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	Source	Assembly	Species	Details
Athaliana_AT1G65486 AT1G65486	Chr1	24349523	24350306	Phytozome	TAIR10	Arabidopsis_thaliana	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	Sequence	Details
Athaliana_AT1G65486.1 AT1G65486.1 PAC:19653759	High	No	326		Get ORF Coding potential... Type: noncoding Potential: -0.934 Folding energies... MFEI: -24.233 AMFE: -0.537 GC content %: 45.092
Athaliana_AT1G65486.2 AT1G65486.2 PAC:19653760	Low	No	474		Get ORF Coding potential... Type: noncoding Potential: -1.249 Folding energies... MFEI: -23.586 AMFE: -0.621 GC content %: 37.975

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_AT1G65486.2	RepBase (RepeatMasker)	2014-01-31	ATLINE1A

Gene models

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