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_AET1Gv20408100 [ AET1Gv20408100]	1D	224526548	224533364	v4	Aegilops tauschii (Ensembl Plants 51)	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	Orthologous group	Sequence	Details
Atauschii_AET1Gv20408100.1 AET1Gv20408100.1	Low	Yes	1123	OG0002324		Get ORF Coding potential... Type: noncoding Potential: -0.854 Folding energies... MFEI: -31.398 AMFE: -0.640 GC content %: 49.065
Atauschii_AET1Gv20408100.2 AET1Gv20408100.2	Low	Yes	946	OG0002324		Get ORF Coding potential... Type: noncoding Potential: -1.004 Folding energies... MFEI: -33.171 AMFE: -0.650 GC content %: 51.057
Atauschii_AET1Gv20408100.3 AET1Gv20408100.3	Low	Yes	516	OG0002324		Get ORF Coding potential... Type: noncoding Potential: -1.093 Folding energies... MFEI: -29.167 AMFE: -0.690 GC content %: 42.248
Atauschii_AET1Gv20408100.4 AET1Gv20408100.4	High	No	400	OG0068328		Get ORF Coding potential... Type: noncoding Potential: -0.827 Folding energies... MFEI: -36.700 AMFE: -0.602 GC content %: 61.000
Atauschii_AET1Gv20408100.5 AET1Gv20408100.5	High	No	306	OG0068329		Get ORF Coding potential... Type: noncoding Potential: -0.841 Folding energies... MFEI: -35.065 AMFE: -0.550 GC content %: 63.725

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_AET1Gv20408100.3	Rfam	14.6	MIR1122	3.5e-7
Atauschii_AET1Gv20408100.1	Rfam	14.6	MIR1122	7.6e-7
Atauschii_AET1Gv20408100.2	Rfam	14.6	MIR1122	6.4e-7

Gene models

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