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mmu_circAmph_1485
Basic information of circular RNA
PanCircBase ID:
mmu_circAmph_1485
mm39_Chr. Position ID:
chr13|19270692|19305501|+
Gene name:
Amph
Transcript:
ENSMUST00000239207.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
13
Exon/intron indexes:
5,6,7,8,9,10,11,12,13,14,15,16,17
Exon/intron offsets:
0,8230,9484,13370,14049,16349,17708,26580,29714,31629,31901,34073,34752
Genomic length:
34809
Exon/intron sizes in nt:
96,108,86,76,83,139,129,117,24,24,513,33,57
Flanking exon/introns:
chr13:19268469-19270692|chr13:19305501-19321705
Splice length:
1485
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AAGTGTGATGTGCTGTGGGAAGACTTCCATCAAAAGCTAGTGGATGGCTCCTTGCTGACACTGGACACCTACCTGGGCCAGTTTCCTGACATAAAGAATCGCATCGCTAAGCGCAGCAGGAAGCTTGTGGATTATGATAGTGCTCGCCATCACCTGGAGGCTCTGCAGAGTTCCAAACGGAAAGATGAGAGTCGGATCTCTAAGGCAGAAGAGGAGTTTCAGAAAGCACAGAAAGTGTTTGAAGAGTTCAATGTTGACTTACAAGAAGAGTTGCCGTCATTGTGGTCAAGTCGAGTTGGCTTTTACGTCAATACTTTCAAAAATGTCTCCAGCCTTGAGGCCAAGTTTCATAAGGAAATCGCAGTGCTTTGCCACAAGCTCTATGAAGTGATGACGAAACTCGGTGATCAGCATGCTGACAAGGCCTTCAGCATTCAAGGAGCTCCCAGTGACTCGGGTCCTCTTCGCATTGCAAAGACACCATCACCTCCAGAGGAGCCTTCTCCCCTGCCCAGCCCCACGGCTAGTCCCAACCACACATTAGCACCTGCATCTCCTGCCCCAGTGCGACCCAGATCACCTTCACAGACAAGGAAAGGGCCTCCTGTCCCACCTCTGCCTAAAGTCACCCCAACAAAGGAACTGAAACAGGAGAACATCATCAATTTCTTTGAGGACAACTTTGTACCAGAAATCAATGTGACAACACCTTCCCAGAACGAAGTCTTGGAGGTGAAGAAGGAAGAGACTTTGCTGGATTTGGACTTTGACCCTTTCAAGCCCGATGTGGCTCCGGCAGGTTCTGCTGCAGCGACCCACTCTCCCATGTCTCAGACATTGCCCTGGGACTTATGGACGACAAGCACTGATTTGGTACAACCAACTGACTCTTCAAAAAGTCTTTCTATGTGTAACCTCATCATGGAGGAAACCCCTGACAGTGGTTTGGCTGAAGAGATTCAAAGATATGAAACTGACATAGGTGCATTCACTTGGGGGCCTCATGCTAGGACAGACAGTGTCAGCCAGGAGATGACCTCAAGTGGGTCCCAAGAAGACATGCTCTGTCTCTCTGAAGCAGAGCAAGACATGAGATTATCCACTGCAATGCTTTCTTCTGCTGACTGTTCTACTGTAGCTGGTCAGGATGAGGATGCTCCTCCAGCTAGAAATGAGCAGCTGTCCTCAGAGCCTGTTCCTGGGGCTGAAGTTGCTATTACTACGTACATGGAGATGGACCAGCCATATGCATTACTTGACTCAGAGCTACCAGCCGTCGGAAAAGCTGACCTGCTCAAAGAAGGTCATGAAGAAGCTAAAATATCAGATGGTGAAATAAAACAGACACAGAAGTTAGAAGATCCTATGTGGGTATGTGTGGAGACATACCAAAGGGCTTCTGGGGGTTCATTTAATGATTTCACCCAGGCCCAGGACACTTCATTATTCACCATGCAGACAGATCAGAATATGGTAGGTGGCTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGATTTCACCCAGGCCCAG
