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_Zm00001d032350 [ Zm00001d032350]	1	223440445	223444783	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_Zm00001d032350_T001 Zm00001d032350_T001	Low	No	2967	[1]		Get ORF Coding potential... Type: noncoding Potential: -0.575 Folding energies... MFEI: -27.708 AMFE: -0.660 GC content %: 41.995
Zmays_Zm00001d032350_T005 Zm00001d032350_T005	Low	No	2089	[2]		Get ORF Coding potential... Type: noncoding Potential: -0.695 Folding energies... MFEI: -28.808 AMFE: -0.678 GC content %: 42.508
Zmays_Zm00001d032350_T006 Zm00001d032350_T006	Low	No	2332	[3]		Get ORF Coding potential... Type: noncoding Potential: -0.536 Folding energies... MFEI: -28.877 AMFE: -0.658 GC content %: 43.911
Zmays_Zm00001d032350_T007 Zm00001d032350_T007	High	No	2321	[4]		Get ORF Coding potential... Type: noncoding Potential: -0.535 Folding energies... MFEI: -29.220 AMFE: -0.669 GC content %: 43.688
Zmays_Zm00001d032350_T009 Zm00001d032350_T009	High	No	2650	[5]		Get ORF Coding potential... Type: noncoding Potential: -0.581 Folding energies... MFEI: -28.257 AMFE: -0.670 GC content %: 42.151

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_Zm00001d032350_T001	RepBase (RepeatMasker)	0000-00-00	DNA/hAT-Ac
Zmays_Zm00001d032350_T005	RepBase (RepeatMasker)	0000-00-00	DNA/hAT-Ac
Zmays_Zm00001d032350_T006	RepBase (RepeatMasker)	0000-00-00	DNA/hAT-Ac

Gene models

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