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
Cpapaya_evm.TU.contig_27558 evm.TU.contig_27558	contig_27558	3606	12111	Phytozome	ASGPBv0.4	Carica_papaya	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
Cpapaya_evm.TU.contig_27558.2 evm.TU.contig_27558.2 PAC:16429510	Low	No	363		Get ORF Coding potential... Type: noncoding Potential: -0.783 Folding energies... MFEI: -26.474 AMFE: -0.604 GC content %: 43.802

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
Cpapaya_evm.TU.contig_27558.2	RepBase (RepeatMasker)	2014-01-31	L1-14_CPa

Gene models

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