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.D04G010833 [ Gohir.D04G010833]	D04	1758086	1760688	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.D04G010833.1 Gohir.D04G010833.1	Low	Yes	1960	OG0002570		Get ORF Coding potential... Type: noncoding Potential: -1.300 Folding energies... MFEI: -25.969 AMFE: -0.650 GC content %: 39.949
Ghirsutum_Gohir.D04G010833.2 Gohir.D04G010833.2	High	No	1116	OG0002570		Get ORF Coding potential... Type: noncoding Potential: -1.265 Folding energies... MFEI: -25.314 AMFE: -0.614 GC content %: 41.219
Ghirsutum_Gohir.D04G010833.3 Gohir.D04G010833.3	High	No	1440	OG0002570		Get ORF Coding potential... Type: noncoding Potential: -1.305 Folding energies... MFEI: -25.569 AMFE: -0.643 GC content %: 39.792
Ghirsutum_Gohir.D04G010833.4 Gohir.D04G010833.4	High	No	1233	OG0002570		Get ORF Coding potential... Type: noncoding Potential: -1.273 Folding energies... MFEI: -24.850 AMFE: -0.603 GC content %: 41.200

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.D04G010833.1	Rfam	14.6	MIR159	1.2e-33

Gene models

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