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_6BS_6311CB06E Traes_6BS_6311CB06E	ta_iwgsc_6bs_v1_3045948	1961	17739	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_6BS_6311CB06E.10 Traes_6BS_6311CB06E.10 PAC:31914929	High	No	989		Get ORF Coding potential... Type: noncoding Potential: -1.157 Folding energies... MFEI: -24.408 AMFE: -0.608 GC content %: 40.142
Taestivum_Traes_6BS_6311CB06E.11 Traes_6BS_6311CB06E.11 PAC:31914931	High	No	657		Get ORF Coding potential... Type: noncoding Potential: -1.073 Folding energies... MFEI: -24.399 AMFE: -0.564 GC content %: 43.227
Taestivum_Traes_6BS_6311CB06E.12 Traes_6BS_6311CB06E.12 PAC:31914934	High	No	821		Get ORF Coding potential... Type: noncoding Potential: -1.121 Folding energies... MFEI: -22.814 AMFE: -0.585 GC content %: 38.977
Taestivum_Traes_6BS_6311CB06E.13 Traes_6BS_6311CB06E.13 PAC:31914933	Low	No	904		Get ORF Coding potential... Type: noncoding Potential: -1.063 Folding energies... MFEI: -23.097 AMFE: -0.578 GC content %: 39.934
Taestivum_Traes_6BS_6311CB06E.14 Traes_6BS_6311CB06E.14 PAC:31914932	Low	No	1434		Get ORF Coding potential... Type: noncoding Potential: -1.214 Folding energies... MFEI: -22.727 AMFE: -0.609 GC content %: 37.308
Taestivum_Traes_6BS_6311CB06E.8 Traes_6BS_6311CB06E.8 PAC:31914928	High	No	680		Get ORF Coding potential... Type: noncoding Potential: -1.081 Folding energies... MFEI: -25.265 AMFE: -0.580 GC content %: 43.529
Taestivum_Traes_6BS_6311CB06E.9 Traes_6BS_6311CB06E.9 PAC:31914930	High	No	1210		Get ORF Coding potential... Type: noncoding Potential: -1.190 Folding energies... MFEI: -24.000 AMFE: -0.618 GC content %: 38.843

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_6BS_6311CB06E.14	RepBase (RepeatMasker)	2014-01-31	Copia1-VV_I-int
Taestivum_Traes_6BS_6311CB06E.13	RepBase (RepeatMasker)	2014-01-31	Copia1-VV_I-int

Gene models

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