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_7AL_5D4028AF1 Traes_7AL_5D4028AF1	ta_iwgsc_7al_v1_4461963	7	5508	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_7AL_5D4028AF1.4 Traes_7AL_5D4028AF1.4 PAC:31848566	Low	Yes	1712		Get ORF Coding potential... Type: noncoding Potential: -1.186 Folding energies... MFEI: -26.846 AMFE: -0.713 GC content %: 37.675
Taestivum_Traes_7AL_5D4028AF1.5 Traes_7AL_5D4028AF1.5 PAC:31848567	High	No	490		Get ORF Coding potential... Type: noncoding Potential: -1.056 Folding energies... MFEI: -21.429 AMFE: -0.574 GC content %: 37.347
Taestivum_Traes_7AL_5D4028AF1.6 Traes_7AL_5D4028AF1.6 PAC:31848568	High	No	374		Get ORF Coding potential... Type: noncoding Potential: -1.255 Folding energies... MFEI: -20.214 AMFE: -0.540 GC content %: 37.433

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_7AL_5D4028AF1.4	Rfam	11.0	MIR1122	3.9e-8

Gene models

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