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_Zm00001d035346 [ Zm00001d035346]	6	22716458	22744646	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_Zm00001d035346_T001 Zm00001d035346_T001	High	No	884	[1]		Get ORF Coding potential... Type: noncoding Potential: -1.190 Folding energies... MFEI: -28.428 AMFE: -0.628 GC content %: 45.249
Zmays_Zm00001d035346_T117 Zm00001d035346_T117	Low	No	1262	[2]		Get ORF Coding potential... Type: noncoding Potential: -1.256 Folding energies... MFEI: -29.342 AMFE: -0.638 GC content %: 45.959
Zmays_Zm00001d035346_T172 Zm00001d035346_T172	Low	No	600	[3]		Get ORF Coding potential... Type: noncoding Potential: -0.507 Folding energies... MFEI: -23.317 AMFE: -0.588 GC content %: 39.667

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_Zm00001d035346_T117	SwissProt	2021-04-01	Q8H930	2.53e-10
Zmays_Zm00001d035346_T172	SwissProt	2021-04-01	Q8H930	7.94e-11

Gene models

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