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.6G027800 Prupe.6G027800	Pp06	2167493	2168487	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.6G027800.1 Prupe.6G027800.1 PAC:32086008	Low	No	797		Get ORF Coding potential... Type: noncoding Potential: -0.770 Folding energies... MFEI: -27.842 AMFE: -0.634 GC content %: 43.915
Ppersica_Prupe.6G027800.2 Prupe.6G027800.2 PAC:32086009	Low	No	744		Get ORF Coding potential... Type: noncoding Potential: -0.757 Folding energies... MFEI: -28.777 AMFE: -0.655 GC content %: 43.952

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.6G027800.1	SwissProt	2015-06-01	F4I171	2.0e-10
Ppersica_Prupe.6G027800.2	SwissProt	2015-06-01	F4I171	1.0e-10
Ppersica_Prupe.6G027800.1	RepBase (RepeatMasker)	2014-01-31	SINE2-1_PTr
Ppersica_Prupe.6G027800.2	RepBase (RepeatMasker)	2014-01-31	SINE2-1_PTr

Gene models

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