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_Zm00001d033584 [ Zm00001d033584]	1	267873372	267875853	v4	Zea mays (Phytozome 13)	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	Orthologous group	Sequence	Details
Zmays_Zm00001d033584_T001 Zm00001d033584_T001	High	No	2031	[1]		Get ORF Coding potential... Type: noncoding Potential: -1.040 Folding energies... MFEI: -28.557 AMFE: -0.611 GC content %: 46.726
Zmays_Zm00001d033584_T002 Zm00001d033584_T002	Low	No	1791	[2]		Get ORF Coding potential... Type: noncoding Potential: -1.028 Folding energies... MFEI: -31.240 AMFE: -0.658 GC content %: 47.460

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_Zm00001d033584_T002	RepBase (RepeatMasker)	0000-00-00	LTR/Gypsy

Gene models

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