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mmu_circAgtpbp1_1224
Basic information of circular RNA
PanCircBase ID:
mmu_circAgtpbp1_1224
mm39_Chr. Position ID:
chr13|59643146|59655870|-
Gene name:
Agtpbp1
Transcript:
ENSMUST00000022040.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
17,16,15,14,13,12
Exon/intron offsets:
0,230,1643,4681,8861,12626
Genomic length:
12724
Exon/intron sizes in nt:
149,87,84,689,117,98
Flanking exon/introns:
chr13:59630418-59643146|chr13:59655870-59660137
Splice length:
1224
Other database IDs:
circBase: mmu_circ_0004714, CIRCpedia: MMU_CIRCpedia_24534, circAtlas: mmu-Agtpbp1_0054
circAtlas: hsa-AGTPBP1_0075, CIRCpedia: HSA_CIRCpedia_170647
Human Ortholog IDs:
Mature spliced Sequence:
TGGACGATGTGGTGGACGAGAGTGACGACAACGACGACATTGATTTAGAAGTGGAAAATGAACTCGAGAATGAAGATGACCTAGATCAGAGTTTTAAGAATGATGATATTGAAACAGATATTAATAAATTAAGACCTCAGCAAGTACCAGGACGAACAATAGAAGAACTAAAAATGTACGAGCACCTTTTCCCCGAGCTTGTTGATGATTTTCAGGACTATGAACTGATCTCTAAGGAACCCAAACCTTTTGTGTTTGAGGGGAAGGCTCGGGGCCCCATTGTAGTTCCCACAGCTGGAGAGGAGGTACCTGGGAATTCAGGGAGCGTAAAGAAAGGAGTGGTAATGAAGGAGAGAGCAAGTCCTAAAGGAGAGGAAGCCAAGGAAGACCCTAAGGGCCACGACAGGACACTGCCGCAGCAGCTGGGTGGCCAGAGCAGAGTGGCCCCCTCAGCCCACAGCTTCAACAATGATCTTGTGAAGGCCCTAGACCGAATCACACTGCAGAATGTTCCTTCGCAAGTAGCCTCGGGCTTGAACGCAGGAATGAGGAAGGACTTTGGTCTCCCTCTCACTGTCCTCTCATGCACGAAAGCTTGTCCTCACGTGGCTAAGTGTGGAAGTACTCTCTTTGAAGGGCGGACGGTACATCTTGGGAAGCTGTGTTGTACTGGAGTTGAAACGGAAGATGACGAAGACACTGAGTCCCACTCATCAACAGAGCAGGCCCCCTCTGTTGAAGCCTCTGATGGACCAACACTGCACGACCCAGACCTCTATATTGAGATTGTGAAAAATACGAAGTCCGTTCCAGAATACTCAGAGGTGGCTTATCCTGATTATTTTGGTCACATTCCACCTCCCTTCAAAGAGCCTATTTTAGAAAGGCCTTATGGTGTACAAAGGACAAAAATTGCCCAAGACATCGAGAGGCTGATACACCAGAACGATATCATAGACCGCGTGGTGTATGACTTAGACAACCCTACCTATACCACTCCAGAAGAAGGAGATACTTTGAAGTTTAACTCAAAATTCGAATCTGGGAATCTGCGCAAAGTAATTCAAATTAGAAAAAGCGAGTACGACCTTATCCTGAACTCTGATATAAACAGTAACCATTACCACCAGTGGTTCTACTTTGAAGTCAGTGGGATGCGGCCTGGTGTGGCATATAGGTTCAACATCATCAACTGTGAGAAGTCCAACAGTCAGTTTAATTATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACCAGTGGTTCTACTTTGAAGT
