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_BBD279E25 Traes_6BS_BBD279E25	ta_iwgsc_6bs_v1_2931695	2	1929	Phytozome	v2.2	Triticum_aestivum	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
Taestivum_Traes_6BS_BBD279E25.1 Traes_6BS_BBD279E25.1 PAC:31842590	Low	No	550		Get ORF Coding potential... Type: noncoding Potential: -0.018 Folding energies... MFEI: -29.964 AMFE: -0.690 GC content %: 43.455
Taestivum_Traes_6BS_BBD279E25.2 Traes_6BS_BBD279E25.2 PAC:31842588	High	No	801		Get ORF Coding potential... Type: noncoding Potential: -1.395 Folding energies... MFEI: -23.508 AMFE: -0.604 GC content %: 38.951
Taestivum_Traes_6BS_BBD279E25.3 Traes_6BS_BBD279E25.3 PAC:31842591	Low	No	1142		Get ORF Coding potential... Type: noncoding Potential: -0.401 Folding energies... MFEI: -29.597 AMFE: -0.683 GC content %: 43.345
Taestivum_Traes_6BS_BBD279E25.4 Traes_6BS_BBD279E25.4 PAC:31842589	Low	No	698		Get ORF Coding potential... Type: noncoding Potential: -0.308 Folding energies... MFEI: -28.954 AMFE: -0.687 GC content %: 42.120
Taestivum_Traes_6BS_BBD279E25.5 Traes_6BS_BBD279E25.5 PAC:31842592	Low	No	578		Get ORF Coding potential... Type: noncoding Potential: -0.089 Folding energies... MFEI: -29.343 AMFE: -0.681 GC content %: 43.080
Taestivum_Traes_6BS_BBD279E25.6 Traes_6BS_BBD279E25.6 PAC:31842593	Low	No	303		Get ORF Coding potential... Type: noncoding Potential: -0.063 Folding energies... MFEI: -23.894 AMFE: -0.540 GC content %: 44.224

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_BBD279E25.3	RepBase (RepeatMasker)	2014-01-31	LINE1-22_ZM

Gene models

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