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_HORVU0Hr1G004270 [ HORVU0Hr1G004270]	chrUn	23446381	23448778	r1	Hordeum vulgare (Phytozome 13)	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
Hvulgare_HORVU0Hr1G004270.1 HORVU0Hr1G004270.1	Low	No	1107	OG0001060		Get ORF Coding potential... Type: noncoding Potential: -1.219 Folding energies... MFEI: -24.426 AMFE: -0.563 GC content %: 43.360
Hvulgare_HORVU0Hr1G004270.2 HORVU0Hr1G004270.2	Low	No	938	OG0001060		Get ORF Coding potential... Type: noncoding Potential: -1.205 Folding energies... MFEI: -24.083 AMFE: -0.554 GC content %: 43.497
Hvulgare_HORVU0Hr1G004270.3 HORVU0Hr1G004270.3	Low	No	917	OG0001060		Get ORF Coding potential... Type: noncoding Potential: -1.259 Folding energies... MFEI: -23.828 AMFE: -0.542 GC content %: 43.948
Hvulgare_HORVU0Hr1G004270.4 HORVU0Hr1G004270.4	Low	No	806	OG0001060		Get ORF Coding potential... Type: noncoding Potential: -1.241 Folding energies... MFEI: -23.623 AMFE: -0.552 GC content %: 42.804
Hvulgare_HORVU0Hr1G004270.5 HORVU0Hr1G004270.5	Low	No	779	OG0001060		Get ORF Coding potential... Type: noncoding Potential: -1.192 Folding energies... MFEI: -23.184 AMFE: -0.527 GC content %: 44.031

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_HORVU0Hr1G004270.3	SwissProt	2021-04-01	Q9LVH5	9.3e-7
Hvulgare_HORVU0Hr1G004270.4	SwissProt	2021-04-01	Q9LVH5	5.18e-7
Hvulgare_HORVU0Hr1G004270.5	SwissProt	2021-04-01	Q9LVH5	1.24e-7
Hvulgare_HORVU0Hr1G004270.1	SwissProt	2021-04-01	Q9LVH5	1.48e-6
Hvulgare_HORVU0Hr1G004270.2	SwissProt	2021-04-01	Q9LVH5	2.23e-7

Gene models

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