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_Thecc1EG037702 Thecc1EG037702	scaffold_9	4853450	4854518	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_Thecc1EG037702t1 Thecc1EG037702t1 PAC:27429265	Low	No	913		Get ORF Coding potential... Type: noncoding Potential: -0.243 Folding energies... MFEI: -23.363 AMFE: -0.654 GC content %: 35.706

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_Thecc1EG037702t1	SwissProt	2015-06-01	Q0J2C6	6.0e-9

Gene models

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