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_HORVU1Hr1G083660 [ HORVU1Hr1G083660]	chr1H	532258356	532276672	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_HORVU1Hr1G083660.1 HORVU1Hr1G083660.1	High	No	730	OG0037255		Get ORF Coding potential... Type: noncoding Potential: -0.575 Folding energies... MFEI: -30.411 AMFE: -0.572 GC content %: 53.151
Hvulgare_HORVU1Hr1G083660.2 HORVU1Hr1G083660.2	Low	No	5242	OG0037256		Get ORF Coding potential... Type: noncoding Potential: -1.098 Folding energies... MFEI: -27.982 AMFE: -0.676 GC content %: 41.396
Hvulgare_HORVU1Hr1G083660.31 HORVU1Hr1G083660.31	Low	No	433	OG0192383		Get ORF Coding potential... Type: noncoding Potential: -0.835 Folding energies... MFEI: -41.386 AMFE: -0.614 GC content %: 67.436
Hvulgare_HORVU1Hr1G083660.36 HORVU1Hr1G083660.36	Low	No	499	OG0037257		Get ORF Coding potential... Type: coding Potential: 0.270 Folding energies... MFEI: -24.469 AMFE: -0.579 GC content %: 42.285
Hvulgare_HORVU1Hr1G083660.37 HORVU1Hr1G083660.37	High	No	1059	OG0019506		Get ORF Coding potential... Type: noncoding Potential: -0.840 Folding energies... MFEI: -25.099 AMFE: -0.639 GC content %: 39.282
Hvulgare_HORVU1Hr1G083660.5 HORVU1Hr1G083660.5	Low	No	3595	OG0037258		Get ORF Coding potential... Type: noncoding Potential: -1.075 Folding energies... MFEI: -29.010 AMFE: -0.690 GC content %: 42.031

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_HORVU1Hr1G083660.31	SwissProt	2021-04-01	Q54GS8	6.96e-8
Hvulgare_HORVU1Hr1G083660.2	RepBase (RepeatMasker)	2014-01-31	DNA/TcMar-Stowaway; LINE/L1
Hvulgare_HORVU1Hr1G083660.5	RepBase (RepeatMasker)	2014-01-31	DNA/TcMar-Stowaway; LINE/L1

Gene models

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