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_GRMZM2G422210 GRMZM2G422210	3	137706864	137710786	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_GRMZM2G422210_T01 GRMZM2G422210_T01 PAC:31033884	Low	No	1101		Get ORF Coding potential... Type: noncoding Potential: -1.072 Folding energies... MFEI: -26.349 AMFE: -0.646 GC content %: 40.781
Zmays_GRMZM2G422210_T02 GRMZM2G422210_T02 PAC:31033883	High	No	1327		Get ORF Coding potential... Type: noncoding Potential: -1.086 Folding energies... MFEI: -28.885 AMFE: -0.674 GC content %: 42.879
Zmays_GRMZM2G422210_T03 GRMZM2G422210_T03 PAC:31033882	High	No	2379		Get ORF Coding potential... Type: noncoding Potential: -1.171 Folding energies... MFEI: -27.987 AMFE: -0.661 GC content %: 42.329

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_GRMZM2G422210_T01	SwissProt	2015-06-01	P56277	1.0e-4
Zmays_GRMZM2G422210_T01	RepBase (RepeatMasker)	2014-01-31	Helitron-4_ZM

Gene models

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