60.03
GGTAGGTGTCCAGTGTCAGC
60.04
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGATTTCACCCAGGCCCAG
60.03
AGGTGTCCAGTGTCAGCAAG
59.89
141
PCR template sequence:
ATACCAAAGGGCTTCTGGGGGTTCATTTAATGATTTCACCCAGGCCCAGGACACTTCATTATTCACCATGCAGACAGATCAGAATATGGTAGGTGGCTTGAAGTGTGATGTGCTGTGGGAAGACTTCCATCAAAAGCTAGTGGATGGCTCCTTGCTGACACTGGACACCTACCTGGGCCAGTTTCCTGACATAAAGAATC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-210-3p(1), mmu-miR-9-5p(1), mmu-miR-223-3p(1), mmu-miR-26a-5p(1), mmu-miR-298-5p(1), mmu-miR-222-3p(1), mmu-miR-138-5p(1), mmu-miR-139-5p(1), mmu-miR-26b-5p(1), mmu-miR-382-5p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGTAGGTGGCTTGAAGTGTGATGTGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAMPH_1485_ORF_1
1.0526
0.206778084
0.999999899
2580
ORF sequence:
ATGACGAAACTCGGTGATCAGCATGCTGACAAGGCCTTCAGCATTCAAGGAGCTCCCAGTGACTCGGGTCCTCTTCGCATTGCAAAGACACCATCACCTCCAGAGGAGCCTTCTCCCCTGCCCAGCCCCACGGCTAGTCCCAACCACACATTAGCACCTGCATCTCCTGCCCCAGTGCGACCCAGATCACCTTCACAGACAAGGAAAGGGCCTCCTGTCCCACCTCTGCCTAAAGTCACCCCAACAAAGGAACTGAAACAGGAGAACATCATCAATTTCTTTGAGGACAACTTTGTACCAGAAATCAATGTGACAACACCTTCCCAGAACGAAGTCTTGGAGGTGAAGAAGGAAGAGACTTTGCTGGATTTGGACTTTGACCCTTTCAAGCCCGATGTGGCTCCGGCAGGTTCTGCTGCAGCGACCCACTCTCCCATGTCTCAGACATTGCCCTGGGACTTATGGACGACAAGCACTGATTTGGTACAACCAACTGACTCTTCAAAAAGTCTTTCTATGTGTAACCTCATCATGGAGGAAACCCCTGACAGTGGTTTGGCTGAAGAGATTCAAAGATATGAAACTGACATAGGTGCATTCACTTGGGGGCCTCATGCTAGGACAGACAGTGTCAGCCAGGAGATGACCTCAAGTGGGTCCCAAGAAGACATGCTCTGTCTCTCTGAAGCAGAGCAAGACATGAGATTATCCACTGCAATGCTTTCTTCTGCTGACTGTTCTACTGTAGCTGGTCAGGATGAGGATGCTCCTCCAGCTAGAAATGAGCAGCTGTCCTCAGAGCCTGTTCCTGGGGCTGAAGTTGCTATTACTACGTACATGGAGATGGACCAGCCATATGCATTACTTGACTCAGAGCTACCAGCCGTCGGAAAAGCTGACCTGCTCAAAGAAGGTCATGAAGAAGCTAAAATATCAGATGGTGAAATAAAACAGACACAGAAGTTAGAAGATCCTATGTGGGTATGTGTGGAGACATACCAAAGGGCTTCTGGGGGTTCATTTAATGATTTCACCCAGGCCCAGGACACTTCATTATTCACCATGCAGACAGATCAGAATATGGTAGGTGGCTTGAAGTGTGATGTGCTGTGGGAAGACTTCCATCAAAAGCTAGTGGATGGCTCCTTGCTGACACTGGACACCTACCTGGGCCAGTTTCCTGACATAAAGAATCGCATCGCTAAGCGCAGCAGGAAGCTTGTGGATTATGATAGTGCTCGCCATCACCTGGAGGCTCTGCAGAGTTCCAAACGGAAAGATGAGAGTCGGATCTCTAAGGCAGAAGAGGAGTTTCAGAAAGCACAGAAAGTGTTTGAAGAGTTCAATGTTGACTTACAAGAAGAGTTGCCGTCATTGTGGTCAAGTCGAGTTGGCTTTTACGTCAATACTTTCAAAAATGTCTCCAGCCTTGAGGCCAAGTTTCATAAGGAAATCGCAGTGCTTTGCCACAAGCTCTATGAAGTGATGACGAAACTCGGTGATCAGCATGCTGACAAGGCCTTCAGCATTCAAGGAGCTCCCAGTGACTCGGGTCCTCTTCGCATTGCAAAGACACCATCACCTCCAGAGGAGCCTTCTCCCCTGCCCAGCCCCACGGCTAGTCCCAACCACACATTAGCACCTGCATCTCCTGCCCCAGTGCGACCCAGATCACCTTCACAGACAAGGAAAGGGCCTCCTGTCCCACCTCTGCCTAAAGTCACCCCAACAAAGGAACTGAAACAGGAGAACATCATCAATTTCTTTGAGGACAACTTTGTACCAGAAATCAATGTGACAACACCTTCCCAGAACGAAGTCTTGGAGGTGAAGAAGGAAGAGACTTTGCTGGATTTGGACTTTGACCCTTTCAAGCCCGATGTGGCTCCGGCAGGTTCTGCTGCAGCGACCCACTCTCCCATGTCTCAGACATTGCCCTGGGACTTATGGACGACAAGCACTGATTTGGTACAACCAACTGACTCTTCAAAAAGTCTTTCTATGTGTAACCTCATCATGGAGGAAACCCCTGACAGTGGTTTGGCTGAAGAGATTCAAAGATATGAAACTGACATAGGTGCATTCACTTGGGGGCCTCATGCTAGGACAGACAGTGTCAGCCAGGAGATGACCTCAAGTGGGTCCCAAGAAGACATGCTCTGTCTCTCTGAAGCAGAGCAAGACATGAGATTATCCACTGCAATGCTTTCTTCTGCTGACTGTTCTACTGTAGCTGGTCAGGATGAGGATGCTCCTCCAGCTAGAAATGAGCAGCTGTCCTCAGAGCCTGTTCCTGGGGCTGAAGTTGCTATTACTACGTACATGGAGATGGACCAGCCATATGCATTACTTGACTCAGAGCTACCAGCCGTCGGAAAAGCTGACCTGCTCAAAGAAGGTCATGAAGAAGCTAAAATATCAGATGGTGAAATAAAACAGACACAGAAGTTAGAAGATCCTATGTGGGTATGTGTGGAGACATACCAAAGGGCTTCTGGGGGTTCATTTAATGATTTCACCCAGGCCCAGGACACTTCATTATTCACCATGCAGACAGATCAGAATATGGTAGGTGGCTTG
Peptide sequence:
MTKLGDQHADKAFSIQGAPSDSGPLRIAKTPSPPEEPSPLPSPTASPNHTLAPASPAPVRPRSPSQTRKGPPVPPLPKVTPTKELKQENIINFFEDNFVPEINVTTPSQNEVLEVKKEETLLDLDFDPFKPDVAPAGSAAATHSPMSQTLPWDLWTTSTDLVQPTDSSKSLSMCNLIMEETPDSGLAEEIQRYETDIGAFTWGPHARTDSVSQEMTSSGSQEDMLCLSEAEQDMRLSTAMLSSADCSTVAGQDEDAPPARNEQLSSEPVPGAEVAITTYMEMDQPYALLDSELPAVGKADLLKEGHEEAKISDGEIKQTQKLEDPMWVCVETYQRASGGSFNDFTQAQDTSLFTMQTDQNMVGGLKCDVLWEDFHQKLVDGSLLTLDTYLGQFPDIKNRIAKRSRKLVDYDSARHHLEALQSSKRKDESRISKAEEEFQKAQKVFEEFNVDLQEELPSLWSSRVGFYVNTFKNVSSLEAKFHKEIAVLCHKLYEVMTKLGDQHADKAFSIQGAPSDSGPLRIAKTPSPPEEPSPLPSPTASPNHTLAPASPAPVRPRSPSQTRKGPPVPPLPKVTPTKELKQENIINFFEDNFVPEINVTTPSQNEVLEVKKEETLLDLDFDPFKPDVAPAGSAAATHSPMSQTLPWDLWTTSTDLVQPTDSSKSLSMCNLIMEETPDSGLAEEIQRYETDIGAFTWGPHARTDSVSQEMTSSGSQEDMLCLSEAEQDMRLSTAMLSSADCSTVAGQDEDAPPARNEQLSSEPVPGAEVAITTYMEMDQPYALLDSELPAVGKADLLKEGHEEAKISDGEIKQTQKLEDPMWVCVETYQRASGGSFNDFTQAQDTSLFTMQTDQNMVGGL
IRESfinder result
IRESfinder score
0.57052605
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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