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_39304 evm.TU.contig_39304	contig_39304	245	724	Phytozome	ASGPBv0.4	Carica_papaya	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
Cpapaya_evm.TU.contig_39304.1 evm.TU.contig_39304.1 PAC:16431318	Low	No	480		Get ORF Coding potential... Type: noncoding Potential: -0.208 Folding energies... MFEI: -25.938 AMFE: -0.585 GC content %: 44.375

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_39304.1	RepBase (RepeatMasker)	2014-01-31	L1-6_CPa

Gene models

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