Gene

Athaliana AT1G01046

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

Athaliana_AT1G01046
AT1G01046
Chr1 28500 28706 Phytozome TAIR10 Arabidopsis_thaliana
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

Athaliana_AT1G01046.1
AT1G01046.1
Low Yes 207
Coding potential...
Type: noncoding Potential: -1.080
Folding energies...
MFEI: -38.744 AMFE: -1.028
GC content
%: 37.681


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
Athaliana_AT1G01046.1  miRBase 20.0 ath-miR838 1.0e-5
Athaliana_AT1G01046.1  miRBase 20.0 aly-miR838-3p 5.0e-4
Athaliana_AT1G01046.1  miRBase 20.0 aly-miR838-5p 0.002
Athaliana_AT1G01046.1  Rfam 11.0 MIR164 1.3e-6


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).

AT1G01046.png