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
Ghirsutum_Gohir.A13G103750 [ Gohir.A13G103750]	A13	70142573	70145368	v2.1	Gossypium hirsutum (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
Ghirsutum_Gohir.A13G103750.1 Gohir.A13G103750.1	Low	No	2295	OG0003192		Get ORF Coding potential... Type: noncoding Potential: -0.292 Folding energies... MFEI: -20.200 AMFE: -0.595 GC content %: 33.943
Ghirsutum_Gohir.A13G103750.2 Gohir.A13G103750.2	High	No	1341	OG0003192		Get ORF Coding potential... Type: noncoding Potential: -1.203 Folding energies... MFEI: -20.723 AMFE: -0.586 GC content %: 35.347
Ghirsutum_Gohir.A13G103750.3 Gohir.A13G103750.3	High	No	1145	OG0003192		Get ORF Coding potential... Type: noncoding Potential: -1.278 Folding energies... MFEI: -20.838 AMFE: -0.583 GC content %: 35.721
Ghirsutum_Gohir.A13G103750.4 Gohir.A13G103750.4	High	No	1420	OG0003192		Get ORF Coding potential... Type: noncoding Potential: -1.258 Folding energies... MFEI: -21.127 AMFE: -0.593 GC content %: 35.634

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
Ghirsutum_Gohir.A13G103750.1	RepBase (RepeatMasker)	2014-01-31	LINE/L1; LTR/Gypsy

Gene models

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