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_7AS_BA2B54EE1 Traes_7AS_BA2B54EE1	ta_iwgsc_7as_v1_4245247	4	2111	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_7AS_BA2B54EE1.1 Traes_7AS_BA2B54EE1.1 PAC:31785389	High	No	1127		Get ORF Coding potential... Type: noncoding Potential: -0.488 Folding energies... MFEI: -32.981 AMFE: -0.667 GC content %: 49.423
Taestivum_Traes_7AS_BA2B54EE1.2 Traes_7AS_BA2B54EE1.2 PAC:31785390	Low	Yes	1053		Get ORF Coding potential... Type: noncoding Potential: -0.479 Folding energies... MFEI: -35.850 AMFE: -0.720 GC content %: 49.763

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_7AS_BA2B54EE1.2	miRBase	21.0	tae-miR5049-3p	0.002
Taestivum_Traes_7AS_BA2B54EE1.2	miRBase	21.0	bdi-miR5049-3p	0.002
Taestivum_Traes_7AS_BA2B54EE1.2	Rfam	11.0	MIR1122	7.4e-14
Taestivum_Traes_7AS_BA2B54EE1.2	RepBase (RepeatMasker)	2014-01-31	ICARUS_TM

Gene models

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