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_GRMZM2G089631 GRMZM2G089631	1	214530556	214536331	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_GRMZM2G089631_T01 GRMZM2G089631_T01 PAC:31012377	Low	No	891		Get ORF Coding potential... Type: noncoding Potential: -0.543 Folding energies... MFEI: -30.988 AMFE: -0.616 GC content %: 50.281
Zmays_GRMZM2G089631_T04 GRMZM2G089631_T04 PAC:31012379	High	No	1502		Get ORF Coding potential... Type: noncoding Potential: -0.945 Folding energies... MFEI: -28.688 AMFE: -0.612 GC content %: 46.871
Zmays_GRMZM2G089631_T05 GRMZM2G089631_T05 PAC:31012378	Low	No	596		Get ORF Coding potential... Type: noncoding Potential: -0.842 Folding energies... MFEI: -30.822 AMFE: -0.633 GC content %: 48.658

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_GRMZM2G089631_T01	SwissProt	2015-06-01	Q5ZI66	4.0e-5
Zmays_GRMZM2G089631_T05	RepBase (RepeatMasker)	2014-01-31	Gypsy-107_ZM-LTR

Gene models

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