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	Source	Assembly	Species	Details
Zmays_GRMZM2G360339 GRMZM2G360339	6	115310129	115311599	Phytozome	6a	Zea_mays	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	Sequence	Details
Zmays_GRMZM2G360339_T01 GRMZM2G360339_T01 PAC:31021614	Low	No	466		Get ORF Coding potential... Type: noncoding Potential: -0.815 Folding energies... MFEI: -30.021 AMFE: -0.498 GC content %: 60.300
Zmays_GRMZM2G360339_T02 GRMZM2G360339_T02 PAC:31021615	High	No	721		Get ORF Coding potential... Type: noncoding Potential: -0.860 Folding energies... MFEI: -32.122 AMFE: -0.603 GC content %: 53.259
Zmays_GRMZM2G360339_T03 GRMZM2G360339_T03 PAC:31021616	Low	No	815		Get ORF Coding potential... Type: noncoding Potential: -0.917 Folding energies... MFEI: -31.067 AMFE: -0.583 GC content %: 53.252
Zmays_GRMZM2G360339_T04 GRMZM2G360339_T04 PAC:31021613	High	No	726		Get ORF Coding potential... Type: noncoding Potential: -1.059 Folding energies... MFEI: -32.287 AMFE: -0.604 GC content %: 53.444

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_GRMZM2G360339_T01	RepBase (RepeatMasker)	2014-01-31	MERMITE18D
Zmays_GRMZM2G360339_T03	RepBase (RepeatMasker)	2014-01-31	MERMITE18D

Gene models

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