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_HORVU5Hr1G040190 [ HORVU5Hr1G040190]	chr5H	296068400	296073717	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_HORVU5Hr1G040190.11 HORVU5Hr1G040190.11	High	No	639	OG0044874		Get ORF Coding potential... Type: noncoding Potential: -1.125 Folding energies... MFEI: -29.562 AMFE: -0.649 GC content %: 45.540
Hvulgare_HORVU5Hr1G040190.17 HORVU5Hr1G040190.17	Low	Yes	1472	OG0044875		Get ORF Coding potential... Type: noncoding Potential: -0.688 Folding energies... MFEI: -27.520 AMFE: -0.670 GC content %: 41.101
Hvulgare_HORVU5Hr1G040190.43 HORVU5Hr1G040190.43	Low	No	1158	OG0012938		Get ORF Coding potential... Type: noncoding Potential: -1.080 Folding energies... MFEI: -31.813 AMFE: -0.724 GC content %: 43.955
Hvulgare_HORVU5Hr1G040190.44 HORVU5Hr1G040190.44	Low	No	872	OG0012938		Get ORF Coding potential... Type: noncoding Potential: -0.982 Folding energies... MFEI: -31.204 AMFE: -0.705 GC content %: 44.266
Hvulgare_HORVU5Hr1G040190.45 HORVU5Hr1G040190.45	High	No	753	OG0044876		Get ORF Coding potential... Type: noncoding Potential: -0.961 Folding energies... MFEI: -29.017 AMFE: -0.672 GC content %: 43.161

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_HORVU5Hr1G040190.17	Rfam	14.6	MIR1122	1.2e-11
Hvulgare_HORVU5Hr1G040190.17	RepBase (RepeatMasker)	2014-01-31	DNA/TcMar-Stowaway
Hvulgare_HORVU5Hr1G040190.43	RepBase (RepeatMasker)	2014-01-31	DNA/hAT-Ac
Hvulgare_HORVU5Hr1G040190.44	RepBase (RepeatMasker)	2014-01-31	DNA/hAT-Ac
Hvulgare_HORVU5Hr1G040190.17	SwissProt	2021-04-01	Q9FNY0	2.06e-10

Gene models

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