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_GRMZM2G029807 GRMZM2G029807	6	49565455	49569827	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_GRMZM2G029807_T01 GRMZM2G029807_T01 PAC:31021226	High	No	2378		Get ORF Coding potential... Type: noncoding Potential: -1.134 Folding energies... MFEI: -29.146 AMFE: -0.682 GC content %: 42.767
Zmays_GRMZM2G029807_T02 GRMZM2G029807_T02 PAC:31021222	Low	No	1628		Get ORF Coding potential... Type: noncoding Potential: -0.318 Folding energies... MFEI: -29.478 AMFE: -0.667 GC content %: 44.226
Zmays_GRMZM2G029807_T03 GRMZM2G029807_T03 PAC:31021225	High	No	1465		Get ORF Coding potential... Type: noncoding Potential: -1.110 Folding energies... MFEI: -29.693 AMFE: -0.665 GC content %: 44.642
Zmays_GRMZM2G029807_T04 GRMZM2G029807_T04 PAC:31021224	High	No	1481		Get ORF Coding potential... Type: noncoding Potential: -1.110 Folding energies... MFEI: -29.588 AMFE: -0.635 GC content %: 46.590
Zmays_GRMZM2G029807_T05 GRMZM2G029807_T05 PAC:31021221	Low	No	714		Get ORF Coding potential... Type: noncoding Potential: -0.250 Folding energies... MFEI: -26.022 AMFE: -0.664 GC content %: 39.216
Zmays_GRMZM2G029807_T06 GRMZM2G029807_T06 PAC:31021223	High	No	571		Get ORF Coding potential... Type: noncoding Potential: -1.049 Folding energies... MFEI: -15.814 AMFE: -0.473 GC content %: 33.450

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_GRMZM2G029807_T05	RepBase (RepeatMasker)	2014-01-31	SINE2-1a_SBi
Zmays_GRMZM2G029807_T02	SwissProt	2015-06-01	Q9ZVS8	5.0e-10
Zmays_GRMZM2G029807_T05	SwissProt	2015-06-01	Q9ZVS8	1.0e-10

Gene models

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