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_4BL_45CA283A7 Traes_4BL_45CA283A7	ta_iwgsc_4bl_v1_6964387	343	13438	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_4BL_45CA283A7.30 Traes_4BL_45CA283A7.30 PAC:32013908	Low	No	1201		Get ORF Coding potential... Type: noncoding Potential: -0.620 Folding energies... MFEI: -30.525 AMFE: -0.627 GC content %: 48.709
Taestivum_Traes_4BL_45CA283A7.32 Traes_4BL_45CA283A7.32 PAC:32013910	Low	No	1301		Get ORF Coding potential... Type: noncoding Potential: -0.103 Folding energies... MFEI: -23.828 AMFE: -0.620 GC content %: 38.432
Taestivum_Traes_4BL_45CA283A7.34 Traes_4BL_45CA283A7.34 PAC:32013916	Low	No	596		Get ORF Coding potential... Type: noncoding Potential: -1.254 Folding energies... MFEI: -28.691 AMFE: -0.626 GC content %: 45.805
Taestivum_Traes_4BL_45CA283A7.35 Traes_4BL_45CA283A7.35 PAC:32013912	High	No	654		Get ORF Coding potential... Type: noncoding Potential: -1.075 Folding energies... MFEI: -19.266 AMFE: -0.500 GC content %: 38.532
Taestivum_Traes_4BL_45CA283A7.36 Traes_4BL_45CA283A7.36 PAC:32013913	Low	No	343		Get ORF Coding potential... Type: noncoding Potential: -1.058 Folding energies... MFEI: -27.376 AMFE: -0.614 GC content %: 44.606
Taestivum_Traes_4BL_45CA283A7.37 Traes_4BL_45CA283A7.37 PAC:32013914	High	No	344		Get ORF Coding potential... Type: noncoding Potential: -1.151 Folding energies... MFEI: -27.297 AMFE: -0.580 GC content %: 47.093
Taestivum_Traes_4BL_45CA283A7.38 Traes_4BL_45CA283A7.38 PAC:32013915	Low	No	732		Get ORF Coding potential... Type: noncoding Potential: -1.147 Folding energies... MFEI: -28.948 AMFE: -0.621 GC content %: 46.585
Taestivum_Traes_4BL_45CA283A7.39 Traes_4BL_45CA283A7.39 PAC:32013917	High	No	312		Get ORF Coding potential... Type: noncoding Potential: -1.259 Folding energies... MFEI: -19.455 AMFE: -0.552 GC content %: 35.256

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_4BL_45CA283A7.36	RepBase (RepeatMasker)	2014-01-31	LINE1-52_ZM

Gene models

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