Gene

Stuberosum PGSC0003DMG400001539

From GreeNC

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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_PGSC0003DMG400001539
PGSC0003DMG400001539
chr02 60855031 60856077 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_PGSC0003DMT400003899
PGSC0003DMT400003899
PAC:24428059
Low No 1047
Coding potential...
Type: noncoding Potential: -1.438
Folding energies...
MFEI: -24.355 AMFE: -0.596
GC content
%: 40.879


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_PGSC0003DMT400003899  SwissProt 2015-06-01 P04323 1.0e-37
Stuberosum_PGSC0003DMT400003899  RepBase (RepeatMasker) 2014-01-31 Gypsy-6_ST-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).

PGSC0003DMG400001539.png