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.D07G224300 [ Gotom.D07G224300]	D07	47699731	47701733	v1.1	Gossypium tomentosum (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
Gtomentosum_Gotom.D07G224300.1 Gotom.D07G224300.1	Low	No	1266	OG0019346		Get ORF Coding potential... Type: noncoding Potential: -1.040 Folding energies... MFEI: -22.788 AMFE: -0.631 GC content %: 36.098
Gtomentosum_Gotom.D07G224300.2 Gotom.D07G224300.2	High	No	786	OG0019346		Get ORF Coding potential... Type: noncoding Potential: -1.086 Folding energies... MFEI: -21.336 AMFE: -0.610 GC content %: 34.987
Gtomentosum_Gotom.D07G224300.3 Gotom.D07G224300.3	High	No	261	OG0182810		Get ORF Coding potential... Type: noncoding Potential: -0.882 Folding energies... MFEI: -17.050 AMFE: -0.368 GC content %: 46.360
Gtomentosum_Gotom.D07G224300.4 Gotom.D07G224300.4	High	No	258	OG0182811		Get ORF Coding potential... Type: noncoding Potential: -0.754 Folding energies... MFEI: -15.349 AMFE: -0.357 GC content %: 43.023

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.D07G224300.1	RepBase (RepeatMasker)	2014-01-31	LTR/ERV1

Gene models

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