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mmu_circAgtpbp1_1080
Basic information of circular RNA
PanCircBase ID:
mmu_circAgtpbp1_1080
mm39_Chr. Position ID:
chr13|59608282|59624952|-
Gene name:
Agtpbp1
Transcript:
ENSMUST00000022040.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
25,24,23,22,21,20,19
Exon/intron offsets:
0,1528,5516,13219,14063,15191,16525
Genomic length:
16670
Exon/intron sizes in nt:
161,177,132,130,181,154,145
Flanking exon/introns:
chr13:59598128-59608282|chr13:59624952-59630330
Splice length:
1080
Other database IDs:
circBase: mmu_circ_0004703, CIRCpedia: MMU_CIRCpedia_24507, circAtlas: mmu-Agtpbp1_0013
circBase: hsa_circ_0139168, circAtlas: hsa-AGTPBP1_0013, CIRCpedia: HSA_CIRCpedia_64554
Human Ortholog IDs:
Mature spliced Sequence:
AAATCACTTCTCACGAAGCTCAGTTGCCGCAGGCGGACAGAAGGGCAAGTCCTACTACACCATCACCTTCACCGTGAACTTCCCGCACAAGGACGATGTCTGCTATTTCGCCTATCACTATCCATACACGTACTCGACTCTGCAGATGCATCTTCAAAAATTGGAATCGGCACACAATCCTCAACAAATCTATTTTCGAAAAGACGTGTTGTGTGAAACCTTGTCTGGAAACATCTGTCCTTTGGTGACCATAACAGCAATGCCAGAGTCCAATTACTATGAACATATCTGTCAGTTCAGAACTCGCCCTTATATTTTCTTGTCTGCTCGGGTCCATCCTGGAGAAACCAATGCAAGCTGGGTAATGAAAGGAACACTGGAGTACCTCATGAGCAATAGCCCGACTGCCCAGAGCCTACGGGAGTCTTACATTTTTAAAATTGTCCCCATGCTAAATCCAGATGGTGTCATCAATGGAAATCACCGCTGCTCCTTAAGTGGAGAGGATTTGAACAGACAGTGGCAAAGTCCAAACCCAGAGTTACACCCCACGATTTATCATGCCAAGGGGCTGCTGCAGTACCTGGCCGCGGTGAAGCGCCTACCTCTGGTTTATTGTGATTACCATGGCCATTCTCGAAAAAAGAATGTATTCATGTACGGCTGCAGCATCAAAGAGACGGTGTGGCACACCCATGACAACTCGGCTTCCTGTGATATTGTGGAAGACATGGGATACAGGACTTTGCCTAAGATACTGAGCCACATTGCTCCGGCATTTTGCATGAGCAGTTGTAGCTTTGTGGTGGAAAAATCTAAAGAATCCACAGCTCGGGTTGTCGTGTGGCGGGAAATTGGAGTTCAGAGGAGCTACACCATGGAGAGTACTTTATGTGGCTGCGATCAGGGTAGATACAAGGGTTTACAGATTGGGACTCGAGAATTGGAAGAGATGGGAGCAAAATTTTGTGTTGGTTTATTGCGTTTGAAACGACTGACTTCTTCATTGGAATATAATCTGCCCTCCAACCTGCTTGACTTTGAAAATGACTTAATTGAATCAAGCTGTAAAGTGACTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCTCCAACCTGCTTGACTT
59.89
GGGAAGTTCACGGTGAAGGT
59.89
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAATCTGCCCTCCAACCTGC
59.74
TCACGGTGAAGGTGATGGTG
59.97
143
PCR template sequence:
TGCGTTTGAAACGACTGACTTCTTCATTGGAATATAATCTGCCCTCCAACCTGCTTGACTTTGAAAATGACTTAATTGAATCAAGCTGTAAAGTGACTAGAAATCACTTCTCACGAAGCTCAGTTGCCGCAGGCGGACAGAAGGGCAAGTCCTACTACACCATCACCTTCACCGTGAACTTCCCGCACAAGGACGATGTC
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
GTAAAGTGACTAGAAATCACTTCTCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAGTPBP1_1080_ORF_1
0.6141
0.13603517
0.999982106
2013
ORF sequence:
