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.D09G153300 [ Gotom.D09G153300]	D09	40197016	40198693	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.D09G153300.1 Gotom.D09G153300.1	Low	No	805	OG0001733		Get ORF Coding potential... Type: noncoding Potential: -0.234 Folding energies... MFEI: -23.168 AMFE: -0.604 GC content %: 38.385
Gtomentosum_Gotom.D09G153300.2 Gotom.D09G153300.2	Low	No	678	OG0001733		Get ORF Coding potential... Type: noncoding Potential: -0.275 Folding energies... MFEI: -23.584 AMFE: -0.625 GC content %: 37.758

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.D09G153300.2	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm
Gtomentosum_Gotom.D09G153300.1	SwissProt	2021-04-01	P46302	3.91e-20
Gtomentosum_Gotom.D09G153300.2	SwissProt	2021-04-01	P46302	1.63e-20
Gtomentosum_Gotom.D09G153300.1	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm

Gene models

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