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mmu_circAmph_929
Basic information of circular RNA
PanCircBase ID:
mmu_circAmph_929
mm39_Chr. Position ID:
chr13|19268374|19297389|+
Gene name:
Amph
Transcript:
ENSMUST00000239207.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
4,5,6,7,8,9,10,11,12
Exon/intron offsets:
0,2318,10548,11802,15688,16367,18667,20026,28898
Genomic length:
29015
Exon/intron sizes in nt:
9,59,61,08,86,76,83,13,00,00,000
Flanking exon/introns:
chr13:19261555-19268374|chr13:19297389-19300406
Splice length:
929
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTATGCAGGAGGCCTCAATGAAGCTCACTGAATCTCTACATGAAGTCTACGAGCCAGACTGGTATGGACGGGAAGATGTAAAGATGGTTGGTGAGAAGTGTGATGTGCTGTGGGAAGACTTCCATCAAAAGCTAGTGGATGGCTCCTTGCTGACACTGGACACCTACCTGGGCCAGTTTCCTGACATAAAGAATCGCATCGCTAAGCGCAGCAGGAAGCTTGTGGATTATGATAGTGCTCGCCATCACCTGGAGGCTCTGCAGAGTTCCAAACGGAAAGATGAGAGTCGGATCTCTAAGGCAGAAGAGGAGTTTCAGAAAGCACAGAAAGTGTTTGAAGAGTTCAATGTTGACTTACAAGAAGAGTTGCCGTCATTGTGGTCAAGTCGAGTTGGCTTTTACGTCAATACTTTCAAAAATGTCTCCAGCCTTGAGGCCAAGTTTCATAAGGAAATCGCAGTGCTTTGCCACAAGCTCTATGAAGTGATGACGAAACTCGGTGATCAGCATGCTGACAAGGCCTTCAGCATTCAAGGAGCTCCCAGTGACTCGGGTCCTCTTCGCATTGCAAAGACACCATCACCTCCAGAGGAGCCTTCTCCCCTGCCCAGCCCCACGGCTAGTCCCAACCACACATTAGCACCTGCATCTCCTGCCCCAGTGCGACCCAGATCACCTTCACAGACAAGGAAAGGGCCTCCTGTCCCACCTCTGCCTAAAGTCACCCCAACAAAGGAACTGAAACAGGAGAACATCATCAATTTCTTTGAGGACAACTTTGTACCAGAAATCAATGTGACAACACCTTCCCAGAACGAAGTCTTGGAGGTGAAGAAGGAAGAGACTTTGCTGGATTTGGACTTTGACCCTTTCAAGCCCGATGTGGCTCCGGCAGGTTCTGCTGCAGCGACCCACTCTCCCATGTCTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTTGACCCTTTCAAGCCCG
59.4
CGTCCATACCAGTCTGGCTC
59.9
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTTGACCCTTTCAAGCCCGA
59.82
TCCCGTCCATACCAGTCTGG
60.69
142
PCR template sequence:
GAAGAAGGAAGAGACTTTGCTGGATTTGGACTTTGACCCTTTCAAGCCCGATGTGGCTCCGGCAGGTTCTGCTGCAGCGACCCACTCTCCCATGTCTCAGGTATGCAGGAGGCCTCAATGAAGCTCACTGAATCTCTACATGAAGTCTACGAGCCAGACTGGTATGGACGGGAAGATGTAAAGATGGTTGGTGAGAAGTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-298-5p(1), mmu-miR-222-3p(1), mmu-miR-149-5p(1), mmu-miR-382-5p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCCATGTCTCAGGTATGCAGGAGGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAMPH_929_ORF_1
1.1217
0.304232266
0.99249299
948
ORF sequence:
ATGCAGGAGGCCTCAATGAAGCTCACTGAATCTCTACATGAAGTCTACGAGCCAGACTGGTATGGACGGGAAGATGTAAAGATGGTTGGTGAGAAGTGTGATGTGCTGTGGGAAGACTTCCATCAAAAGCTAGTGGATGGCTCCTTGCTGACACTGGACACCTACCTGGGCCAGTTTCCTGACATAAAGAATCGCATCGCTAAGCGCAGCAGGAAGCTTGTGGATTATGATAGTGCTCGCCATCACCTGGAGGCTCTGCAGAGTTCCAAACGGAAAGATGAGAGTCGGATCTCTAAGGCAGAAGAGGAGTTTCAGAAAGCACAGAAAGTGTTTGAAGAGTTCAATGTTGACTTACAAGAAGAGTTGCCGTCATTGTGGTCAAGTCGAGTTGGCTTTTACGTCAATACTTTCAAAAATGTCTCCAGCCTTGAGGCCAAGTTTCATAAGGAAATCGCAGTGCTTTGCCACAAGCTCTATGAAGTGATGACGAAACTCGGTGATCAGCATGCTGACAAGGCCTTCAGCATTCAAGGAGCTCCCAGTGACTCGGGTCCTCTTCGCATTGCAAAGACACCATCACCTCCAGAGGAGCCTTCTCCCCTGCCCAGCCCCACGGCTAGTCCCAACCACACATTAGCACCTGCATCTCCTGCCCCAGTGCGACCCAGATCACCTTCACAGACAAGGAAAGGGCCTCCTGTCCCACCTCTGCCTAAAGTCACCCCAACAAAGGAACTGAAACAGGAGAACATCATCAATTTCTTTGAGGACAACTTTGTACCAGAAATCAATGTGACAACACCTTCCCAGAACGAAGTCTTGGAGGTGAAGAAGGAAGAGACTTTGCTGGATTTGGACTTTGACCCTTTCAAGCCCGATGTGGCTCCGGCAGGTTCTGCTGCAGCGACCCACTCTCCCATGTCTCAGGTATGCAGGAGGCCTCAATGA
Peptide sequence:
MQEASMKLTESLHEVYEPDWYGREDVKMVGEKCDVLWEDFHQKLVDGSLLTLDTYLGQFPDIKNRIAKRSRKLVDYDSARHHLEALQSSKRKDESRISKAEEEFQKAQKVFEEFNVDLQEELPSLWSSRVGFYVNTFKNVSSLEAKFHKEIAVLCHKLYEVMTKLGDQHADKAFSIQGAPSDSGPLRIAKTPSPPEEPSPLPSPTASPNHTLAPASPAPVRPRSPSQTRKGPPVPPLPKVTPTKELKQENIINFFEDNFVPEINVTTPSQNEVLEVKKEETLLDLDFDPFKPDVAPAGSAAATHSPMSQVCRRPQ
IRESfinder result
IRESfinder score
0.49321857
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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