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_GRMZM2G448927 GRMZM2G448927	1	287819575	287827612	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_GRMZM2G448927_T02 GRMZM2G448927_T02 PAC:31015451	High	No	1466		Get ORF Coding potential... Type: noncoding Potential: -1.180 Folding energies... MFEI: -26.105 AMFE: -0.640 GC content %: 40.791
Zmays_GRMZM2G448927_T09 GRMZM2G448927_T09 PAC:31015452	Low	No	682		Get ORF Coding potential... Type: noncoding Potential: -1.265 Folding energies... MFEI: -30.704 AMFE: -0.578 GC content %: 53.079

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_GRMZM2G448927_T09	RepBase (RepeatMasker)	2014-01-31	CASTAWAY

Gene models

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