top of page
mmu_circAgtpbp1_1126
Basic information of circular RNA
PanCircBase ID:
mmu_circAgtpbp1_1126
mm39_Chr. Position ID:
chr13|59643146|59652124|-
Gene name:
Agtpbp1
Transcript:
ENSMUST00000022040.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
17,16,15,14,13
Exon/intron offsets:
0,230,1643,4681,8861
Genomic length:
8978
Exon/intron sizes in nt:
149,87,84,689,117
Flanking exon/introns:
chr13:59630418-59643146|chr13:59652124-59655772
Splice length:
1126
Other database IDs:
circBase: mmu_circ_0004713, CIRCpedia: MMU_CIRCpedia_24533, circAtlas: mmu-Agtpbp1_0009
circBase: hsa_circ_0139196, circAtlas: hsa-AGTPBP1_0012, CIRCpedia: HSA_CIRCpedia_64567
Human Ortholog IDs:
Mature spliced Sequence:
AATGATGATATTGAAACAGATATTAATAAATTAAGACCTCAGCAAGTACCAGGACGAACAATAGAAGAACTAAAAATGTACGAGCACCTTTTCCCCGAGCTTGTTGATGATTTTCAGGACTATGAACTGATCTCTAAGGAACCCAAACCTTTTGTGTTTGAGGGGAAGGCTCGGGGCCCCATTGTAGTTCCCACAGCTGGAGAGGAGGTACCTGGGAATTCAGGGAGCGTAAAGAAAGGAGTGGTAATGAAGGAGAGAGCAAGTCCTAAAGGAGAGGAAGCCAAGGAAGACCCTAAGGGCCACGACAGGACACTGCCGCAGCAGCTGGGTGGCCAGAGCAGAGTGGCCCCCTCAGCCCACAGCTTCAACAATGATCTTGTGAAGGCCCTAGACCGAATCACACTGCAGAATGTTCCTTCGCAAGTAGCCTCGGGCTTGAACGCAGGAATGAGGAAGGACTTTGGTCTCCCTCTCACTGTCCTCTCATGCACGAAAGCTTGTCCTCACGTGGCTAAGTGTGGAAGTACTCTCTTTGAAGGGCGGACGGTACATCTTGGGAAGCTGTGTTGTACTGGAGTTGAAACGGAAGATGACGAAGACACTGAGTCCCACTCATCAACAGAGCAGGCCCCCTCTGTTGAAGCCTCTGATGGACCAACACTGCACGACCCAGACCTCTATATTGAGATTGTGAAAAATACGAAGTCCGTTCCAGAATACTCAGAGGTGGCTTATCCTGATTATTTTGGTCACATTCCACCTCCCTTCAAAGAGCCTATTTTAGAAAGGCCTTATGGTGTACAAAGGACAAAAATTGCCCAAGACATCGAGAGGCTGATACACCAGAACGATATCATAGACCGCGTGGTGTATGACTTAGACAACCCTACCTATACCACTCCAGAAGAAGGAGATACTTTGAAGTTTAACTCAAAATTCGAATCTGGGAATCTGCGCAAAGTAATTCAAATTAGAAAAAGCGAGTACGACCTTATCCTGAACTCTGATATAAACAGTAACCATTACCACCAGTGGTTCTACTTTGAAGTCAGTGGGATGCGGCCTGGTGTGGCATATAGGTTCAACATCATCAACTGTGAGAAGTCCAACAGTCAGTTTAATTATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGAAGTCAGTGGGATGCGG
60.32
GGGGAAAAGGTGCTCGTACA
59.96
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGAAGTCAGTGGGATGCGG
60.32
CGTCCTGGTACTTGCTGAGG
60.11
140
PCR template sequence:
