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_HORVU4Hr1G056950 [ HORVU4Hr1G056950]	chr4H	478351972	478354766	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_HORVU4Hr1G056950.11 HORVU4Hr1G056950.11	Low	No	901	OG0043561		Get ORF Coding potential... Type: noncoding Potential: -0.263 Folding energies... MFEI: -30.533 AMFE: -0.605 GC content %: 50.499
Hvulgare_HORVU4Hr1G056950.3 HORVU4Hr1G056950.3	Low	No	497	OG0043562		Get ORF Coding potential... Type: noncoding Potential: -0.997 Folding energies... MFEI: -31.670 AMFE: -0.612 GC content %: 51.710

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_HORVU4Hr1G056950.3	RepBase (RepeatMasker)	2014-01-31	LTR/ERV1
Hvulgare_HORVU4Hr1G056950.11	SwissProt	2021-04-01	P43125	3.15e-16
Hvulgare_HORVU4Hr1G056950.3	SwissProt	2021-04-01	Q6ZPQ6	3.99e-9

Gene models

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