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.A13G116950 [ Gohir.A13G116950]	A13	82494462	82499433	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.A13G116950.1 Gohir.A13G116950.1	High	No	705	OG0033972		Get ORF Coding potential... Type: noncoding Potential: -0.960 Folding energies... MFEI: -21.277 AMFE: -0.647 GC content %: 32.908
Ghirsutum_Gohir.A13G116950.2 Gohir.A13G116950.2	Low	No	1318	OG0033972		Get ORF Coding potential... Type: noncoding Potential: -1.156 Folding energies... MFEI: -22.686 AMFE: -0.717 GC content %: 31.639

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.A13G116950.2	RepBase (RepeatMasker)	2014-01-31	DNA/PIF-Harbinger

Gene models

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