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_GRMZM2G042881 GRMZM2G042881	1	75150359	75154220	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_GRMZM2G042881_T01 GRMZM2G042881_T01 PAC:31013980	Low	Yes	2376		Get ORF Coding potential... Type: noncoding Potential: -1.053 Folding energies... MFEI: -27.891 AMFE: -0.655 GC content %: 42.551
Zmays_GRMZM2G042881_T02 GRMZM2G042881_T02 PAC:31013982	High	No	208		Get ORF Coding potential... Type: noncoding Potential: -1.406 Folding energies... MFEI: -31.587 AMFE: -0.626 GC content %: 50.481
Zmays_GRMZM2G042881_T03 GRMZM2G042881_T03 PAC:31013981	High	No	683		Get ORF Coding potential... Type: noncoding Potential: -0.753 Folding energies... MFEI: -28.770 AMFE: -0.614 GC content %: 46.852

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_GRMZM2G042881_T01	Rfam	11.0	MIR1122	2.0e-4
Zmays_GRMZM2G042881_T01	RepBase (RepeatMasker)	2014-01-31	STOWAWAY1_SB

Gene models

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