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_GRMZM2G527028 GRMZM2G527028	8	64089015	64090929	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_GRMZM2G527028_T01 GRMZM2G527028_T01 PAC:30981876	Low	Yes	1788		Get ORF Coding potential... Type: noncoding Potential: -1.088 Folding energies... MFEI: -32.176 AMFE: -0.716 GC content %: 44.911
Zmays_GRMZM2G527028_T02 GRMZM2G527028_T02 PAC:30981874	Low	Yes	543		Get ORF Coding potential... Type: noncoding Potential: -1.151 Folding energies... MFEI: -34.162 AMFE: -0.779 GC content %: 43.831
Zmays_GRMZM2G527028_T03 GRMZM2G527028_T03 PAC:30981875	High	No	903		Get ORF Coding potential... Type: noncoding Potential: -1.011 Folding energies... MFEI: -30.631 AMFE: -0.660 GC content %: 46.401

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_GRMZM2G527028_T01	RepBase (RepeatMasker)	2014-01-31	Gypsy-13_Mad-I
Zmays_GRMZM2G527028_T02	RepBase (RepeatMasker)	2014-01-31	Gypsy-13_Mad-I

Gene models

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