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_Thecc1EG031211 Thecc1EG031211	scaffold_7	3424663	3499238	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_Thecc1EG031211t1 Thecc1EG031211t1 PAC:27445227	Low	No	309		Get ORF Coding potential... Type: noncoding Potential: -0.641 Folding energies... MFEI: -22.557 AMFE: -0.536 GC content %: 42.071
Tcacao_Thecc1EG031211t2 Thecc1EG031211t2 PAC:27445226	Low	No	255		Get ORF Coding potential... Type: noncoding Potential: -0.621 Folding energies... MFEI: -18.824 AMFE: -0.471 GC content %: 40.000

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_Thecc1EG031211t1	SwissProt	2015-06-01	O81833	5.0e-7
Tcacao_Thecc1EG031211t2	SwissProt	2015-06-01	Q9SXB5	4.0e-6

Gene models

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