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_GRMZM2G001572 GRMZM2G001572	6	141136206	141138045	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_GRMZM2G001572_T01 GRMZM2G001572_T01 PAC:31026424	High	No	1370		Get ORF Coding potential... Type: noncoding Potential: -1.163 Folding energies... MFEI: -23.526 AMFE: -0.556 GC content %: 42.336
Zmays_GRMZM2G001572_T02 GRMZM2G001572_T02 PAC:31026423	High	No	786		Get ORF Coding potential... Type: noncoding Potential: -1.073 Folding energies... MFEI: -24.593 AMFE: -0.546 GC content %: 45.038
Zmays_GRMZM2G001572_T03 GRMZM2G001572_T03 PAC:31026422	High	No	1370		Get ORF Coding potential... Type: noncoding Potential: -1.163 Folding energies... MFEI: -23.526 AMFE: -0.556 GC content %: 42.336
Zmays_GRMZM2G001572_T04 GRMZM2G001572_T04 PAC:31026421	Low	No	1558		Get ORF Coding potential... Type: noncoding Potential: -1.178 Folding energies... MFEI: -24.281 AMFE: -0.580 GC content %: 41.849

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_GRMZM2G001572_T04	RepBase (RepeatMasker)	2014-01-31	Helitron-3_ZM

Gene models

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