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
Atauschii_AET3Gv20587300 [ AET3Gv20587300]	3D	342401402	342409349	v4	Aegilops tauschii (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
Atauschii_AET3Gv20587300.39 AET3Gv20587300.39	Low	No	7944	OG0001155		Get ORF Coding potential... Type: noncoding Potential: -0.145 Folding energies... MFEI: -25.950 AMFE: -0.670 GC content %: 38.734
Atauschii_AET3Gv20587300.43 AET3Gv20587300.43	Low	No	6893	OG0001155		Get ORF Coding potential... Type: noncoding Potential: -0.140 Folding energies... MFEI: -26.227 AMFE: -0.671 GC content %: 39.098
Atauschii_AET3Gv20587300.45 AET3Gv20587300.45	High	No	263	OG0001155		Get ORF Coding potential... Type: noncoding Potential: -1.264 Folding energies... MFEI: -31.483 AMFE: -0.575 GC content %: 54.753
Atauschii_AET3Gv20587300.56 AET3Gv20587300.56	Low	No	1619	OG0001155		Get ORF Coding potential... Type: noncoding Potential: -0.256 Folding energies... MFEI: -25.170 AMFE: -0.650 GC content %: 38.728
Atauschii_AET3Gv20587300.57 AET3Gv20587300.57	Low	No	1149	OG0001155		Get ORF Coding potential... Type: noncoding Potential: -0.117 Folding energies... MFEI: -26.902 AMFE: -0.656 GC content %: 40.992
Atauschii_AET3Gv20587300.58 AET3Gv20587300.58	Low	No	1916	OG0001155		Get ORF Coding potential... Type: noncoding Potential: -0.220 Folding energies... MFEI: -27.552 AMFE: -0.694 GC content %: 39.718
Atauschii_AET3Gv20587300.59 AET3Gv20587300.59	High	No	822	OG0001155		Get ORF Coding potential... Type: noncoding Potential: -1.101 Folding energies... MFEI: -24.258 AMFE: -0.629 GC content %: 38.564
Atauschii_AET3Gv20587300.60 AET3Gv20587300.60	High	No	923	OG0001155		Get ORF Coding potential... Type: noncoding Potential: -1.118 Folding energies... MFEI: -24.399 AMFE: -0.638 GC content %: 38.245
Atauschii_AET3Gv20587300.61 AET3Gv20587300.61	High	No	856	OG0001155		Get ORF Coding potential... Type: noncoding Potential: -1.301 Folding energies... MFEI: -25.783 AMFE: -0.663 GC content %: 38.902
Atauschii_AET3Gv20587300.62 AET3Gv20587300.62	High	No	539	OG0001155		Get ORF Coding potential... Type: noncoding Potential: -1.028 Folding energies... MFEI: -22.801 AMFE: -0.597 GC content %: 38.219
Atauschii_AET3Gv20587300.63 AET3Gv20587300.63	High	No	789	OG0001155		Get ORF Coding potential... Type: noncoding Potential: -1.309 Folding energies... MFEI: -23.295 AMFE: -0.615 GC content %: 37.896

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
Atauschii_AET3Gv20587300.58	SwissProt	2021-04-01	Q8RXL8	1.22e-14
Atauschii_AET3Gv20587300.39	RepBase (RepeatMasker)	2014-01-31	LINE/L1
Atauschii_AET3Gv20587300.39	SwissProt	2021-04-01	P51138	2.59e-25
Atauschii_AET3Gv20587300.43	RepBase (RepeatMasker)	2014-01-31	LINE/L1
Atauschii_AET3Gv20587300.43	SwissProt	2021-04-01	P51138	2.24e-25
Atauschii_AET3Gv20587300.56	SwissProt	2021-04-01	Q8RXL8	1.1e-14
Atauschii_AET3Gv20587300.57	SwissProt	2021-04-01	Q8RXL8	2.35e-15

Gene models

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