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
Gmustelinum_Gomus.D11G236300 [ Gomus.D11G236300]	D11	31097004	31099291	v1.1	Gossypium mustelinum (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
Gmustelinum_Gomus.D11G236300.1 Gomus.D11G236300.1	High	No	943	OG0011763		Get ORF Coding potential... Type: noncoding Potential: -0.942 Folding energies... MFEI: -21.421 AMFE: -0.627 GC content %: 34.146
Gmustelinum_Gomus.D11G236300.2 Gomus.D11G236300.2	High	No	1752	OG0011868		Get ORF Coding potential... Type: noncoding Potential: -1.071 Folding energies... MFEI: -21.507 AMFE: -0.668 GC content %: 32.192
Gmustelinum_Gomus.D11G236300.3 Gomus.D11G236300.3	Low	Yes	1302	OG0011868		Get ORF Coding potential... Type: noncoding Potential: -1.024 Folding energies... MFEI: -23.848 AMFE: -0.690 GC content %: 34.562
Gmustelinum_Gomus.D11G236300.4 Gomus.D11G236300.4	High	No	1414	OG0011868		Get ORF Coding potential... Type: noncoding Potential: -1.034 Folding energies... MFEI: -24.257 AMFE: -0.703 GC content %: 34.512
Gmustelinum_Gomus.D11G236300.5 Gomus.D11G236300.5	Low	Yes	942	OG0011868		Get ORF Coding potential... Type: noncoding Potential: -0.978 Folding energies... MFEI: -24.246 AMFE: -0.701 GC content %: 34.607

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
Gmustelinum_Gomus.D11G236300.5	Rfam	14.6	mir-891	0.0067
Gmustelinum_Gomus.D11G236300.3	Rfam	14.6	mir-891	0.0092

Gene models

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