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
Osativa_LOC_Os05g38219 LOC_Os05g38219	Chr5	22406439	22412412	Phytozome	v7.0	Oryza_sativa_Japonica_Group	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
Osativa_LOC_Os05g38219.1 LOC_Os05g38219.1 PAC:24150592	Low	No	3084		Get ORF Coding potential... Type: noncoding Potential: -1.194 Folding energies... MFEI: -32.059 AMFE: -0.650 GC content %: 49.351
Osativa_LOC_Os05g38219.2 LOC_Os05g38219.2 PAC:24150593	Low	No	2719		Get ORF Coding potential... Type: noncoding Potential: -1.180 Folding energies... MFEI: -28.871 AMFE: -0.628 GC content %: 45.973

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
Osativa_LOC_Os05g38219.1	SwissProt	2015-06-01	Q84TF0	2.0e-4
Osativa_LOC_Os05g38219.2	SwissProt	2015-06-01	O80944	1.0e-18

Gene models

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