Brapa Brara.I05337

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 Assembly Species Details

Brapa_Brara.I05337
[ Brara.I05337]
A09 43417809 43418566 v1.3 Brassica rapa (Phytozome 13)
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 Orthologous group Sequence Details

Brapa_Brara.I05337.1
Brara.I05337.1
Low No 450 OG0017463
Coding potential...
Type: noncoding Potential: -0.634
Folding energies...
MFEI: -34.911 AMFE: -0.708
GC content
%: 49.333
Brapa_Brara.I05337.2
Brara.I05337.2
Low No 412 OG0017463
Coding potential...
Type: noncoding Potential: -0.643
Folding energies...
MFEI: -33.519 AMFE: -0.674
GC content
%: 49.757
Brapa_Brara.I05337.3
Brara.I05337.3
Low No 389 OG0017463
Coding potential...
Type: noncoding Potential: -0.634
Folding energies...
MFEI: -32.494 AMFE: -0.698
GC content
%: 46.530


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
Brapa_Brara.I05337.1  RepBase (RepeatMasker) 2014-01-31 LTR/Gypsy
Brapa_Brara.I05337.2  RepBase (RepeatMasker) 2014-01-31 LTR/Gypsy
Brapa_Brara.I05337.3  RepBase (RepeatMasker) 2014-01-31 LTR/Gypsy
Brapa_Brara.I05337.1  SwissProt 2021-04-01 Q8K2Y7 2.19e-8
Brapa_Brara.I05337.2  SwissProt 2021-04-01 Q8K2Y7 1.21e-8
Brapa_Brara.I05337.3  SwissProt 2021-04-01 Q8K2Y7 1.26e-8


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).

Brapa_Brara.I05337.png