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_AT1G56220 AT1G56220	Chr1	21043348	21044738	Phytozome	TAIR10	Arabidopsis_thaliana	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	Sequence	Details
Athaliana_AT1G56220.2 AT1G56220.2 PAC:19653046	Low	No	762		Get ORF Coding potential... Type: noncoding Potential: -1.152 Folding energies... MFEI: -26.864 AMFE: -0.599 GC content %: 44.882
Athaliana_AT1G56220.4 AT1G56220.4 PAC:19653047	Low	No	752		Get ORF Coding potential... Type: noncoding Potential: -1.100 Folding energies... MFEI: -26.941 AMFE: -0.601 GC content %: 44.814

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_AT1G56220.2	SwissProt	2015-06-01	Q05349	5.0e-5
Athaliana_AT1G56220.4	SwissProt	2015-06-01	Q05349	5.0e-5

Gene models

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