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_AT1G22140 AT1G22140	Chr1	7814763	7815631	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_AT1G22140.1 AT1G22140.1 PAC:19650830	Low	No	476		Get ORF Coding potential... Type: noncoding Potential: -0.771 Folding energies... MFEI: -22.899 AMFE: -0.583 GC content %: 39.286
Athaliana_AT1G22140.2 AT1G22140.2 PAC:19650831	High	No	503		Get ORF Coding potential... Type: noncoding Potential: -0.965 Folding energies... MFEI: -22.684 AMFE: -0.604 GC content %: 37.575

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_AT1G22140.1	SwissProt	2015-06-01	Q7JWR9	5.0e-4

Gene models

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