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
Acoerulea_Aquca_2051_00001 Aquca_2051_00001	scaffold_2051	669	1691	Phytozome		[[Species:|]]"Species:" cannot be used as a page name in this wiki.	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
Acoerulea_Aquca_2051_00001.1 Aquca_2051_00001.1 PAC:22042713	Low	No	575		Get ORF Coding potential... Type: noncoding Potential: -0.799 Folding energies... MFEI: -17.287 AMFE: -0.526 GC content %: 32.870
Acoerulea_Aquca_2051_00001.2 Aquca_2051_00001.2 PAC:22042714	High	No	420		Get ORF Coding potential... Type: noncoding Potential: -0.708 Folding energies... MFEI: -18.762 AMFE: -0.597 GC content %: 31.429

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
Acoerulea_Aquca_2051_00001.1	RepBase (RepeatMasker)	2014-01-31	ATENSPM5

Gene models

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