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_HORVU3Hr1G011260 [ HORVU3Hr1G011260]	chr3H	24492785	24497173	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_HORVU3Hr1G011260.10 HORVU3Hr1G011260.10	Low	No	1396	OG0040418		Get ORF Coding potential... Type: noncoding Potential: -0.711 Folding energies... MFEI: -27.042 AMFE: -0.659 GC content %: 41.046
Hvulgare_HORVU3Hr1G011260.3 HORVU3Hr1G011260.3	Low	No	641	OG0040419		Get ORF Coding potential... Type: noncoding Potential: -0.776 Folding energies... MFEI: -32.262 AMFE: -0.614 GC content %: 52.574
Hvulgare_HORVU3Hr1G011260.4 HORVU3Hr1G011260.4	High	No	883	OG0012503		Get ORF Coding potential... Type: noncoding Potential: -0.348 Folding energies... MFEI: -30.272 AMFE: -0.625 GC content %: 48.471
Hvulgare_HORVU3Hr1G011260.5 HORVU3Hr1G011260.5	High	No	770	OG0012503		Get ORF Coding potential... Type: noncoding Potential: -0.343 Folding energies... MFEI: -29.143 AMFE: -0.600 GC content %: 48.571
Hvulgare_HORVU3Hr1G011260.7 HORVU3Hr1G011260.7	High	No	331	OG0040420		Get ORF Coding potential... Type: noncoding Potential: -0.721 Folding energies... MFEI: -24.743 AMFE: -0.573 GC content %: 43.202
Hvulgare_HORVU3Hr1G011260.8 HORVU3Hr1G011260.8	High	No	338	OG0040421		Get ORF Coding potential... Type: noncoding Potential: -0.924 Folding energies... MFEI: -22.278 AMFE: -0.542 GC content %: 41.124
Hvulgare_HORVU3Hr1G011260.9 HORVU3Hr1G011260.9	High	No	295	OG0192621		Get ORF Coding potential... Type: noncoding Potential: -1.149 Folding energies... MFEI: -21.559 AMFE: -0.553 GC content %: 38.983

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_HORVU3Hr1G011260.3	RepBase (RepeatMasker)	2014-01-31	SINE
Hvulgare_HORVU3Hr1G011260.10	RepBase (RepeatMasker)	2014-01-31	SINE

Gene models

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