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_4DS_BABF96DAF Traes_4DS_BABF96DAF	ta_iwgsc_4ds_v1_2280789	3528	7019	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_4DS_BABF96DAF.1 Traes_4DS_BABF96DAF.1 PAC:31954873	High	No	285		Get ORF Coding potential... Type: noncoding Potential: -0.450 Folding energies... MFEI: -40.772 AMFE: -0.628 GC content %: 64.912
Taestivum_Traes_4DS_BABF96DAF.2 Traes_4DS_BABF96DAF.2 PAC:31954870	High	No	308		Get ORF Coding potential... Type: noncoding Potential: -0.875 Folding energies... MFEI: -39.253 AMFE: -0.611 GC content %: 64.286
Taestivum_Traes_4DS_BABF96DAF.3 Traes_4DS_BABF96DAF.3 PAC:31954872	High	No	2152		Get ORF Coding potential... Type: noncoding Potential: -1.051 Folding energies... MFEI: -31.106 AMFE: -0.636 GC content %: 48.885
Taestivum_Traes_4DS_BABF96DAF.4 Traes_4DS_BABF96DAF.4 PAC:31954871	High	No	2074		Get ORF Coding potential... Type: noncoding Potential: -1.046 Folding energies... MFEI: -32.507 AMFE: -0.641 GC content %: 50.723
Taestivum_Traes_4DS_BABF96DAF.5 Traes_4DS_BABF96DAF.5 PAC:31954874	Low	Yes	281		Get ORF Coding potential... Type: noncoding Potential: -1.243 Folding energies... MFEI: -30.854 AMFE: -0.850 GC content %: 36.299
Taestivum_Traes_4DS_BABF96DAF.6 Traes_4DS_BABF96DAF.6 PAC:31954875	High	No	828		Get ORF Coding potential... Type: noncoding Potential: -1.149 Folding energies... MFEI: -25.978 AMFE: -0.613 GC content %: 42.391

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_4DS_BABF96DAF.5	Rfam	11.0	MIR1122	1.1e-9

Gene models

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