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	Assembly	Species	Details
Tdicoccoides_TRIDC6BG003200 [ TRIDC6BG003200]	6B	16398376	16409665	v1	Triticum dicoccoides (Ensembl Plants 51)	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	Orthologous group	Sequence	Details
Tdicoccoides_TRIDC6BG003200.16 TRIDC6BG003200.16	Low	No	3445	OG0015415		Get ORF Coding potential... Type: noncoding Potential: -0.024 Folding energies... MFEI: -28.473 AMFE: -0.684 GC content %: 41.626
Tdicoccoides_TRIDC6BG003200.20 TRIDC6BG003200.20	High	No	2808	OG0015415		Get ORF Coding potential... Type: noncoding Potential: -1.261 Folding energies... MFEI: -27.507 AMFE: -0.664 GC content %: 41.417
Tdicoccoides_TRIDC6BG003200.27 TRIDC6BG003200.27	High	No	2472	OG0015415		Get ORF Coding potential... Type: noncoding Potential: -1.248 Folding energies... MFEI: -26.622 AMFE: -0.672 GC content %: 39.604
Tdicoccoides_TRIDC6BG003200.35 TRIDC6BG003200.35	Low	No	2538	OG0015415		Get ORF Coding potential... Type: noncoding Potential: -0.973 Folding energies... MFEI: -26.584 AMFE: -0.658 GC content %: 40.426
Tdicoccoides_TRIDC6BG003200.36 TRIDC6BG003200.36	Low	No	808	OG0365003		Get ORF Coding potential... Type: noncoding Potential: -0.350 Folding energies... MFEI: -26.807 AMFE: -0.683 GC content %: 39.233

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
Tdicoccoides_TRIDC6BG003200.16	SwissProt	2021-04-01	Q6VAK3	1.86e-16
Tdicoccoides_TRIDC6BG003200.35	SwissProt	2021-04-01	Q6VAK3	1.08e-8
Tdicoccoides_TRIDC6BG003200.36	SwissProt	2021-04-01	Q6VAK4	6.64e-12

Gene models

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