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
Sbicolor_Sobic.004G286900 Sobic.004G286900	Chr04	62920504	62923636	Phytozome	v3.1	Sorghum_bicolor	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
Sbicolor_Sobic.004G286900.1 Sobic.004G286900.1 PAC:32748425	Low	No	2344		Get ORF Coding potential... Type: noncoding Potential: -1.103 Folding energies... MFEI: -26.169 AMFE: -0.705 GC content %: 37.116
Sbicolor_Sobic.004G286900.2 Sobic.004G286900.2 PAC:32748424	Low	Yes	2825		Get ORF Coding potential... Type: noncoding Potential: -0.985 Folding energies... MFEI: -28.135 AMFE: -0.717 GC content %: 39.257

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
Sbicolor_Sobic.004G286900.2	RepBase (RepeatMasker)	2014-01-31	LINE1-62B_SBi
Sbicolor_Sobic.004G286900.2	Rfam	11.0	MIR394	2.6e-18
Sbicolor_Sobic.004G286900.1	RepBase (RepeatMasker)	2014-01-31	LINE1-62B_SBi

Gene models

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