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
Csativus_Cucsa.369900 Cucsa.369900	scaffold03665	196	1440	Phytozome	v1.0	Cucumis_sativus	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
Csativus_Cucsa.369900.1 Cucsa.369900.1 PAC:16981744	Low	No	520		Get ORF Coding potential... Type: noncoding Potential: -0.027 Folding energies... MFEI: -21.442 AMFE: -0.483 GC content %: 44.423
Csativus_Cucsa.369900.2 Cucsa.369900.2 PAC:16981745	Low	No	863		Get ORF Coding potential... Type: noncoding Potential: -0.036 Folding energies... MFEI: -23.511 AMFE: -0.562 GC content %: 41.831

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
Csativus_Cucsa.369900.2	SwissProt	2015-06-01	O65399	1.0e-14
Csativus_Cucsa.369900.1	SwissProt	2015-06-01	O65399	1.0e-15

Gene models

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