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
Zmays_GRMZM2G426140 GRMZM2G426140	5	102550539	102556475	Phytozome	6a	Zea_mays	Coding? Yes

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
Zmays_GRMZM2G426140_T02 GRMZM2G426140_T02 PAC:30990771	High	No	343		Get ORF Coding potential... Type: noncoding Potential: -1.236 Folding energies... MFEI: -20.758 AMFE: -0.556 GC content %: 37.318
Zmays_GRMZM2G426140_T03 GRMZM2G426140_T03 PAC:30990770	Low	No	302		Get ORF Coding potential... Type: noncoding Potential: -1.204 Folding energies... MFEI: -22.781 AMFE: -0.510 GC content %: 44.702

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
Zmays_GRMZM2G426140_T03	RepBase (RepeatMasker)	2014-01-31	Helitron-3_ZM

Gene models

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