ATGCATCTTCAAAAATTGGAATCGGCACACAATCCTCAACAAATCTATTTTCGAAAAGACGTGTTGTGTGAAACCTTGTCTGGAAACATCTGTCCTTTGGTGACCATAACAGCAATGCCAGAGTCCAATTACTATGAACATATCTGTCAGTTCAGAACTCGCCCTTATATTTTCTTGTCTGCTCGGGTCCATCCTGGAGAAACCAATGCAAGCTGGGTAATGAAAGGAACACTGGAGTACCTCATGAGCAATAGCCCGACTGCCCAGAGCCTACGGGAGTCTTACATTTTTAAAATTGTCCCCATGCTAAATCCAGATGGTGTCATCAATGGAAATCACCGCTGCTCCTTAAGTGGAGAGGATTTGAACAGACAGTGGCAAAGTCCAAACCCAGAGTTACACCCCACGATTTATCATGCCAAGGGGCTGCTGCAGTACCTGGCCGCGGTGAAGCGCCTACCTCTGGTTTATTGTGATTACCATGGCCATTCTCGAAAAAAGAATGTATTCATGTACGGCTGCAGCATCAAAGAGACGGTGTGGCACACCCATGACAACTCGGCTTCCTGTGATATTGTGGAAGACATGGGATACAGGACTTTGCCTAAGATACTGAGCCACATTGCTCCGGCATTTTGCATGAGCAGTTGTAGCTTTGTGGTGGAAAAATCTAAAGAATCCACAGCTCGGGTTGTCGTGTGGCGGGAAATTGGAGTTCAGAGGAGCTACACCATGGAGAGTACTTTATGTGGCTGCGATCAGGGTAGATACAAGGGTTTACAGATTGGGACTCGAGAATTGGAAGAGATGGGAGCAAAATTTTGTGTTGGTTTATTGCGTTTGAAACGACTGACTTCTTCATTGGAATATAATCTGCCCTCCAACCTGCTTGACTTTGAAAATGACTTAATTGAATCAAGCTGTAAAGTGACTAGAAATCACTTCTCACGAAGCTCAGTTGCCGCAGGCGGACAGAAGGGCAAGTCCTACTACACCATCACCTTCACCGTGAACTTCCCGCACAAGGACGATGTCTGCTATTTCGCCTATCACTATCCATACACGTACTCGACTCTGCAGATGCATCTTCAAAAATTGGAATCGGCACACAATCCTCAACAAATCTATTTTCGAAAAGACGTGTTGTGTGAAACCTTGTCTGGAAACATCTGTCCTTTGGTGACCATAACAGCAATGCCAGAGTCCAATTACTATGAACATATCTGTCAGTTCAGAACTCGCCCTTATATTTTCTTGTCTGCTCGGGTCCATCCTGGAGAAACCAATGCAAGCTGGGTAATGAAAGGAACACTGGAGTACCTCATGAGCAATAGCCCGACTGCCCAGAGCCTACGGGAGTCTTACATTTTTAAAATTGTCCCCATGCTAAATCCAGATGGTGTCATCAATGGAAATCACCGCTGCTCCTTAAGTGGAGAGGATTTGAACAGACAGTGGCAAAGTCCAAACCCAGAGTTACACCCCACGATTTATCATGCCAAGGGGCTGCTGCAGTACCTGGCCGCGGTGAAGCGCCTACCTCTGGTTTATTGTGATTACCATGGCCATTCTCGAAAAAAGAATGTATTCATGTACGGCTGCAGCATCAAAGAGACGGTGTGGCACACCCATGACAACTCGGCTTCCTGTGATATTGTGGAAGACATGGGATACAGGACTTTGCCTAAGATACTGAGCCACATTGCTCCGGCATTTTGCATGAGCAGTTGTAGCTTTGTGGTGGAAAAATCTAAAGAATCCACAGCTCGGGTTGTCGTGTGGCGGGAAATTGGAGTTCAGAGGAGCTACACCATGGAGAGTACTTTATGTGGCTGCGATCAGGGTAGATACAAGGGTTTACAGATTGGGACTCGAGAATTGGAAGAGATGGGAGCAAAATTTTGTGTTGGTTTATTGCGTTTGAAACGACTGACTTCTTCATTGGAATATAATCTGCCCTCCAACCTGCTTGACTTTGAAAATGACTTAATTGAATCAAGCTGTAAAGTGACT
Peptide sequence:
MHLQKLESAHNPQQIYFRKDVLCETLSGNICPLVTITAMPESNYYEHICQFRTRPYIFLSARVHPGETNASWVMKGTLEYLMSNSPTAQSLRESYIFKIVPMLNPDGVINGNHRCSLSGEDLNRQWQSPNPELHPTIYHAKGLLQYLAAVKRLPLVYCDYHGHSRKKNVFMYGCSIKETVWHTHDNSASCDIVEDMGYRTLPKILSHIAPAFCMSSCSFVVEKSKESTARVVVWREIGVQRSYTMESTLCGCDQGRYKGLQIGTRELEEMGAKFCVGLLRLKRLTSSLEYNLPSNLLDFENDLIESSCKVTRNHFSRSSVAAGGQKGKSYYTITFTVNFPHKDDVCYFAYHYPYTYSTLQMHLQKLESAHNPQQIYFRKDVLCETLSGNICPLVTITAMPESNYYEHICQFRTRPYIFLSARVHPGETNASWVMKGTLEYLMSNSPTAQSLRESYIFKIVPMLNPDGVINGNHRCSLSGEDLNRQWQSPNPELHPTIYHAKGLLQYLAAVKRLPLVYCDYHGHSRKKNVFMYGCSIKETVWHTHDNSASCDIVEDMGYRTLPKILSHIAPAFCMSSCSFVVEKSKESTARVVVWREIGVQRSYTMESTLCGCDQGRYKGLQIGTRELEEMGAKFCVGLLRLKRLTSSLEYNLPSNLLDFENDLIESSCKVT
IRESfinder result
IRESfinder score
0.569061523
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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