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_GRMZM2G015906 GRMZM2G015906	8	109484696	109491322	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_GRMZM2G015906_T02 GRMZM2G015906_T02 PAC:30976195	High	No	849		Get ORF Coding potential... Type: noncoding Potential: -1.137 Folding energies... MFEI: -21.508 AMFE: -0.578 GC content %: 37.220
Zmays_GRMZM2G015906_T03 GRMZM2G015906_T03 PAC:30976194	Low	No	342		Get ORF Coding potential... Type: noncoding Potential: -1.303 Folding energies... MFEI: -30.234 AMFE: -0.525 GC content %: 57.602

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_GRMZM2G015906_T03	RepBase (RepeatMasker)	2014-01-31	EnSpm-35_SBi

Gene models

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