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.A05G319300 [ Gotom.A05G319300]	A05	34750956	34766132	v1.1	Gossypium tomentosum (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
Gtomentosum_Gotom.A05G319300.3 Gotom.A05G319300.3	High	No	755	OG0001193		Get ORF Coding potential... Type: noncoding Potential: -0.978 Folding energies... MFEI: -22.689 AMFE: -0.522 GC content %: 43.444
Gtomentosum_Gotom.A05G319300.5 Gotom.A05G319300.5	High	No	623	OG0001193		Get ORF Coding potential... Type: noncoding Potential: -0.924 Folding energies... MFEI: -19.422 AMFE: -0.450 GC content %: 43.178
Gtomentosum_Gotom.A05G319300.6 Gotom.A05G319300.6	Low	No	1335	OG0001193		Get ORF Coding potential... Type: noncoding Potential: -1.113 Folding energies... MFEI: -20.022 AMFE: -0.601 GC content %: 33.333
Gtomentosum_Gotom.A05G319300.7 Gotom.A05G319300.7	Low	No	1286	OG0180843		Get ORF Coding potential... Type: noncoding Potential: -1.208 Folding energies... MFEI: -19.712 AMFE: -0.596 GC content %: 33.048
Gtomentosum_Gotom.A05G319300.8 Gotom.A05G319300.8	Low	No	1252	OG0001193		Get ORF Coding potential... Type: noncoding Potential: -1.100 Folding energies... MFEI: -19.449 AMFE: -0.592 GC content %: 32.827

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.A05G319300.6	RepBase (RepeatMasker)	2014-01-31	LTR/Copia; LTR/Gypsy
Gtomentosum_Gotom.A05G319300.7	RepBase (RepeatMasker)	2014-01-31	LTR/Copia; LTR/Gypsy
Gtomentosum_Gotom.A05G319300.8	RepBase (RepeatMasker)	2014-01-31	LTR/Copia; LTR/Gypsy

Gene models

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