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mmu_circAgtpbp1_2779
Basic information of circular RNA
PanCircBase ID:
mmu_circAgtpbp1_2779
mm39_Chr. Position ID:
chr13|59608282|59662109|-
Gene name:
Agtpbp1
Transcript:
ENSMUST00000022040.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
16
Exon/intron indexes:
25,24,23,22,21,20,19,18,17,16,15,14,13,12,11,10
Exon/intron offsets:
0,1528,5516,13219,14063,15191,16525,22048,34864,35094,36507,39545,43725,47490,51855,53618
Genomic length:
53827
Exon/intron sizes in nt:
1,61,17,71,32,13,01,81,00,00,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr13:59598128-59608282|chr13:59662109-59665466
Splice length:
2779
Other database IDs:
circAtlas: mmu-Agtpbp1_0007
circBase: hsa_circ_0139174, circAtlas: hsa-AGTPBP1_0007, CIRCpedia: HSA_CIRCpedia_160311
Human Ortholog IDs:
Mature spliced Sequence:
AGACAAACGCCAGGAGAGCGGTGGACAGAGGGTACGTTCAAGTGCTTCTAACCATCTATGTAGATTGGCACCGGCATGATAATCGGCATAGAAACATGCTCATTCGGAAGGGGATTCTACAGAGCTTAAAAAGTGTCACGAACATCAAGTTGGGCAGAAAAGCATTTATTGATGCGAATGGGATGAAAATTCTGTATAACACTTCTCAAGAGTGCTTGGCGGTCAGGACTCTTGATCCTCTTGTCAACACATCCAGTCTGATAATGAGAAAATGCTTCCCCAAAAACCGCCTTCCGCTCCCCACCATTAAAAGTTCTTTCCACTTCCAATTGCCAATTATCCCTGTGACTGGACCTGTGGCCCAGCTCTACAGCTTGCCGCCTGAAGTGGACGATGTGGTGGACGAGAGTGACGACAACGACGACATTGATTTAGAAGTGGAAAATGAACTCGAGAATGAAGATGACCTAGATCAGAGTTTTAAGAATGATGATATTGAAACAGATATTAATAAATTAAGACCTCAGCAAGTACCAGGACGAACAATAGAAGAACTAAAAATGTACGAGCACCTTTTCCCCGAGCTTGTTGATGATTTTCAGGACTATGAACTGATCTCTAAGGAACCCAAACCTTTTGTGTTTGAGGGGAAGGCTCGGGGCCCCATTGTAGTTCCCACAGCTGGAGAGGAGGTACCTGGGAATTCAGGGAGCGTAAAGAAAGGAGTGGTAATGAAGGAGAGAGCAAGTCCTAAAGGAGAGGAAGCCAAGGAAGACCCTAAGGGCCACGACAGGACACTGCCGCAGCAGCTGGGTGGCCAGAGCAGAGTGGCCCCCTCAGCCCACAGCTTCAACAATGATCTTGTGAAGGCCCTAGACCGAATCACACTGCAGAATGTTCCTTCGCAAGTAGCCTCGGGCTTGAACGCAGGAATGAGGAAGGACTTTGGTCTCCCTCTCACTGTCCTCTCATGCACGAAAGCTTGTCCTCACGTGGCTAAGTGTGGAAGTACTCTCTTTGAAGGGCGGACGGTACATCTTGGGAAGCTGTGTTGTACTGGAGTTGAAACGGAAGATGACGAAGACACTGAGTCCCACTCATCAACAGAGCAGGCCCCCTCTGTTGAAGCCTCTGATGGACCAACACTGCACGACCCAGACCTCTATATTGAGATTGTGAAAAATACGAAGTCCGTTCCAGAATACTCAGAGGTGGCTTATCCTGATTATTTTGGTCACATTCCACCTCCCTTCAAAGAGCCTATTTTAGAAAGGCCTTATGGTGTACAAAGGACAAAAATTGCCCAAGACATCGAGAGGCTGATACACCAGAACGATATCATAGACCGCGTGGTGTATGACTTAGACAACCCTACCTATACCACTCCAGAAGAAGGAGATACTTTGAAGTTTAACTCAAAATTCGAATCTGGGAATCTGCGCAAAGTAATTCAAATTAGAAAAAGCGAGTACGACCTTATCCTGAACTCTGATATAAACAGTAACCATTACCACCAGTGGTTCTACTTTGAAGTCAGTGGGATGCGGCCTGGTGTGGCATATAGGTTCAACATCATCAACTGTGAGAAGTCCAACAGTCAGTTTAATTATGGTATGCAGCCACTTATGTATTCAGTTCAGGAAGCACTAAATGCCAGACCATGGTGGATCCGTATGGGCACTGACATTTGTTACTACAAAAATCACTTCTCACGAAGCTCAGTTGCCGCAGGCGGACAGAAGGGCAAGTCCTACTACACCATCACCTTCACCGTGAACTTCCCGCACAAGGACGATGTCTGCTATTTCGCCTATCACTATCCATACACGTACTCGACTCTGCAGATGCATCTTCAAAAATTGGAATCGGCACACAATCCTCAACAAATCTATTTTCGAAAAGACGTGTTGTGTGAAACCTTGTCTGGAAACATCTGTCCTTTGGTGACCATAACAGCAATGCCAGAGTCCAATTACTATGAACATATCTGTCAGTTCAGAACTCGCCCTTATATTTTCTTGTCTGCTCGGGTCCATCCTGGAGAAACCAATGCAAGCTGGGTAATGAAAGGAACACTGGAGTACCTCATGAGCAATAGCCCGACTGCCCAGAGCCTACGGGAGTCTTACATTTTTAAAATTGTCCCCATGCTAAATCCAGATGGTGTCATCAATGGAAATCACCGCTGCTCCTTAAGTGGAGAGGATTTGAACAGACAGTGGCAAAGTCCAAACCCAGAGTTACACCCCACGATTTATCATGCCAAGGGGCTGCTGCAGTACCTGGCCGCGGTGAAGCGCCTACCTCTGGTTTATTGTGATTACCATGGCCATTCTCGAAAAAAGAATGTATTCATGTACGGCTGCAGCATCAAAGAGACGGTGTGGCACACCCATGACAACTCGGCTTCCTGTGATATTGTGGAAGACATGGGATACAGGACTTTGCCTAAGATACTGAGCCACATTGCTCCGGCATTTTGCATGAGCAGTTGTAGCTTTGTGGTGGAAAAATCTAAAGAATCCACAGCTCGGGTTGTCGTGTGGCGGGAAATTGGAGTTCAGAGGAGCTACACCATGGAGAGTACTTTATGTGGCTGCGATCAGGGTAGATACAAGGGTTTACAGATTGGGACTCGAGAATTGGAAGAGATGGGAGCAAAATTTTGTGTTGGTTTATTGCGTTTGAAACGACTGACTTCTTCATTGGAATATAATCTGCCCTCCAACCTGCTTGACTTTGAAAATGACTTAATTGAATCAAGCTGTAAAGTGACTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCTCCAACCTGCTTGACTT
59.89
ATGCCGATTATCATGCCGGT
59.96
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAATCTGCCCTCCAACCTGC
59.74
ATGCCGATTATCATGCCGGT
59.96
155
PCR template sequence:
TGCGTTTGAAACGACTGACTTCTTCATTGGAATATAATCTGCCCTCCAACCTGCTTGACTTTGAAAATGACTTAATTGAATCAAGCTGTAAAGTGACTAGAGACAAACGCCAGGAGAGCGGTGGACAGAGGGTACGTTCAAGTGCTTCTAACCATCTATGTAGATTGGCACCGGCATGATAATCGGCATAGAAACATGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
25
