Get ORF Coding potential... Type: noncoding Potential: -0.984 Folding energies... MFEI: -28.675 AMFE: -0.591 GC content %: 48.500
Hvulgare_HORVU6Hr1G060870.6 HORVU6Hr1G060870.6	High	No	569	OG0005979		Get ORF Coding potential... Type: noncoding Potential: -0.783 Folding energies... MFEI: -31.160 AMFE: -0.526 GC content %: 59.227
Hvulgare_HORVU6Hr1G060870.9 HORVU6Hr1G060870.9	Low	No	384	OG0193149		Get ORF Coding potential... Type: noncoding Potential: -0.510 Folding energies... MFEI: -35.625 AMFE: -0.565 GC content %: 63.021

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_HORVU6Hr1G060870.10	SwissProt	2021-04-01	Q9LT71	9.54e-6
Hvulgare_HORVU6Hr1G060870.9	SwissProt	2021-04-01	Q9LT71	1.7e-5

Gene models

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