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mmu_circAgtpbp1_742
Basic information of circular RNA
PanCircBase ID:
mmu_circAgtpbp1_742
mm39_Chr. Position ID:
chr13|59613798|59624952|-
Gene name:
Agtpbp1
Transcript:
ENSMUST00000022040.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
23,22,21,20,19
Exon/intron offsets:
0,7703,8547,9675,11009
Genomic length:
11154
Exon/intron sizes in nt:
132,130,181,154,145
Flanking exon/introns:
chr13:59609987-59613798|chr13:59624952-59630330
Splice length:
742
Other database IDs:
CIRCpedia: MMU_CIRCpedia_215463, circAtlas: mmu-Agtpbp1_0071
CIRCpedia: HSA_CIRCpedia_175194
Human Ortholog IDs:
Mature spliced Sequence:
AAATCACTTCTCACGAAGCTCAGTTGCCGCAGGCGGACAGAAGGGCAAGTCCTACTACACCATCACCTTCACCGTGAACTTCCCGCACAAGGACGATGTCTGCTATTTCGCCTATCACTATCCATACACGTACTCGACTCTGCAGATGCATCTTCAAAAATTGGAATCGGCACACAATCCTCAACAAATCTATTTTCGAAAAGACGTGTTGTGTGAAACCTTGTCTGGAAACATCTGTCCTTTGGTGACCATAACAGCAATGCCAGAGTCCAATTACTATGAACATATCTGTCAGTTCAGAACTCGCCCTTATATTTTCTTGTCTGCTCGGGTCCATCCTGGAGAAACCAATGCAAGCTGGGTAATGAAAGGAACACTGGAGTACCTCATGAGCAATAGCCCGACTGCCCAGAGCCTACGGGAGTCTTACATTTTTAAAATTGTCCCCATGCTAAATCCAGATGGTGTCATCAATGGAAATCACCGCTGCTCCTTAAGTGGAGAGGATTTGAACAGACAGTGGCAAAGTCCAAACCCAGAGTTACACCCCACGATTTATCATGCCAAGGGGCTGCTGCAGTACCTGGCCGCGGTGAAGCGCCTACCTCTGGTTTATTGTGATTACCATGGCCATTCTCGAAAAAAGAATGTATTCATGTACGGCTGCAGCATCAAAGAGACGGTGTGGCACACCCATGACAACTCGGCTTCCTGTGATATTGTGGAAGACATGGGATACAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAGCATCAAAGAGACGGT
59.96
TCACGGTGAAGGTGATGGTG
59.97
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TACGGCTGCAGCATCAAAGA
60.04
TCACGGTGAAGGTGATGGTG
59.97
161
PCR template sequence:
AAAGAATGTATTCATGTACGGCTGCAGCATCAAAGAGACGGTGTGGCACACCCATGACAACTCGGCTTCCTGTGATATTGTGGAAGACATGGGATACAGGAAATCACTTCTCACGAAGCTCAGTTGCCGCAGGCGGACAGAAGGGCAAGTCCTACTACACCATCACCTTCACCGTGAACTTCCCGCACAAGGACGATGTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-9-5p(1), mmu-miR-199a-5p(1), mmu-let-7e-5p(1), mmu-miR-18a-5p(1), mmu-let-7d-5p(1), mmu-miR-425-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-377-3p(1), mmu-miR-190b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATGGGATACAGGAAATCACTTCTCA
siRNA sets
AAGTGATTTCCTGTATCCC, AGTGATTTCCTGTATCCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAGTPBP1_742_ORF_1
0.6214
0.175490887
0.941961965
858
ORF sequence:
ATGGCCATTCTCGAAAAAAGAATGTATTCATGTACGGCTGCAGCATCAAAGAGACGGTGTGGCACACCCATGACAACTCGGCTTCCTGTGATATTGTGGAAGACATGGGATACAGGAAATCACTTCTCACGAAGCTCAGTTGCCGCAGGCGGACAGAAGGGCAAGTCCTACTACACCATCACCTTCACCGTGAACTTCCCGCACAAGGACGATGTCTGCTATTTCGCCTATCACTATCCATACACGTACTCGACTCTGCAGATGCATCTTCAAAAATTGGAATCGGCACACAATCCTCAACAAATCTATTTTCGAAAAGACGTGTTGTGTGAAACCTTGTCTGGAAACATCTGTCCTTTGGTGACCATAACAGCAATGCCAGAGTCCAATTACTATGAACATATCTGTCAGTTCAGAACTCGCCCTTATATTTTCTTGTCTGCTCGGGTCCATCCTGGAGAAACCAATGCAAGCTGGGTAATGAAAGGAACACTGGAGTACCTCATGAGCAATAGCCCGACTGCCCAGAGCCTACGGGAGTCTTACATTTTTAAAATTGTCCCCATGCTAAATCCAGATGGTGTCATCAATGGAAATCACCGCTGCTCCTTAAGTGGAGAGGATTTGAACAGACAGTGGCAAAGTCCAAACCCAGAGTTACACCCCACGATTTATCATGCCAAGGGGCTGCTGCAGTACCTGGCCGCGGTGAAGCGCCTACCTCTGGTTTATTGTGATTACCATGGCCATTCTCGAAAAAAGAATGTATTCATGTACGGCTGCAGCATCAAAGAGACGGTGTGGCACACCCATGACAACTCGGCTTCCTGTGATATTGTGGAAGACATGGGATACAGG
Peptide sequence:
MAILEKRMYSCTAAASKRRCGTPMTTRLPVILWKTWDTGNHFSRSSVAAGGQKGKSYYTITFTVNFPHKDDVCYFAYHYPYTYSTLQMHLQKLESAHNPQQIYFRKDVLCETLSGNICPLVTITAMPESNYYEHICQFRTRPYIFLSARVHPGETNASWVMKGTLEYLMSNSPTAQSLRESYIFKIVPMLNPDGVINGNHRCSLSGEDLNRQWQSPNPELHPTIYHAKGLLQYLAAVKRLPLVYCDYHGHSRKKNVFMYGCSIKETVWHTHDNSASCDIVEDMGYR
IRESfinder result
IRESfinder score
0.488922598
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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