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	Assembly	Species	Details
Zmays_Zm00001d027257 [ Zm00001d027257]	1	560956	568038	v4	Zea mays (Phytozome 13)	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	Orthologous group	Sequence	Details
Zmays_Zm00001d027257_T003 Zm00001d027257_T003	High	No	2139	[1]		Get ORF Coding potential... Type: noncoding Potential: -0.696 Folding energies... MFEI: -32.375 AMFE: -0.693 GC content %: 46.704
Zmays_Zm00001d027257_T006 Zm00001d027257_T006	High	No	2565	[2]		Get ORF Coding potential... Type: noncoding Potential: -0.713 Folding energies... MFEI: -31.875 AMFE: -0.679 GC content %: 46.940
Zmays_Zm00001d027257_T007 Zm00001d027257_T007	Low	No	3900	[3]		Get ORF Coding potential... Type: noncoding Potential: -0.628 Folding energies... MFEI: -31.618 AMFE: -0.659 GC content %: 48.000

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_Zm00001d027257_T007	RepBase (RepeatMasker)	0000-00-00	LINE/L1

Gene models

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