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_GRMZM2G164233 GRMZM2G164233	1	277123723	277127542	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_GRMZM2G164233_T01 GRMZM2G164233_T01 PAC:31018517	High	No	1743		Get ORF Coding potential... Type: noncoding Potential: -0.985 Folding energies... MFEI: -23.769 AMFE: -0.600 GC content %: 39.644
Zmays_GRMZM2G164233_T03 GRMZM2G164233_T03 PAC:31018518	Low	No	483		Get ORF Coding potential... Type: noncoding Potential: -1.134 Folding energies... MFEI: -31.532 AMFE: -0.503 GC content %: 62.733

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_GRMZM2G164233_T03	SwissProt	2015-06-01	Q9M8J2	2.0e-17

Gene models

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