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	Assembly	Species	Details
Ncolorata_Nycol.E00289 [ Nycol.E00289]	GWHAAYW00000005	3025837	3030035	v1.2	Nymphaea colorata (Phytozome 13)	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	Orthologous group	Sequence	Details
Ncolorata_Nycol.E00289.2 Nycol.E00289.2	High	No	1405	OG0003397		Get ORF Coding potential... Type: noncoding Potential: -0.570 Folding energies... MFEI: -26.790 AMFE: -0.603 GC content %: 44.413
Ncolorata_Nycol.E00289.3 Nycol.E00289.3	High	No	1485	OG0003397		Get ORF Coding potential... Type: noncoding Potential: -0.581 Folding energies... MFEI: -26.808 AMFE: -0.611 GC content %: 43.906
Ncolorata_Nycol.E00289.4 Nycol.E00289.4	Low	No	1512	OG0003397		Get ORF Coding potential... Type: noncoding Potential: -0.585 Folding energies... MFEI: -26.700 AMFE: -0.601 GC content %: 44.444
Ncolorata_Nycol.E00289.5 Nycol.E00289.5	High	No	1375	OG0003397		Get ORF Coding potential... Type: noncoding Potential: -0.566 Folding energies... MFEI: -26.887 AMFE: -0.605 GC content %: 44.436
Ncolorata_Nycol.E00289.6 Nycol.E00289.6	High	No	1454	OG0003397		Get ORF Coding potential... Type: noncoding Potential: -0.577 Folding energies... MFEI: -26.919 AMFE: -0.613 GC content %: 43.948
Ncolorata_Nycol.E00289.7 Nycol.E00289.7	High	No	962	OG0003397		Get ORF Coding potential... Type: noncoding Potential: -0.481 Folding energies... MFEI: -28.067 AMFE: -0.615 GC content %: 45.634
Ncolorata_Nycol.E00289.8 Nycol.E00289.8	High	No	992	OG0003397		Get ORF Coding potential... Type: noncoding Potential: -0.489 Folding energies... MFEI: -27.702 AMFE: -0.608 GC content %: 45.565
Ncolorata_Nycol.E00289.9 Nycol.E00289.9	High	No	932	OG0003397		Get ORF Coding potential... Type: noncoding Potential: -0.473 Folding energies... MFEI: -27.811 AMFE: -0.606 GC content %: 45.923

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
Ncolorata_Nycol.E00289.4	RepBase (RepeatMasker)	2014-01-31	LTR/Gypsy

Gene models

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