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_GRMZM2G098857 GRMZM2G098857	5	87156733	87160116	Phytozome	6a	Zea_mays	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	Sequence	Details
Zmays_GRMZM2G098857_T03 GRMZM2G098857_T03 PAC:30985336	Low	No	942		Get ORF Coding potential... Type: noncoding Potential: -0.419 Folding energies... MFEI: -27.155 AMFE: -0.622 GC content %: 43.631
Zmays_GRMZM2G098857_T05 GRMZM2G098857_T05 PAC:30985337	Low	No	751		Get ORF Coding potential... Type: noncoding Potential: -0.057 Folding energies... MFEI: -26.138 AMFE: -0.650 GC content %: 40.213

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_GRMZM2G098857_T03	RepBase (RepeatMasker)	2014-01-31	STOWAWAY40_OS
Zmays_GRMZM2G098857_T03	SwissProt	2015-06-01	Q9LV09	3.0e-6
Zmays_GRMZM2G098857_T05	SwissProt	2015-06-01	Q5M823	3.0e-10

Gene models

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