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_27001.1 evm.TU.contig_27001.1	contig_27001	3181	3793	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_27001.1 evm.TU.contig_27001.1 PAC:16429477	Low	No	303		Get ORF Coding potential... Type: noncoding Potential: -1.112 Folding energies... MFEI: -34.950 AMFE: -0.683 GC content %: 51.155

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_27001.1	RepBase (RepeatMasker)	2014-01-31	Gypsy-7_CP-I

Gene models

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