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
Ahalleri_Araha.19412s0001 Araha.19412s0001	Scaffold19412	15	1314	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
Ahalleri_Araha.19412s0001.1 Araha.19412s0001.1 PAC:28840317	Low	No	809		Get ORF Coding potential... Type: coding Potential: 0.017 Folding energies... MFEI: -23.288 AMFE: -0.636 GC content %: 36.588
Ahalleri_Araha.19412s0001.2 Araha.19412s0001.2 PAC:28840318	Low	No	759		Get ORF Coding potential... Type: coding Potential: 0.036 Folding energies... MFEI: -23.900 AMFE: -0.650 GC content %: 36.759

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
Ahalleri_Araha.19412s0001.1	RepBase (RepeatMasker)	2014-01-31	ATCopia24I
Ahalleri_Araha.19412s0001.2	RepBase (RepeatMasker)	2014-01-31	ATCopia24I

Gene models

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