CACCAGTGGTTCTACTTTGAAGTCAGTGGGATGCGGCCTGGTGTGGCATATAGGTTCAACATCATCAACTGTGAGAAGTCCAACAGTCAGTTTAATTATGAATGATGATATTGAAACAGATATTAATAAATTAAGACCTCAGCAAGTACCAGGACGAACAATAGAAGAACTAAAAATGTACGAGCACCTTTTCCCCGAGC
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
CAGTTTAATTATGAATGATGATATTG
siRNA sets
CATCATTCATAATTAAACT, TATCATCATTCATAATTAA, AATATCATCATTCATAATT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAGTPBP1_1126_ORF_1
1.0594
0.239217116
0.996958748
1128
ORF sequence:
ATGAATGATGATATTGAAACAGATATTAATAAATTAAGACCTCAGCAAGTACCAGGACGAACAATAGAAGAACTAAAAATGTACGAGCACCTTTTCCCCGAGCTTGTTGATGATTTTCAGGACTATGAACTGATCTCTAAGGAACCCAAACCTTTTGTGTTTGAGGGGAAGGCTCGGGGCCCCATTGTAGTTCCCACAGCTGGAGAGGAGGTACCTGGGAATTCAGGGAGCGTAAAGAAAGGAGTGGTAATGAAGGAGAGAGCAAGTCCTAAAGGAGAGGAAGCCAAGGAAGACCCTAAGGGCCACGACAGGACACTGCCGCAGCAGCTGGGTGGCCAGAGCAGAGTGGCCCCCTCAGCCCACAGCTTCAACAATGATCTTGTGAAGGCCCTAGACCGAATCACACTGCAGAATGTTCCTTCGCAAGTAGCCTCGGGCTTGAACGCAGGAATGAGGAAGGACTTTGGTCTCCCTCTCACTGTCCTCTCATGCACGAAAGCTTGTCCTCACGTGGCTAAGTGTGGAAGTACTCTCTTTGAAGGGCGGACGGTACATCTTGGGAAGCTGTGTTGTACTGGAGTTGAAACGGAAGATGACGAAGACACTGAGTCCCACTCATCAACAGAGCAGGCCCCCTCTGTTGAAGCCTCTGATGGACCAACACTGCACGACCCAGACCTCTATATTGAGATTGTGAAAAATACGAAGTCCGTTCCAGAATACTCAGAGGTGGCTTATCCTGATTATTTTGGTCACATTCCACCTCCCTTCAAAGAGCCTATTTTAGAAAGGCCTTATGGTGTACAAAGGACAAAAATTGCCCAAGACATCGAGAGGCTGATACACCAGAACGATATCATAGACCGCGTGGTGTATGACTTAGACAACCCTACCTATACCACTCCAGAAGAAGGAGATACTTTGAAGTTTAACTCAAAATTCGAATCTGGGAATCTGCGCAAAGTAATTCAAATTAGAAAAAGCGAGTACGACCTTATCCTGAACTCTGATATAAACAGTAACCATTACCACCAGTGGTTCTACTTTGAAGTCAGTGGGATGCGGCCTGGTGTGGCATATAGGTTCAACATCATCAACTGTGAGAAGTCCAACAGTCAGTTTAATTAT
Peptide sequence:
MNDDIETDINKLRPQQVPGRTIEELKMYEHLFPELVDDFQDYELISKEPKPFVFEGKARGPIVVPTAGEEVPGNSGSVKKGVVMKERASPKGEEAKEDPKGHDRTLPQQLGGQSRVAPSAHSFNNDLVKALDRITLQNVPSQVASGLNAGMRKDFGLPLTVLSCTKACPHVAKCGSTLFEGRTVHLGKLCCTGVETEDDEDTESHSSTEQAPSVEASDGPTLHDPDLYIEIVKNTKSVPEYSEVAYPDYFGHIPPPFKEPILERPYGVQRTKIAQDIERLIHQNDIIDRVVYDLDNPTYTTPEEGDTLKFNSKFESGNLRKVIQIRKSEYDLILNSDINSNHYHQWFYFEVSGMRPGVAYRFNIINCEKSNSQFNY
IRESfinder result
IRESfinder score
0.599195911
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page