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_GRMZM2G110374 GRMZM2G110374	10	9846262	9847350	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_GRMZM2G110374_T02 GRMZM2G110374_T02 PAC:31005641	Low	No	647		Get ORF Coding potential... Type: noncoding Potential: -0.669 Folding energies... MFEI: -30.201 AMFE: -0.594 GC content %: 50.850
Zmays_GRMZM2G110374_T03 GRMZM2G110374_T03 PAC:31005642	Low	No	755		Get ORF Coding potential... Type: noncoding Potential: -0.714 Folding energies... MFEI: -29.086 AMFE: -0.624 GC content %: 46.623

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_GRMZM2G110374_T03	SwissProt	2015-06-01	Q6P6Z8	7.0e-14
Zmays_GRMZM2G110374_T02	SwissProt	2015-06-01	Q6P6Z8	2.0e-11

Gene models

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