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_AET3Gv20630500 [ AET3Gv20630500]	3D	369701274	369706722	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_AET3Gv20630500.19 AET3Gv20630500.19	High	No	1003	OG0072988		Get ORF Coding potential... Type: noncoding Potential: -1.062 Folding energies... MFEI: -29.541 AMFE: -0.689 GC content %: 42.871
Atauschii_AET3Gv20630500.25 AET3Gv20630500.25	High	No	802	OG0072989		Get ORF Coding potential... Type: noncoding Potential: -1.049 Folding energies... MFEI: -27.793 AMFE: -0.635 GC content %: 43.766
Atauschii_AET3Gv20630500.26 AET3Gv20630500.26	High	No	456	OG0016217		Get ORF Coding potential... Type: noncoding Potential: -1.029 Folding energies... MFEI: -29.605 AMFE: -0.634 GC content %: 46.711
Atauschii_AET3Gv20630500.30 AET3Gv20630500.30	High	No	411	OG0016217		Get ORF Coding potential... Type: noncoding Potential: -1.158 Folding energies... MFEI: -29.805 AMFE: -0.631 GC content %: 47.202
Atauschii_AET3Gv20630500.31 AET3Gv20630500.31	Low	No	554	OG0016217		Get ORF Coding potential... Type: noncoding Potential: -0.323 Folding energies... MFEI: -29.332 AMFE: -0.640 GC content %: 45.848
Atauschii_AET3Gv20630500.36 AET3Gv20630500.36	Low	Yes	1292	OG0025043		Get ORF Coding potential... Type: noncoding Potential: -1.037 Folding energies... MFEI: -28.885 AMFE: -0.702 GC content %: 41.176

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_AET3Gv20630500.36	Rfam	14.6	MIR1122	1.6e-7
Atauschii_AET3Gv20630500.31	SwissProt	2021-04-01	O22315	3.42e-14
Atauschii_AET3Gv20630500.36	SwissProt	2021-04-01	O22315	5.26e-4

Gene models

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