Gene

Stuberosum PGSC0003DMG400002682

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_PGSC0003DMG400002682
PGSC0003DMG400002682
chr09 8152959 8156135 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_PGSC0003DMT400006914
PGSC0003DMT400006914
PAC:24399837
High No 279
Coding potential...
Type: noncoding Potential: -0.393
Folding energies...
MFEI: -15.842 AMFE: -0.460
GC content
%: 34.409
Stuberosum_PGSC0003DMT400006915
PGSC0003DMT400006915
PAC:24399836
Low No 585
Coding potential...
Type: noncoding Potential: -0.345
Folding energies...
MFEI: -15.915 AMFE: -0.571
GC content
%: 27.863
Stuberosum_PGSC0003DMT400006916
PGSC0003DMT400006916
PAC:24399838
Low No 993
Coding potential...
Type: noncoding Potential: -0.836
Folding energies...
MFEI: -17.462 AMFE: -0.635
GC content
%: 27.492


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_PGSC0003DMT400006915  SwissProt 2015-06-01 Q8LA14 7.0e-10
Stuberosum_PGSC0003DMT400006916  SwissProt 2015-06-01 Q8LA14 2.0e-7


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).

PGSC0003DMG400002682.png