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_5AS_D170DC83A Traes_5AS_D170DC83A	ta_iwgsc_5as_v1_141085	4	1552	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_5AS_D170DC83A.1 Traes_5AS_D170DC83A.1 PAC:31898479	Low	Yes	295		Get ORF Coding potential... Type: noncoding Potential: -0.818 Folding energies... MFEI: -33.898 AMFE: -0.633 GC content %: 53.559
Taestivum_Traes_5AS_D170DC83A.2 Traes_5AS_D170DC83A.2 PAC:31898480	Low	Yes	637		Get ORF Coding potential... Type: noncoding Potential: -0.857 Folding energies... MFEI: -29.309 AMFE: -0.627 GC content %: 46.782

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_5AS_D170DC83A.2	Rfam	11.0	mir-598	0.0035
Taestivum_Traes_5AS_D170DC83A.1	Rfam	11.0	mir-598	0.0016

Gene models

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