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mmu_circAtad2b_860
Basic information of circular RNA
PanCircBase ID:
mmu_circAtad2b_860
mm39_Chr. Position ID:
chr12|4987386|5002706|+
Gene name:
Atad2b
Transcript:
ENSMUST00000045664.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
2,3,4,5,6,7,8,9
Exon/intron offsets:
0,2269,2705,4585,5768,7519,13132,15221
Genomic length:
15320
Exon/intron sizes in nt:
152,50,154,103,109,117,76,99
Flanking exon/introns:
chr12:4967921-4987386|chr12:5002706-5004545
Splice length:
860
Other database IDs:
circAtlas: mmu-Atad2b_0021
circAtlas: hsa-ATAD2B_0030
Human Ortholog IDs:
Mature spliced Sequence:
AAGGCTGAAGTTGACGGAAGCTTAAGTGATAGCCACGTATCTCCTCCAGCCAAACGCACTTTGAAACAGCCGGATTCTGTTTGCAAAGACAAATCAAAATCACGAAGTACTGGTCAGCGAGAAGAATGGAACATACCATCTGGTCAGACCAGGTTAACTTCTCAGCCTGGTGCTACATTACCAAACGGACATAGTAGCTTGTCACTTCGAAGCCACCCCCTTCGAGGGGAAAAGAAAGGAGATGGCGACCTTTCATGTATAAATGGTGACATAGAAGTCAGAAAAAGTTGTCGGTCCAGGAAAAACAGATTTGAAAGTGTGAATCAGAGTTTATTATTTGATCAGCTAGTAAATAGTACTGCTGAAGCTGTATTACAAGAAATGGATAATATTAATATCCGACGAAACCGTCGATCAGGCGAAGTAGAGAGGCTTCGAATGTGGACAGATACAGAATTTGAAAATATGGATATGTATTCAAGGGTAAAAAGACGAAGAAAATCACTGAGAAGAAATAGTTATGGGATACAGAATCATCATGAGGTTTCCACTGAGGGCGAGGAAGAAGAATCTCAAGAGGAGGATGGAGACATAGAGGTTGAAGAGGCAGAAGGAGAAGAAAATGATAGACCATATAACTTGAGACAAAGAAAAACAGTGGATCGATACCAAGCACCGCCTATAGTACCGGCTCATCAAAAAAAGAGGGAAAATACACTATTTGATATTCACAGGTCTCCAGCAAGAAGAAGCCATATCAGGAGAAAGAAACATGCCATTCACAGTAGTGATACAACTTCTTCTGATGAGGAACGCTTTGAAAGAAGGAAATCGAAAAGCATGGCAAGAGCAAGAAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTTCTTCTGATGAGGAACGCT
59.44
TTGCAAACAGAATCCGGCTG
59.4
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTTCTTCTGATGAGGAACGCT
59.44
ATCCGGCTGTTTCAAAGTGC
59.4
140
PCR template sequence:
GGAGAAAGAAACATGCCATTCACAGTAGTGATACAACTTCTTCTGATGAGGAACGCTTTGAAAGAAGGAAATCGAAAAGCATGGCAAGAGCAAGAAACAGAAGGCTGAAGTTGACGGAAGCTTAAGTGATAGCCACGTATCTCCTCCAGCCAAACGCACTTTGAAACAGCCGGATTCTGTTTGCAAAGACAAATCAAAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-135a-5p(1), mmu-miR-29a-3p(1), mmu-miR-382-5p(1), mmu-miR-207(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGCAAGAAACAGAAGGCTGAAGTTG
siRNA sets
TCAGCCTTCTGTTTCTTGC, CAGCCTTCTGTTTCTTGCT, AACTTCAGCCTTCTGTTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATAD2B_860_ORF_1
0.9223
0.081034593
0.598730778
504
ORF sequence:
ATGGATAATATTAATATCCGACGAAACCGTCGATCAGGCGAAGTAGAGAGGCTTCGAATGTGGACAGATACAGAATTTGAAAATATGGATATGTATTCAAGGGTAAAAAGACGAAGAAAATCACTGAGAAGAAATAGTTATGGGATACAGAATCATCATGAGGTTTCCACTGAGGGCGAGGAAGAAGAATCTCAAGAGGAGGATGGAGACATAGAGGTTGAAGAGGCAGAAGGAGAAGAAAATGATAGACCATATAACTTGAGACAAAGAAAAACAGTGGATCGATACCAAGCACCGCCTATAGTACCGGCTCATCAAAAAAAGAGGGAAAATACACTATTTGATATTCACAGGTCTCCAGCAAGAAGAAGCCATATCAGGAGAAAGAAACATGCCATTCACAGTAGTGATACAACTTCTTCTGATGAGGAACGCTTTGAAAGAAGGAAATCGAAAAGCATGGCAAGAGCAAGAAACAGAAGGCTGAAGTTGACGGAAGCTTAA
Peptide sequence:
MDNINIRRNRRSGEVERLRMWTDTEFENMDMYSRVKRRRKSLRRNSYGIQNHHEVSTEGEEEESQEEDGDIEVEEAEGEENDRPYNLRQRKTVDRYQAPPIVPAHQKKRENTLFDIHRSPARRSHIRRKKHAIHSSDTTSSDEERFERRKSKSMARARNRRLKLTEA
IRESfinder result
IRESfinder score
0.412095018
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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