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	Source	Assembly	Species	Details
Tcacao_Thecc1EG010146 Thecc1EG010146	scaffold_2	31048169	31049446	Phytozome	v1.1	Theobroma_cacao	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	Sequence	Details
Tcacao_Thecc1EG010146t1 Thecc1EG010146t1 PAC:27463938	Low	No	1278		Get ORF Coding potential... Type: noncoding Potential: -0.994 Folding energies... MFEI: -22.034 AMFE: -0.521 GC content %: 42.332

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
Tcacao_Thecc1EG010146t1	RepBase (RepeatMasker)	2014-01-31	Gypsy-2_TC-I

Gene models

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