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.005G156900 Sobic.005G156900	Chr05	62879980	62882027	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.005G156900.1 Sobic.005G156900.1 PAC:32738594	Low	No	890		Get ORF Coding potential... Type: noncoding Potential: -1.330 Folding energies... MFEI: -29.191 AMFE: -0.654 GC content %: 44.607
Sbicolor_Sobic.005G156900.2 Sobic.005G156900.2 PAC:32738599	High	No	699		Get ORF Coding potential... Type: noncoding Potential: -1.302 Folding energies... MFEI: -29.485 AMFE: -0.634 GC content %: 46.495
Sbicolor_Sobic.005G156900.3 Sobic.005G156900.3 PAC:32738595	High	No	765		Get ORF Coding potential... Type: noncoding Potential: -1.313 Folding energies... MFEI: -30.301 AMFE: -0.657 GC content %: 46.144
Sbicolor_Sobic.005G156900.4 Sobic.005G156900.4 PAC:32738596	High	No	738		Get ORF Coding potential... Type: noncoding Potential: -1.309 Folding energies... MFEI: -29.729 AMFE: -0.643 GC content %: 46.206
Sbicolor_Sobic.005G156900.5 Sobic.005G156900.5 PAC:32738597	Low	No	863		Get ORF Coding potential... Type: noncoding Potential: -1.327 Folding energies... MFEI: -28.725 AMFE: -0.644 GC content %: 44.612
Sbicolor_Sobic.005G156900.6 Sobic.005G156900.6 PAC:32738598	Low	No	896		Get ORF Coding potential... Type: noncoding Potential: -1.331 Folding energies... MFEI: -27.879 AMFE: -0.636 GC content %: 43.862

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.005G156900.5	RepBase (RepeatMasker)	2014-01-31	EnSpm-N17_SBi
Sbicolor_Sobic.005G156900.6	RepBase (RepeatMasker)	2014-01-31	EnSpm-N17_SBi
Sbicolor_Sobic.005G156900.1	RepBase (RepeatMasker)	2014-01-31	EnSpm-N17_SBi

Gene models

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