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_AET0Gv20036500 [ AET0Gv20036500]	jcf7190000001345	99809	102141	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_AET0Gv20036500.1 AET0Gv20036500.1	Low	Yes	1097	OG0024177		Get ORF Coding potential... Type: noncoding Potential: -0.065 Folding energies... MFEI: -37.967 AMFE: -0.700 GC content %: 54.239
Atauschii_AET0Gv20036500.3 AET0Gv20036500.3	Low	No	831	OG0024177		Get ORF Coding potential... Type: noncoding Potential: -0.055 Folding energies... MFEI: -30.890 AMFE: -0.625 GC content %: 49.458

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_AET0Gv20036500.1	SwissProt	2021-04-01	Q9LQU2	5.61e-6
Atauschii_AET0Gv20036500.3	SwissProt	2021-04-01	D9HP27	4.04e-18
Atauschii_AET0Gv20036500.1	Rfam	14.6	MIR1122	2.6e-12

Gene models

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