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-9-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-1a-3p(1), mmu-miR-199a-5p(1), mmu-miR-375-3p(1), mmu-let-7e-5p(1), mmu-miR-34a-5p(1), mmu-miR-205-5p(1), mmu-miR-18a-5p(1), mmu-miR-328-3p(1), mmu-miR-298-5p(1), mmu-miR-320-3p(1), mmu-let-7d-5p(1), mmu-miR-127-3p(1), mmu-miR-676-3p(1), mmu-miR-127-5p(1), mmu-miR-182-5p(1), mmu-miR-425-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-377-3p(1), mmu-miR-190b-5p(1), mmu-miR-670-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTAAAGTGACTAGAGACAAACGCCAG
siRNA sets
TTGTCTCTAGTCACTTTAC, TTTGTCTCTAGTCACTTTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAGTPBP1_2779_ORF_1
0.8683
0.193062646
0.999999957
2763
ORF sequence:
ATGCTCATTCGGAAGGGGATTCTACAGAGCTTAAAAAGTGTCACGAACATCAAGTTGGGCAGAAAAGCATTTATTGATGCGAATGGGATGAAAATTCTGTATAACACTTCTCAAGAGTGCTTGGCGGTCAGGACTCTTGATCCTCTTGTCAACACATCCAGTCTGATAATGAGAAAATGCTTCCCCAAAAACCGCCTTCCGCTCCCCACCATTAAAAGTTCTTTCCACTTCCAATTGCCAATTATCCCTGTGACTGGACCTGTGGCCCAGCTCTACAGCTTGCCGCCTGAAGTGGACGATGTGGTGGACGAGAGTGACGACAACGACGACATTGATTTAGAAGTGGAAAATGAACTCGAGAATGAAGATGACCTAGATCAGAGTTTTAAGAATGATGATATTGAAACAGATATTAATAAATTAAGACCTCAGCAAGTACCAGGACGAACAATAGAAGAACTAAAAATGTACGAGCACCTTTTCCCCGAGCTTGTTGATGATTTTCAGGACTATGAACTGATCTCTAAGGAACCCAAACCTTTTGTGTTTGAGGGGAAGGCTCGGGGCCCCATTGTAGTTCCCACAGCTGGAGAGGAGGTACCTGGGAATTCAGGGAGCGTAAAGAAAGGAGTGGTAATGAAGGAGAGAGCAAGTCCTAAAGGAGAGGAAGCCAAGGAAGACCCTAAGGGCCACGACAGGACACTGCCGCAGCAGCTGGGTGGCCAGAGCAGAGTGGCCCCCTCAGCCCACAGCTTCAACAATGATCTTGTGAAGGCCCTAGACCGAATCACACTGCAGAATGTTCCTTCGCAAGTAGCCTCGGGCTTGAACGCAGGAATGAGGAAGGACTTTGGTCTCCCTCTCACTGTCCTCTCATGCACGAAAGCTTGTCCTCACGTGGCTAAGTGTGGAAGTACTCTCTTTGAAGGGCGGACGGTACATCTTGGGAAGCTGTGTTGTACTGGAGTTGAAACGGAAGATGACGAAGACACTGAGTCCCACTCATCAACAGAGCAGGCCCCCTCTGTTGAAGCCTCTGATGGACCAACACTGCACGACCCAGACCTCTATATTGAGATTGTGAAAAATACGAAGTCCGTTCCAGAATACTCAGAGGTGGCTTATCCTGATTATTTTGGTCACATTCCACCTCCCTTCAAAGAGCCTATTTTAGAAAGGCCTTATGGTGTACAAAGGACAAAAATTGCCCAAGACATCGAGAGGCTGATACACCAGAACGATATCATAGACCGCGTGGTGTATGACTTAGACAACCCTACCTATACCACTCCAGAAGAAGGAGATACTTTGAAGTTTAACTCAAAATTCGAATCTGGGAATCTGCGCAAAGTAATTCAAATTAGAAAAAGCGAGTACGACCTTATCCTGAACTCTGATATAAACAGTAACCATTACCACCAGTGGTTCTACTTTGAAGTCAGTGGGATGCGGCCTGGTGTGGCATATAGGTTCAACATCATCAACTGTGAGAAGTCCAACAGTCAGTTTAATTATGGTATGCAGCCACTTATGTATTCAGTTCAGGAAGCACTAAATGCCAGACCATGGTGGATCCGTATGGGCACTGACATTTGTTACTACAAAAATCACTTCTCACGAAGCTCAGTTGCCGCAGGCGGACAGAAGGGCAAGTCCTACTACACCATCACCTTCACCGTGAACTTCCCGCACAAGGACGATGTCTGCTATTTCGCCTATCACTATCCATACACGTACTCGACTCTGCAGATGCATCTTCAAAAATTGGAATCGGCACACAATCCTCAACAAATCTATTTTCGAAAAGACGTGTTGTGTGAAACCTTGTCTGGAAACATCTGTCCTTTGGTGACCATAACAGCAATGCCAGAGTCCAATTACTATGAACATATCTGTCAGTTCAGAACTCGCCCTTATATTTTCTTGTCTGCTCGGGTCCATCCTGGAGAAACCAATGCAAGCTGGGTAATGAAAGGAACACTGGAGTACCTCATGAGCAATAGCCCGACTGCCCAGAGCCTACGGGAGTCTTACATTTTTAAAATTGTCCCCATGCTAAATCCAGATGGTGTCATCAATGGAAATCACCGCTGCTCCTTAAGTGGAGAGGATTTGAACAGACAGTGGCAAAGTCCAAACCCAGAGTTACACCCCACGATTTATCATGCCAAGGGGCTGCTGCAGTACCTGGCCGCGGTGAAGCGCCTACCTCTGGTTTATTGTGATTACCATGGCCATTCTCGAAAAAAGAATGTATTCATGTACGGCTGCAGCATCAAAGAGACGGTGTGGCACACCCATGACAACTCGGCTTCCTGTGATATTGTGGAAGACATGGGATACAGGACTTTGCCTAAGATACTGAGCCACATTGCTCCGGCATTTTGCATGAGCAGTTGTAGCTTTGTGGTGGAAAAATCTAAAGAATCCACAGCTCGGGTTGTCGTGTGGCGGGAAATTGGAGTTCAGAGGAGCTACACCATGGAGAGTACTTTATGTGGCTGCGATCAGGGTAGATACAAGGGTTTACAGATTGGGACTCGAGAATTGGAAGAGATGGGAGCAAAATTTTGTGTTGGTTTATTGCGTTTGAAACGACTGACTTCTTCATTGGAATATAATCTGCCCTCCAACCTGCTTGACTTTGAAAATGACTTAATTGAATCAAGCTGTAAAGTGACTAGAGACAAACGCCAGGAGAGCGGTGGACAGAGGGTACGTTCAAGTGCTTCTAACCATCTATGTAGATTGGCACCGGCATGA
Peptide sequence:
MLIRKGILQSLKSVTNIKLGRKAFIDANGMKILYNTSQECLAVRTLDPLVNTSSLIMRKCFPKNRLPLPTIKSSFHFQLPIIPVTGPVAQLYSLPPEVDDVVDESDDNDDIDLEVENELENEDDLDQSFKNDDIETDINKLRPQQVPGRTIEELKMYEHLFPELVDDFQDYELISKEPKPFVFEGKARGPIVVPTAGEEVPGNSGSVKKGVVMKERASPKGEEAKEDPKGHDRTLPQQLGGQSRVAPSAHSFNNDLVKALDRITLQNVPSQVASGLNAGMRKDFGLPLTVLSCTKACPHVAKCGSTLFEGRTVHLGKLCCTGVETEDDEDTESHSSTEQAPSVEASDGPTLHDPDLYIEIVKNTKSVPEYSEVAYPDYFGHIPPPFKEPILERPYGVQRTKIAQDIERLIHQNDIIDRVVYDLDNPTYTTPEEGDTLKFNSKFESGNLRKVIQIRKSEYDLILNSDINSNHYHQWFYFEVSGMRPGVAYRFNIINCEKSNSQFNYGMQPLMYSVQEALNARPWWIRMGTDICYYKNHFSRSSVAAGGQKGKSYYTITFTVNFPHKDDVCYFAYHYPYTYSTLQMHLQKLESAHNPQQIYFRKDVLCETLSGNICPLVTITAMPESNYYEHICQFRTRPYIFLSARVHPGETNASWVMKGTLEYLMSNSPTAQSLRESYIFKIVPMLNPDGVINGNHRCSLSGEDLNRQWQSPNPELHPTIYHAKGLLQYLAAVKRLPLVYCDYHGHSRKKNVFMYGCSIKETVWHTHDNSASCDIVEDMGYRTLPKILSHIAPAFCMSSCSFVVEKSKESTARVVVWREIGVQRSYTMESTLCGCDQGRYKGLQIGTRELEEMGAKFCVGLLRLKRLTSSLEYNLPSNLLDFENDLIESSCKVTRDKRQESGGQRVRSSASNHLCRLAPA
IRESfinder result
IRESfinder score
0.577595849
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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