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_GRMZM2G035356 GRMZM2G035356	2	214320662	214324612	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_GRMZM2G035356_T01 GRMZM2G035356_T01 PAC:30969793	Low	No	825		Get ORF Coding potential... Type: noncoding Potential: -0.281 Folding energies... MFEI: -29.855 AMFE: -0.630 GC content %: 47.394
Zmays_GRMZM2G035356_T02 GRMZM2G035356_T02 PAC:30969794	Low	No	718		Get ORF Coding potential... Type: noncoding Potential: -0.384 Folding energies... MFEI: -25.446 AMFE: -0.609 GC content %: 41.783
Zmays_GRMZM2G035356_T03 GRMZM2G035356_T03 PAC:30969795	High	No	1766		Get ORF Coding potential... Type: noncoding Potential: -0.733 Folding energies... MFEI: -30.504 AMFE: -0.674 GC content %: 45.243

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_GRMZM2G035356_T01	RepBase (RepeatMasker)	2014-01-31	Gypsy-106_ZM-I
Zmays_GRMZM2G035356_T02	RepBase (RepeatMasker)	2014-01-31	Gypsy-106_ZM-I

Gene models

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