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_AET2Gv20604600 [ AET2Gv20604600]	2D	327080126	327110862	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_AET2Gv20604600.19 AET2Gv20604600.19	High	No	708	OG0070565		Get ORF Coding potential... Type: noncoding Potential: -0.855 Folding energies... MFEI: -38.573 AMFE: -0.698 GC content %: 55.226
Atauschii_AET2Gv20604600.3 AET2Gv20604600.3	Low	No	482	OG0070566		Get ORF Coding potential... Type: noncoding Potential: -0.377 Folding energies... MFEI: -40.983 AMFE: -0.631 GC content %: 64.938
Atauschii_AET2Gv20604600.56 AET2Gv20604600.56	Low	No	337	OG0070567		Get ORF Coding potential... Type: noncoding Potential: -0.582 Folding energies... MFEI: -22.493 AMFE: -0.579 GC content %: 38.872
Atauschii_AET2Gv20604600.57 AET2Gv20604600.57	High	No	810	OG0016022		Get ORF Coding potential... Type: noncoding Potential: -0.523 Folding energies... MFEI: -24.370 AMFE: -0.654 GC content %: 37.284
Atauschii_AET2Gv20604600.58 AET2Gv20604600.58	High	No	1103	OG0016022		Get ORF Coding potential... Type: noncoding Potential: -0.561 Folding energies... MFEI: -23.418 AMFE: -0.647 GC content %: 36.174
Atauschii_AET2Gv20604600.59 AET2Gv20604600.59	Low	No	633	OG0016022		Get ORF Coding potential... Type: noncoding Potential: -1.164 Folding energies... MFEI: -23.681 AMFE: -0.627 GC content %: 37.757

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_AET2Gv20604600.59	RepBase (RepeatMasker)	2014-01-31	LINE/L1
Atauschii_AET2Gv20604600.3	SwissProt	2021-04-01	Q54R62	4.3e-10
Atauschii_AET2Gv20604600.56	SwissProt	2021-04-01	Q54R62	4.8e-5

Gene models

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