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_AET1Gv20078300 [ AET1Gv20078300]	1D	19184800	19189110	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_AET1Gv20078300.1 AET1Gv20078300.1	Low	No	1060	OG0015802		Get ORF Coding potential... Type: noncoding Potential: -1.089 Folding energies... MFEI: -28.321 AMFE: -0.611 GC content %: 46.321
Atauschii_AET1Gv20078300.2 AET1Gv20078300.2	Low	No	1710	OG0015802		Get ORF Coding potential... Type: noncoding Potential: -1.222 Folding energies... MFEI: -22.497 AMFE: -0.639 GC content %: 35.205
Atauschii_AET1Gv20078300.3 AET1Gv20078300.3	Low	No	679	OG0015802		Get ORF Coding potential... Type: noncoding Potential: -0.843 Folding energies... MFEI: -31.473 AMFE: -0.609 GC content %: 51.694
Atauschii_AET1Gv20078300.4 AET1Gv20078300.4	Low	No	1777	OG0024219		Get ORF Coding potential... Type: noncoding Potential: -0.994 Folding energies... MFEI: -33.056 AMFE: -0.925 GC content %: 35.734
Atauschii_AET1Gv20078300.5 AET1Gv20078300.5	Low	No	1985	OG0024219		Get ORF Coding potential... Type: noncoding Potential: -1.028 Folding energies... MFEI: -33.018 AMFE: -0.846 GC content %: 39.043

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_AET1Gv20078300.5	RepBase (RepeatMasker)	2014-01-31	LTR/Caulimovirus
Atauschii_AET1Gv20078300.1	RepBase (RepeatMasker)	2014-01-31	LTR/Caulimovirus
Atauschii_AET1Gv20078300.2	RepBase (RepeatMasker)	2014-01-31	LTR/Caulimovirus
Atauschii_AET1Gv20078300.3	RepBase (RepeatMasker)	2014-01-31	LTR/Caulimovirus
Atauschii_AET1Gv20078300.4	RepBase (RepeatMasker)	2014-01-31	LTR/Caulimovirus

Gene models

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