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
Gtomentosum_Gotom.A04G008600 [ Gotom.A04G008600]	A04	819985	821810	v1.1	Gossypium tomentosum (Phytozome 13)	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	Orthologous group	Sequence	Details
Gtomentosum_Gotom.A04G008600.1 Gotom.A04G008600.1	Low	No	1069	OG0011605		Get ORF Coding potential... Type: noncoding Potential: -0.907 Folding energies... MFEI: -26.268 AMFE: -0.690 GC content %: 38.073
Gtomentosum_Gotom.A04G008600.2 Gotom.A04G008600.2	High	No	935	OG0011605		Get ORF Coding potential... Type: noncoding Potential: -0.881 Folding energies... MFEI: -25.722 AMFE: -0.679 GC content %: 37.861
Gtomentosum_Gotom.A04G008600.3 Gotom.A04G008600.3	High	No	219	OG0011606		Get ORF Coding potential... Type: noncoding Potential: -0.699 Folding energies... MFEI: -22.740 AMFE: -0.519 GC content %: 43.836

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
Gtomentosum_Gotom.A04G008600.1	RepBase (RepeatMasker)	2014-01-31	LTR/Copia

Gene models

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