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_AET1Gv20421200 [ AET1Gv20421200]	1D	232680681	232851569	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_AET1Gv20421200.2 AET1Gv20421200.2	High	No	1025	OG0009724		Get ORF Coding potential... Type: noncoding Potential: -1.041 Folding energies... MFEI: -36.332 AMFE: -0.669 GC content %: 54.341
Atauschii_AET1Gv20421200.3 AET1Gv20421200.3	High	No	1974	OG0009724		Get ORF Coding potential... Type: noncoding Potential: -1.225 Folding energies... MFEI: -24.615 AMFE: -0.664 GC content %: 37.082
Atauschii_AET1Gv20421200.4 AET1Gv20421200.4	High	No	1125	OG0009724		Get ORF Coding potential... Type: noncoding Potential: -1.135 Folding energies... MFEI: -35.209 AMFE: -0.669 GC content %: 52.622
Atauschii_AET1Gv20421200.5 AET1Gv20421200.5	Low	Yes	3735	OG0009725		Get ORF Coding potential... Type: noncoding Potential: -1.022 Folding energies... MFEI: -26.442 AMFE: -0.693 GC content %: 38.179
Atauschii_AET1Gv20421200.9 AET1Gv20421200.9	High	No	1123	OG0009724		Get ORF Coding potential... Type: noncoding Potential: -1.096 Folding energies... MFEI: -33.954 AMFE: -0.653 GC content %: 52.004

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_AET1Gv20421200.5	RepBase (RepeatMasker)	2014-01-31	DNA; DNA/Maverick; DNA/TcMar-Stowaway; LINE/RTE-BovB
Atauschii_AET1Gv20421200.5	Rfam	14.6	MIR1122	1.0e-14

Gene models

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