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_GRMZM2G168909 GRMZM2G168909	6	159346429	159371692	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_GRMZM2G168909_T01 GRMZM2G168909_T01 PAC:31025371	High	No	980		Get ORF Coding potential... Type: noncoding Potential: -1.021 Folding energies... MFEI: -25.112 AMFE: -0.646 GC content %: 38.878
Zmays_GRMZM2G168909_T02 GRMZM2G168909_T02 PAC:31025370	Low	Yes	880		Get ORF Coding potential... Type: noncoding Potential: -0.818 Folding energies... MFEI: -34.875 AMFE: -0.699 GC content %: 49.886
Zmays_GRMZM2G168909_T03 GRMZM2G168909_T03 PAC:31025369	Low	Yes	732		Get ORF Coding potential... Type: noncoding Potential: -0.369 Folding energies... MFEI: -34.522 AMFE: -0.692 GC content %: 49.863

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_GRMZM2G168909_T02	RepBase (RepeatMasker)	2014-01-31	ATDNAI27T9C
Zmays_GRMZM2G168909_T03	RepBase (RepeatMasker)	2014-01-31	ATDNAI27T9C

Gene models

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