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_GRMZM2G068531 GRMZM2G068531	5	28214792	28217007	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_GRMZM2G068531_T01 GRMZM2G068531_T01 PAC:30984729	Low	No	1292		Get ORF Coding potential... Type: noncoding Potential: -1.074 Folding energies... MFEI: -27.314 AMFE: -0.556 GC content %: 49.149
Zmays_GRMZM2G068531_T02 GRMZM2G068531_T02 PAC:30984730	High	No	441		Get ORF Coding potential... Type: noncoding Potential: -1.144 Folding energies... MFEI: -30.590 AMFE: -0.477 GC content %: 64.172
Zmays_GRMZM2G068531_T03 GRMZM2G068531_T03 PAC:30984731	Low	No	1043		Get ORF Coding potential... Type: noncoding Potential: -1.166 Folding energies... MFEI: -25.973 AMFE: -0.554 GC content %: 46.884

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_GRMZM2G068531_T03	RepBase (RepeatMasker)	2014-01-31	DNA-1_FV
Zmays_GRMZM2G068531_T01	RepBase (RepeatMasker)	2014-01-31	Copia-141_SB-LTR

Gene models

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