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.1G012500 Prupe.1G012500	Pp01	950246	955472	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.1G012500.1 Prupe.1G012500.1 PAC:32117065	Low	No	1178		Get ORF Coding potential... Type: noncoding Potential: -0.923 Folding energies... MFEI: -23.185 AMFE: -0.569 GC content %: 40.747
Ppersica_Prupe.1G012500.2 Prupe.1G012500.2 PAC:32117066	Low	No	1083		Get ORF Coding potential... Type: noncoding Potential: -0.913 Folding energies... MFEI: -23.335 AMFE: -0.562 GC content %: 41.551

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.1G012500.2	SwissProt	2015-06-01	O81832	4.0e-11
Ppersica_Prupe.1G012500.1	RepBase (RepeatMasker)	2014-01-31	EnSpm-3_TA
Ppersica_Prupe.1G012500.2	RepBase (RepeatMasker)	2014-01-31	EnSpm-3_TA
Ppersica_Prupe.1G012500.1	SwissProt	2015-06-01	O81832	5.0e-11

Gene models

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