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_HORVU7Hr1G047600 [ HORVU7Hr1G047600]	chr7H	160220309	160221565	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_HORVU7Hr1G047600.1 HORVU7Hr1G047600.1	Low	No	282	OG0000514		Get ORF Coding potential... Type: noncoding Potential: -1.465 Folding energies... MFEI: -36.560 AMFE: -0.606 GC content %: 60.284
Hvulgare_HORVU7Hr1G047600.2 HORVU7Hr1G047600.2	High	No	261	OG0000514		Get ORF Coding potential... Type: noncoding Potential: -1.137 Folding energies... MFEI: -38.582 AMFE: -0.596 GC content %: 64.751
Hvulgare_HORVU7Hr1G047600.3 HORVU7Hr1G047600.3	High	No	213	OG0005824		Get ORF Coding potential... Type: noncoding Potential: -1.136 Folding energies... MFEI: -37.136 AMFE: -0.557 GC content %: 66.667
Hvulgare_HORVU7Hr1G047600.5 HORVU7Hr1G047600.5	High	No	243	OG0013315		Get ORF Coding potential... Type: noncoding Potential: -1.129 Folding energies... MFEI: -34.650 AMFE: -0.606 GC content %: 57.202
Hvulgare_HORVU7Hr1G047600.6 HORVU7Hr1G047600.6	Low	No	300	OG0049106		Get ORF Coding potential... Type: noncoding Potential: -1.160 Folding energies... MFEI: -40.333 AMFE: -0.665 GC content %: 60.667
Hvulgare_HORVU7Hr1G047600.7 HORVU7Hr1G047600.7	Low	No	291	OG0003318		Get ORF Coding potential... Type: noncoding Potential: -1.182 Folding energies... MFEI: -45.120 AMFE: -0.702 GC content %: 64.261

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_HORVU7Hr1G047600.1	RepBase (RepeatMasker)	2014-01-31	LINE/L1
Hvulgare_HORVU7Hr1G047600.6	RepBase (RepeatMasker)	2014-01-31	LINE/L1
Hvulgare_HORVU7Hr1G047600.7	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).