58.55
ATGTCGTCGTTGTCGTCACT
59.69
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGAAGTCAGTGGGATGCGG
60.32
AGGTCATCTTCATTCTCGAGTTCA
59.54
166
PCR template sequence:
CACCAGTGGTTCTACTTTGAAGTCAGTGGGATGCGGCCTGGTGTGGCATATAGGTTCAACATCATCAACTGTGAGAAGTCCAACAGTCAGTTTAATTATGTGGACGATGTGGTGGACGAGAGTGACGACAACGACGACATTGATTTAGAAGTGGAAAATGAACTCGAGAATGAAGATGACCTAGATCAGAGTTTTAAGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-1a-3p(1), mmu-miR-375-3p(1), mmu-miR-34a-5p(1), mmu-miR-205-5p(1), mmu-miR-328-3p(1), mmu-miR-298-5p(1), mmu-miR-320-3p(1), mmu-miR-676-3p(1), mmu-miR-127-5p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGTTTAATTATGTGGACGATGTGGT
siRNA sets
ATCGTCCACATAATTAAAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAGTPBP1_1224_ORF_1
1.1828
0.270253628
0.99999945
2274
ORF sequence:
ATGTACGAGCACCTTTTCCCCGAGCTTGTTGATGATTTTCAGGACTATGAACTGATCTCTAAGGAACCCAAACCTTTTGTGTTTGAGGGGAAGGCTCGGGGCCCCATTGTAGTTCCCACAGCTGGAGAGGAGGTACCTGGGAATTCAGGGAGCGTAAAGAAAGGAGTGGTAATGAAGGAGAGAGCAAGTCCTAAAGGAGAGGAAGCCAAGGAAGACCCTAAGGGCCACGACAGGACACTGCCGCAGCAGCTGGGTGGCCAGAGCAGAGTGGCCCCCTCAGCCCACAGCTTCAACAATGATCTTGTGAAGGCCCTAGACCGAATCACACTGCAGAATGTTCCTTCGCAAGTAGCCTCGGGCTTGAACGCAGGAATGAGGAAGGACTTTGGTCTCCCTCTCACTGTCCTCTCATGCACGAAAGCTTGTCCTCACGTGGCTAAGTGTGGAAGTACTCTCTTTGAAGGGCGGACGGTACATCTTGGGAAGCTGTGTTGTACTGGAGTTGAAACGGAAGATGACGAAGACACTGAGTCCCACTCATCAACAGAGCAGGCCCCCTCTGTTGAAGCCTCTGATGGACCAACACTGCACGACCCAGACCTCTATATTGAGATTGTGAAAAATACGAAGTCCGTTCCAGAATACTCAGAGGTGGCTTATCCTGATTATTTTGGTCACATTCCACCTCCCTTCAAAGAGCCTATTTTAGAAAGGCCTTATGGTGTACAAAGGACAAAAATTGCCCAAGACATCGAGAGGCTGATACACCAGAACGATATCATAGACCGCGTGGTGTATGACTTAGACAACCCTACCTATACCACTCCAGAAGAAGGAGATACTTTGAAGTTTAACTCAAAATTCGAATCTGGGAATCTGCGCAAAGTAATTCAAATTAGAAAAAGCGAGTACGACCTTATCCTGAACTCTGATATAAACAGTAACCATTACCACCAGTGGTTCTACTTTGAAGTCAGTGGGATGCGGCCTGGTGTGGCATATAGGTTCAACATCATCAACTGTGAGAAGTCCAACAGTCAGTTTAATTATGTGGACGATGTGGTGGACGAGAGTGACGACAACGACGACATTGATTTAGAAGTGGAAAATGAACTCGAGAATGAAGATGACCTAGATCAGAGTTTTAAGAATGATGATATTGAAACAGATATTAATAAATTAAGACCTCAGCAAGTACCAGGACGAACAATAGAAGAACTAAAAATGTACGAGCACCTTTTCCCCGAGCTTGTTGATGATTTTCAGGACTATGAACTGATCTCTAAGGAACCCAAACCTTTTGTGTTTGAGGGGAAGGCTCGGGGCCCCATTGTAGTTCCCACAGCTGGAGAGGAGGTACCTGGGAATTCAGGGAGCGTAAAGAAAGGAGTGGTAATGAAGGAGAGAGCAAGTCCTAAAGGAGAGGAAGCCAAGGAAGACCCTAAGGGCCACGACAGGACACTGCCGCAGCAGCTGGGTGGCCAGAGCAGAGTGGCCCCCTCAGCCCACAGCTTCAACAATGATCTTGTGAAGGCCCTAGACCGAATCACACTGCAGAATGTTCCTTCGCAAGTAGCCTCGGGCTTGAACGCAGGAATGAGGAAGGACTTTGGTCTCCCTCTCACTGTCCTCTCATGCACGAAAGCTTGTCCTCACGTGGCTAAGTGTGGAAGTACTCTCTTTGAAGGGCGGACGGTACATCTTGGGAAGCTGTGTTGTACTGGAGTTGAAACGGAAGATGACGAAGACACTGAGTCCCACTCATCAACAGAGCAGGCCCCCTCTGTTGAAGCCTCTGATGGACCAACACTGCACGACCCAGACCTCTATATTGAGATTGTGAAAAATACGAAGTCCGTTCCAGAATACTCAGAGGTGGCTTATCCTGATTATTTTGGTCACATTCCACCTCCCTTCAAAGAGCCTATTTTAGAAAGGCCTTATGGTGTACAAAGGACAAAAATTGCCCAAGACATCGAGAGGCTGATACACCAGAACGATATCATAGACCGCGTGGTGTATGACTTAGACAACCCTACCTATACCACTCCAGAAGAAGGAGATACTTTGAAGTTTAACTCAAAATTCGAATCTGGGAATCTGCGCAAAGTAATTCAAATTAGAAAAAGCGAGTACGACCTTATCCTGAACTCTGATATAAACAGTAACCATTACCACCAGTGGTTCTACTTTGAAGTCAGTGGGATGCGGCCTGGTGTGGCATATAGGTTCAACATCATCAACTGTGAGAAGTCCAACAGTCAGTTTAATTAT
Peptide sequence:
MYEHLFPELVDDFQDYELISKEPKPFVFEGKARGPIVVPTAGEEVPGNSGSVKKGVVMKERASPKGEEAKEDPKGHDRTLPQQLGGQSRVAPSAHSFNNDLVKALDRITLQNVPSQVASGLNAGMRKDFGLPLTVLSCTKACPHVAKCGSTLFEGRTVHLGKLCCTGVETEDDEDTESHSSTEQAPSVEASDGPTLHDPDLYIEIVKNTKSVPEYSEVAYPDYFGHIPPPFKEPILERPYGVQRTKIAQDIERLIHQNDIIDRVVYDLDNPTYTTPEEGDTLKFNSKFESGNLRKVIQIRKSEYDLILNSDINSNHYHQWFYFEVSGMRPGVAYRFNIINCEKSNSQFNYVDDVVDESDDNDDIDLEVENELENEDDLDQSFKNDDIETDINKLRPQQVPGRTIEELKMYEHLFPELVDDFQDYELISKEPKPFVFEGKARGPIVVPTAGEEVPGNSGSVKKGVVMKERASPKGEEAKEDPKGHDRTLPQQLGGQSRVAPSAHSFNNDLVKALDRITLQNVPSQVASGLNAGMRKDFGLPLTVLSCTKACPHVAKCGSTLFEGRTVHLGKLCCTGVETEDDEDTESHSSTEQAPSVEASDGPTLHDPDLYIEIVKNTKSVPEYSEVAYPDYFGHIPPPFKEPILERPYGVQRTKIAQDIERLIHQNDIIDRVVYDLDNPTYTTPEEGDTLKFNSKFESGNLRKVIQIRKSEYDLILNSDINSNHYHQWFYFEVSGMRPGVAYRFNIINCEKSNSQFNY
IRESfinder result
IRESfinder score
0.574305511
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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