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mmu_circAgtpbp1_1963
Basic information of circular RNA
PanCircBase ID:
mmu_circAgtpbp1_1963
mm39_Chr. Position ID:
chr13|59630330|59676332|-
Gene name:
Agtpbp1
Transcript:
ENSMUST00000022040.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
18,17,16,15,14,13,12,11,10,9,8,7
Exon/intron offsets:
0,12816,13046,14459,17497,21677,25442,29807,31570,35136,42629,45870
Genomic length:
46002
Exon/intron sizes in nt:
88,149,87,84,689,117,98,178,209,38,94,132
Flanking exon/introns:
chr13:59624952-59630330|chr13:59676332-59678870
Splice length:
1963
Other database IDs:
CIRCpedia: MMU_CIRCpedia_24528, circAtlas: mmu-Agtpbp1_0064
Human Ortholog IDs:
Mature spliced Sequence:
ATAAGAAATTTGGAGTGAAAGCTCGAGTTAACGGGGCACTGACTGTGACTCTGAACTTGGTAAAGCAGCACTTTCAGAACTACCGCTTGGTTCTTCCTTGTCTTCAGCTCTTGCGAGTCTATTCTACCAACTCTGTGAACTCAGTATCTTTAGGTAAAAATGGAGTTGTGGAGTTGATGTTTAAAATCATTGGGCCATTCAGTAAGAAGAATTCGGGTCTCATGAAGGTTGCTTTAGACACTCTTGCTGCATTGCTAAAATCAAAGACAAACGCCAGGAGAGCGGTGGACAGAGGGTACGTTCAAGTGCTTCTAACCATCTATGTAGATTGGCACCGGCATGATAATCGGCATAGAAACATGCTCATTCGGAAGGGGATTCTACAGAGCTTAAAAAGTGTCACGAACATCAAGTTGGGCAGAAAAGCATTTATTGATGCGAATGGGATGAAAATTCTGTATAACACTTCTCAAGAGTGCTTGGCGGTCAGGACTCTTGATCCTCTTGTCAACACATCCAGTCTGATAATGAGAAAATGCTTCCCCAAAAACCGCCTTCCGCTCCCCACCATTAAAAGTTCTTTCCACTTCCAATTGCCAATTATCCCTGTGACTGGACCTGTGGCCCAGCTCTACAGCTTGCCGCCTGAAGTGGACGATGTGGTGGACGAGAGTGACGACAACGACGACATTGATTTAGAAGTGGAAAATGAACTCGAGAATGAAGATGACCTAGATCAGAGTTTTAAGAATGATGATATTGAAACAGATATTAATAAATTAAGACCTCAGCAAGTACCAGGACGAACAATAGAAGAACTAAAAATGTACGAGCACCTTTTCCCCGAGCTTGTTGATGATTTTCAGGACTATGAACTGATCTCTAAGGAACCCAAACCTTTTGTGTTTGAGGGGAAGGCTCGGGGCCCCATTGTAGTTCCCACAGCTGGAGAGGAGGTACCTGGGAATTCAGGGAGCGTAAAGAAAGGAGTGGTAATGAAGGAGAGAGCAAGTCCTAAAGGAGAGGAAGCCAAGGAAGACCCTAAGGGCCACGACAGGACACTGCCGCAGCAGCTGGGTGGCCAGAGCAGAGTGGCCCCCTCAGCCCACAGCTTCAACAATGATCTTGTGAAGGCCCTAGACCGAATCACACTGCAGAATGTTCCTTCGCAAGTAGCCTCGGGCTTGAACGCAGGAATGAGGAAGGACTTTGGTCTCCCTCTCACTGTCCTCTCATGCACGAAAGCTTGTCCTCACGTGGCTAAGTGTGGAAGTACTCTCTTTGAAGGGCGGACGGTACATCTTGGGAAGCTGTGTTGTACTGGAGTTGAAACGGAAGATGACGAAGACACTGAGTCCCACTCATCAACAGAGCAGGCCCCCTCTGTTGAAGCCTCTGATGGACCAACACTGCACGACCCAGACCTCTATATTGAGATTGTGAAAAATACGAAGTCCGTTCCAGAATACTCAGAGGTGGCTTATCCTGATTATTTTGGTCACATTCCACCTCCCTTCAAAGAGCCTATTTTAGAAAGGCCTTATGGTGTACAAAGGACAAAAATTGCCCAAGACATCGAGAGGCTGATACACCAGAACGATATCATAGACCGCGTGGTGTATGACTTAGACAACCCTACCTATACCACTCCAGAAGAAGGAGATACTTTGAAGTTTAACTCAAAATTCGAATCTGGGAATCTGCGCAAAGTAATTCAAATTAGAAAAAGCGAGTACGACCTTATCCTGAACTCTGATATAAACAGTAACCATTACCACCAGTGGTTCTACTTTGAAGTCAGTGGGATGCGGCCTGGTGTGGCATATAGGTTCAACATCATCAACTGTGAGAAGTCCAACAGTCAGTTTAATTATGGTATGCAGCCACTTATGTATTCAGTTCAGGAAGCACTAAATGCCAGACCATGGTGGATCCGTATGGGCACTGACATTTGTTACTACAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTATGCAGCCACTTATGT
56.9
AGCGGTAGTTCTGAAAGTGCT
59.66
177
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTATGCAGCCACTTATGT
56.9
CGGTAGTTCTGAAAGTGCTGC
59.54
175
PCR template sequence:
AGTTTAATTATGGTATGCAGCCACTTATGTATTCAGTTCAGGAAGCACTAAATGCCAGACCATGGTGGATCCGTATGGGCACTGACATTTGTTACTACAAATAAGAAATTTGGAGTGAAAGCTCGAGTTAACGGGGCACTGACTGTGACTCTGAACTTGGTAAAGCAGCACTTTCAGAACTACCGCTTGGTTCTTCCTTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
23
Interacting miRNAs (#binding sites)
mmu-miR-205-5p(2), mmu-miR-20b-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-1a-3p(1), mmu-miR-375-3p(1), mmu-miR-34a-5p(1), mmu-miR-106b-5p(1), mmu-miR-335-5p(1), mmu-miR-328-3p(1), mmu-miR-298-5p(1), mmu-miR-320-3p(1), mmu-miR-136-5p(1), mmu-miR-127-3p(1), mmu-miR-676-3p(1), mmu-miR-127-5p(1), mmu-miR-182-5p(1), mmu-miR-670-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTGTTACTACAAATAAGAAATTTGG
siRNA sets
TTTCTTATTTGTAGTAACA, AATTTCTTATTTGTAGTAA, ATTTCTTATTTGTAGTAAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAGTPBP1_1963_ORF_1
1.0986
0.198161065
0.999993997
2010
ORF sequence:
ATGCCAGACCATGGTGGATCCGTATGGGCACTGACATTTGTTACTACAAATAAGAAATTTGGAGTGAAAGCTCGAGTTAACGGGGCACTGACTGTGACTCTGAACTTGGTAAAGCAGCACTTTCAGAACTACCGCTTGGTTCTTCCTTGTCTTCAGCTCTTGCGAGTCTATTCTACCAACTCTGTGAACTCAGTATCTTTAGGTAAAAATGGAGTTGTGGAGTTGATGTTTAAAATCATTGGGCCATTCAGTAAGAAGAATTCGGGTCTCATGAAGGTTGCTTTAGACACTCTTGCTGCATTGCTAAAATCAAAGACAAACGCCAGGAGAGCGGTGGACAGAGGGTACGTTCAAGTGCTTCTAACCATCTATGTAGATTGGCACCGGCATGATAATCGGCATAGAAACATGCTCATTCGGAAGGGGATTCTACAGAGCTTAAAAAGTGTCACGAACATCAAGTTGGGCAGAAAAGCATTTATTGATGCGAATGGGATGAAAATTCTGTATAACACTTCTCAAGAGTGCTTGGCGGTCAGGACTCTTGATCCTCTTGTCAACACATCCAGTCTGATAATGAGAAAATGCTTCCCCAAAAACCGCCTTCCGCTCCCCACCATTAAAAGTTCTTTCCACTTCCAATTGCCAATTATCCCTGTGACTGGACCTGTGGCCCAGCTCTACAGCTTGCCGCCTGAAGTGGACGATGTGGTGGACGAGAGTGACGACAACGACGACATTGATTTAGAAGTGGAAAATGAACTCGAGAATGAAGATGACCTAGATCAGAGTTTTAAGAATGATGATATTGAAACAGATATTAATAAATTAAGACCTCAGCAAGTACCAGGACGAACAATAGAAGAACTAAAAATGTACGAGCACCTTTTCCCCGAGCTTGTTGATGATTTTCAGGACTATGAACTGATCTCTAAGGAACCCAAACCTTTTGTGTTTGAGGGGAAGGCTCGGGGCCCCATTGTAGTTCCCACAGCTGGAGAGGAGGTACCTGGGAATTCAGGGAGCGTAAAGAAAGGAGTGGTAATGAAGGAGAGAGCAAGTCCTAAAGGAGAGGAAGCCAAGGAAGACCCTAAGGGCCACGACAGGACACTGCCGCAGCAGCTGGGTGGCCAGAGCAGAGTGGCCCCCTCAGCCCACAGCTTCAACAATGATCTTGTGAAGGCCCTAGACCGAATCACACTGCAGAATGTTCCTTCGCAAGTAGCCTCGGGCTTGAACGCAGGAATGAGGAAGGACTTTGGTCTCCCTCTCACTGTCCTCTCATGCACGAAAGCTTGTCCTCACGTGGCTAAGTGTGGAAGTACTCTCTTTGAAGGGCGGACGGTACATCTTGGGAAGCTGTGTTGTACTGGAGTTGAAACGGAAGATGACGAAGACACTGAGTCCCACTCATCAACAGAGCAGGCCCCCTCTGTTGAAGCCTCTGATGGACCAACACTGCACGACCCAGACCTCTATATTGAGATTGTGAAAAATACGAAGTCCGTTCCAGAATACTCAGAGGTGGCTTATCCTGATTATTTTGGTCACATTCCACCTCCCTTCAAAGAGCCTATTTTAGAAAGGCCTTATGGTGTACAAAGGACAAAAATTGCCCAAGACATCGAGAGGCTGATACACCAGAACGATATCATAGACCGCGTGGTGTATGACTTAGACAACCCTACCTATACCACTCCAGAAGAAGGAGATACTTTGAAGTTTAACTCAAAATTCGAATCTGGGAATCTGCGCAAAGTAATTCAAATTAGAAAAAGCGAGTACGACCTTATCCTGAACTCTGATATAAACAGTAACCATTACCACCAGTGGTTCTACTTTGAAGTCAGTGGGATGCGGCCTGGTGTGGCATATAGGTTCAACATCATCAACTGTGAGAAGTCCAACAGTCAGTTTAATTATGGTATGCAGCCACTTATGTATTCAGTTCAGGAAGCACTAAATGCCAGACCATGGTGGATCCGTATGGGCACTGACATTTGTTACTAC
Peptide sequence:
MPDHGGSVWALTFVTTNKKFGVKARVNGALTVTLNLVKQHFQNYRLVLPCLQLLRVYSTNSVNSVSLGKNGVVELMFKIIGPFSKKNSGLMKVALDTLAALLKSKTNARRAVDRGYVQVLLTIYVDWHRHDNRHRNMLIRKGILQSLKSVTNIKLGRKAFIDANGMKILYNTSQECLAVRTLDPLVNTSSLIMRKCFPKNRLPLPTIKSSFHFQLPIIPVTGPVAQLYSLPPEVDDVVDESDDNDDIDLEVENELENEDDLDQSFKNDDIETDINKLRPQQVPGRTIEELKMYEHLFPELVDDFQDYELISKEPKPFVFEGKARGPIVVPTAGEEVPGNSGSVKKGVVMKERASPKGEEAKEDPKGHDRTLPQQLGGQSRVAPSAHSFNNDLVKALDRITLQNVPSQVASGLNAGMRKDFGLPLTVLSCTKACPHVAKCGSTLFEGRTVHLGKLCCTGVETEDDEDTESHSSTEQAPSVEASDGPTLHDPDLYIEIVKNTKSVPEYSEVAYPDYFGHIPPPFKEPILERPYGVQRTKIAQDIERLIHQNDIIDRVVYDLDNPTYTTPEEGDTLKFNSKFESGNLRKVIQIRKSEYDLILNSDINSNHYHQWFYFEVSGMRPGVAYRFNIINCEKSNSQFNYGMQPLMYSVQEALNARPWWIRMGTDICYY
IRESfinder result
IRESfinder score
0.624907531
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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