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
Ppersica_Prupe.6G031100 Prupe.6G031100	Pp06	2419987	2422247	Phytozome	v2.1	Prunus_persica	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
Ppersica_Prupe.6G031100.1 Prupe.6G031100.1 PAC:32086616	High	No	765		Get ORF Coding potential... Type: noncoding Potential: -0.233 Folding energies... MFEI: -21.333 AMFE: -0.573 GC content %: 37.255
Ppersica_Prupe.6G031100.2 Prupe.6G031100.2 PAC:32086617	Low	No	826		Get ORF Coding potential... Type: noncoding Potential: -0.294 Folding energies... MFEI: -21.295 AMFE: -0.511 GC content %: 41.646

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
Ppersica_Prupe.6G031100.2	RepBase (RepeatMasker)	2014-01-31	Copia-29_FV-LTR

Gene models

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