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_HORVU2Hr1G094810 [ HORVU2Hr1G094810]	chr2H	666837932	666840632	r1	Hordeum vulgare (Phytozome 13)	Coding? No

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_HORVU2Hr1G094810.1 HORVU2Hr1G094810.1	Low	Yes	2440	OG0039535		Get ORF Coding potential... Type: noncoding Potential: -1.299 Folding energies... MFEI: -32.357 AMFE: -0.786 GC content %: 41.189
Hvulgare_HORVU2Hr1G094810.2 HORVU2Hr1G094810.2	Low	No	389	OG0039536		Get ORF Coding potential... Type: noncoding Potential: -0.090 Folding energies... MFEI: -38.766 AMFE: -0.642 GC content %: 60.411

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_HORVU2Hr1G094810.2	SwissProt	2021-04-01	Q9M080	1.14e-11
Hvulgare_HORVU2Hr1G094810.1	Rfam	14.6	MIR1122	1.6e-9
Hvulgare_HORVU2Hr1G094810.1	RepBase (RepeatMasker)	2014-01-31	DNA/PIF-Harbinger; DNA/TcMar-Stowaway
Hvulgare_HORVU2Hr1G094810.1	SwissProt	2021-04-01	Q9CAN9	1.06e-9

Gene models

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