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_Zm00001d021335 [ Zm00001d021335]	7	149129974	149134091	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_Zm00001d021335_T004 Zm00001d021335_T004	Low	No	2851	[1]		Get ORF Coding potential... Type: noncoding Potential: -0.690 Folding energies... MFEI: -29.162 AMFE: -0.679 GC content %: 42.967
Zmays_Zm00001d021335_T005 Zm00001d021335_T005	Low	No	3549	[2]		Get ORF Coding potential... Type: noncoding Potential: -1.040 Folding energies... MFEI: -28.397 AMFE: -0.699 GC content %: 40.631

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_Zm00001d021335_T004	SwissProt	2021-04-01	O94285	4.9e-5
Zmays_Zm00001d021335_T005	SwissProt	2021-04-01	Q9D2C6	2.95e-8
Zmays_Zm00001d021335_T004	RepBase (RepeatMasker)	0000-00-00	LINE/L1
Zmays_Zm00001d021335_T005	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).