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_GRMZM5G873681 GRMZM5G873681	5	28214819	28216875	Phytozome	6a	Zea_mays	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
Zmays_GRMZM5G873681_T01 GRMZM5G873681_T01 PAC:30986023	High	No	304		Get ORF Coding potential... Type: noncoding Potential: -0.698 Folding energies... MFEI: -29.737 AMFE: -0.529 GC content %: 56.250
Zmays_GRMZM5G873681_T02 GRMZM5G873681_T02 PAC:30986022	Low	No	2057		Get ORF Coding potential... Type: noncoding Potential: -1.186 Folding energies... MFEI: -31.565 AMFE: -0.640 GC content %: 49.344

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_GRMZM5G873681_T02	RepBase (RepeatMasker)	2014-01-31	DNA-1_FV

Gene models

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