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_Thecc1EG032082 Thecc1EG032082	scaffold_7	8732009	8734829	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_Thecc1EG032082t1 Thecc1EG032082t1 PAC:27444780	Low	No	596		Get ORF Coding potential... Type: noncoding Potential: -0.446 Folding energies... MFEI: -19.111 AMFE: -0.542 GC content %: 35.235

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_Thecc1EG032082t1	RepBase (RepeatMasker)	2014-01-31	POPCOP2_I-int

Gene models

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