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_GRMZM2G428197 GRMZM2G428197	6	169176822	169184545	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_GRMZM2G428197_T01 GRMZM2G428197_T01 PAC:31025453	Low	No	1597		Get ORF Coding potential... Type: noncoding Potential: -1.060 Folding energies... MFEI: -26.669 AMFE: -0.594 GC content %: 44.897
Zmays_GRMZM2G428197_T04 GRMZM2G428197_T04 PAC:31025455	High	No	939		Get ORF Coding potential... Type: noncoding Potential: -0.928 Folding energies... MFEI: -26.528 AMFE: -0.555 GC content %: 47.817
Zmays_GRMZM2G428197_T06 GRMZM2G428197_T06 PAC:31025458	High	No	931		Get ORF Coding potential... Type: noncoding Potential: -0.928 Folding energies... MFEI: -25.639 AMFE: -0.628 GC content %: 40.816

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_GRMZM2G428197_T01	RepBase (RepeatMasker)	2014-01-31	Copia12-ZM_I-int

Gene models

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