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
Cclementina_Ciclev10029678m.g Ciclev10029678m.g	scaffold_8	20361175	20363775	Phytozome	v1.0	Citrus_clementina	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
Cclementina_Ciclev10029675m Ciclev10029675m PAC:20812688	Low	No	538		Get ORF Coding potential... Type: noncoding Potential: -0.953 Folding energies... MFEI: -21.840 AMFE: -0.590 GC content %: 36.989
Cclementina_Ciclev10029678m Ciclev10029678m PAC:20812687	Low	No	620		Get ORF Coding potential... Type: noncoding Potential: -0.994 Folding energies... MFEI: -22.258 AMFE: -0.603 GC content %: 36.935

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
Cclementina_Ciclev10029678m	RepBase (RepeatMasker)	2014-01-31	Copia-41_GM-I
Cclementina_Ciclev10029675m	SwissProt	2015-06-01	Q97I51	4.0e-5
Cclementina_Ciclev10029678m	SwissProt	2015-06-01	Q97I51	7.0e-5
Cclementina_Ciclev10029675m	RepBase (RepeatMasker)	2014-01-31	Copia-41_GM-I

Gene models

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