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
Athaliana_AT5G64687 AT5G64687	Chr5	25858584	25861909	v11	Arabidopsis thaliana (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
Athaliana_AT5G64687.1 AT5G64687.1	Low	No	1198	OG0024133		Get ORF Coding potential... Type: noncoding Potential: -0.366 Folding energies... MFEI: -23.013 AMFE: -0.594 GC content %: 38.731
Athaliana_AT5G64687.2 AT5G64687.2	Low	No	1583	OG0024133		Get ORF Coding potential... Type: noncoding Potential: -0.336 Folding energies... MFEI: -22.672 AMFE: -0.585 GC content %: 38.724

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
Athaliana_AT5G64687.2	SwissProt	2021-04-01	Q39219	5.01e-13
Athaliana_AT5G64687.1	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm
Athaliana_AT5G64687.2	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm
Athaliana_AT5G64687.1	SwissProt	2021-04-01	Q39219	9.26e-12

Gene models

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