Gene

Stuberosum PGSC0003DMG400014737

From GreeNC


Gene information
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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 Source Assembly Species Details

Stuberosum_PGSC0003DMG400014737
PGSC0003DMG400014737
chr01 5951882 5954110 Phytozome v3.4 Solanum_tuberosum
Coding?
No


Transcript features
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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 Sequence Details

Stuberosum_PGSC0003DMT400038210
PGSC0003DMT400038210
PAC:24423347
High No 835
Coding potential...
Type: noncoding Potential: -1.293
Folding energies...
MFEI: -22.647 AMFE: -0.641
GC content
%: 35.329
Stuberosum_PGSC0003DMT400038212
PGSC0003DMT400038212
PAC:24423348
Low No 2229
Coding potential...
Type: noncoding Potential: -1.253
Folding energies...
MFEI: -22.607 AMFE: -0.678
GC content
%: 33.333


Matches to external databases
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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
Stuberosum_PGSC0003DMT400038212  RepBase (RepeatMasker) 2014-01-31 HarbN_I


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

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