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
Taestivum_Traes_4DL_1A406A566 Traes_4DL_1A406A566	ta_iwgsc_4dl_v3_14394155	5	10255	Phytozome	v2.2	Triticum_aestivum	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
Taestivum_Traes_4DL_1A406A566.7 Traes_4DL_1A406A566.7 PAC:31871863	Low	No	519		Get ORF Coding potential... Type: noncoding Potential: -1.073 Folding energies... MFEI: -24.046 AMFE: -0.538 GC content %: 44.701
Taestivum_Traes_4DL_1A406A566.8 Traes_4DL_1A406A566.8 PAC:31871864	High	No	453		Get ORF Coding potential... Type: noncoding Potential: -1.125 Folding energies... MFEI: -20.552 AMFE: -0.625 GC content %: 32.892

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
Taestivum_Traes_4DL_1A406A566.7	RepBase (RepeatMasker)	2014-01-31	DS-RICE4N

Gene models

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