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_Thecc1EG041383 Thecc1EG041383	scaffold_9	37342304	37346349	Phytozome	v1.1	Theobroma_cacao	Coding? Yes

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_Thecc1EG041383t1 Thecc1EG041383t1 PAC:27429794	Low	No	651		Get ORF Coding potential... Type: noncoding Potential: -0.147 Folding energies... MFEI: -24.562 AMFE: -0.627 GC content %: 39.171
Tcacao_Thecc1EG041383t2 Thecc1EG041383t2 PAC:27429795	Low	No	460		Get ORF Coding potential... Type: noncoding Potential: -0.052 Folding energies... MFEI: -25.261 AMFE: -0.584 GC content %: 43.261

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_Thecc1EG041383t1	SwissProt	2015-06-01	Q9ZUX4	2.0e-13
Tcacao_Thecc1EG041383t2	SwissProt	2015-06-01	Q9ZUX4	9.0e-14

Gene models

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