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
Hvulgare_HORVU0Hr1G000960 [ HORVU0Hr1G000960]	chrUn	5682510	5685186	r1	Hordeum vulgare (Phytozome 13)	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
Hvulgare_HORVU0Hr1G000960.1 HORVU0Hr1G000960.1	Low	No	1384	OG0035153		Get ORF Coding potential... Type: noncoding Potential: -1.149 Folding energies... MFEI: -26.069 AMFE: -0.629 GC content %: 41.474
Hvulgare_HORVU0Hr1G000960.12 HORVU0Hr1G000960.12	Low	No	1370	OG0035154		Get ORF Coding potential... Type: noncoding Potential: -0.694 Folding energies... MFEI: -30.759 AMFE: -0.626 GC content %: 49.124
Hvulgare_HORVU0Hr1G000960.14 HORVU0Hr1G000960.14	High	No	1076	OG0035155		Get ORF Coding potential... Type: noncoding Potential: -0.739 Folding energies... MFEI: -30.623 AMFE: -0.592 GC content %: 51.766
Hvulgare_HORVU0Hr1G000960.15 HORVU0Hr1G000960.15	High	No	618	OG0035156		Get ORF Coding potential... Type: noncoding Potential: -1.205 Folding energies... MFEI: -26.909 AMFE: -0.594 GC content %: 45.307
Hvulgare_HORVU0Hr1G000960.17 HORVU0Hr1G000960.17	High	No	1285	OG0035157		Get ORF Coding potential... Type: noncoding Potential: -0.684 Folding energies... MFEI: -30.405 AMFE: -0.604 GC content %: 50.350
Hvulgare_HORVU0Hr1G000960.3 HORVU0Hr1G000960.3	Low	No	1490	OG0035158		Get ORF Coding potential... Type: noncoding Potential: -1.275 Folding energies... MFEI: -26.973 AMFE: -0.657 GC content %: 41.074

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
Hvulgare_HORVU0Hr1G000960.3	RepBase (RepeatMasker)	2014-01-31	LINE/L1; LTR/Copia
Hvulgare_HORVU0Hr1G000960.1	RepBase (RepeatMasker)	2014-01-31	LINE/L1; LTR/Copia
Hvulgare_HORVU0Hr1G000960.12	RepBase (RepeatMasker)	2014-01-31	LINE/L1

Gene models

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