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_HORVU5Hr1G101010 [ HORVU5Hr1G101010]	chr5H	612296412	612298786	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_HORVU5Hr1G101010.2 HORVU5Hr1G101010.2	Low	Yes	1709	OG0046035		Get ORF Coding potential... Type: noncoding Potential: -0.915 Folding energies... MFEI: -29.936 AMFE: -0.705 GC content %: 42.481
Hvulgare_HORVU5Hr1G101010.5 HORVU5Hr1G101010.5	High	No	639	OG0046036		Get ORF Coding potential... Type: noncoding Potential: -1.074 Folding energies... MFEI: -33.568 AMFE: -0.677 GC content %: 49.609
Hvulgare_HORVU5Hr1G101010.6 HORVU5Hr1G101010.6	High	No	599	OG0046037		Get ORF Coding potential... Type: noncoding Potential: -0.642 Folding energies... MFEI: -33.038 AMFE: -0.671 GC content %: 49.249
Hvulgare_HORVU5Hr1G101010.7 HORVU5Hr1G101010.7	High	No	621	OG0046038		Get ORF Coding potential... Type: noncoding Potential: -0.703 Folding energies... MFEI: -33.671 AMFE: -0.679 GC content %: 49.597
Hvulgare_HORVU5Hr1G101010.9 HORVU5Hr1G101010.9	High	No	245	OG0046039		Get ORF Coding potential... Type: noncoding Potential: -1.051 Folding energies... MFEI: -25.429 AMFE: -0.566 GC content %: 44.898

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_HORVU5Hr1G101010.2	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm; DNA/TcMar-Stowaway
Hvulgare_HORVU5Hr1G101010.2	Rfam	14.6	MIR1122	8.7e-15

Gene models

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