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
Ahalleri_g09911 [ g09911]	FJVB01000023.1	294888	295519	v2.2	Arabidopsis halleri (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
Ahalleri_g09911.t1 g09911.t1	Low	No	466	OG0026834		Get ORF Coding potential... Type: noncoding Potential: -0.147 Folding energies... MFEI: -21.223 AMFE: -0.582 GC content %: 36.481
Ahalleri_g09911.t2 g09911.t2	Low	No	448	OG0026834		Get ORF Coding potential... Type: noncoding Potential: -0.021 Folding energies... MFEI: -22.254 AMFE: -0.601 GC content %: 37.054

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
Ahalleri_g09911.t2	RepBase (RepeatMasker)	2014-01-31	LTR/Copia
Ahalleri_g09911.t1	SwissProt	2021-04-01	O23654	1.74e-14
Ahalleri_g09911.t2	SwissProt	2021-04-01	O23654	4.26e-15
Ahalleri_g09911.t1	RepBase (RepeatMasker)	2014-01-31	LTR/Copia

Gene models

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