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_AT3G27340 AT3G27340	Chr3	10121234	10123128	v11	Arabidopsis thaliana (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
Athaliana_AT3G27340.2 AT3G27340.2	High	No	690	OG0024056		Get ORF Coding potential... Type: noncoding Potential: -1.056 Folding energies... MFEI: -26.652 AMFE: -0.679 GC content %: 39.275
Athaliana_AT3G27340.4 AT3G27340.4	Low	No	1051	OG0024056		Get ORF Coding potential... Type: noncoding Potential: -1.071 Folding energies... MFEI: -25.300 AMFE: -0.677 GC content %: 37.393

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_AT3G27340.4	RepBase (RepeatMasker)	2014-01-31	SINE

Gene models

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