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mmu_circRad50_1529
Basic information of circular RNA
PanCircBase ID:
mmu_circRad50_1529
mm39_Chr. Position ID:
chr11|53560456|53577134|-
Gene name:
Rad50
Transcript:
ENSMUST00000020649.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
20,19,18,17,16,15,14,13,12,11
Exon/intron offsets:
0,5068,5273,6272,9235,9760,10403,13572,14496,16520
Genomic length:
16678
Exon/intron sizes in nt:
12,81,14,93,11,11,94,10,00,00,00,00,00,000
Flanking exon/introns:
chr11:53559073-53560456|chr11:53577134-53578921
Splice length:
1529
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ACTGACAAAGATGAACAGATCAGAAAAATAAAGTCTAGGCACAGTGATGAACTAACTTCACTGTTGGGGTACTTTCCTAACAAAAAACAGCTTGAAGACTGGCTTCATTCTAAATCCAAAGAAATTAATCAGACCAGGGACAGACTTGCCAAACTGAACAAAGAGCTAGCTTCAGCTGAACAAAATAAAAATCATATAAATAATGAGCTAAAGAAAAAGGAAGAACAGTTGTCCAGTTATGAAGATAAGCTATTTGATGTTTGTGGTAGCCAAGATTTGGAAAGTGATTTGGGCAGACTTAAAGAAGAAATTGAAAAGTCCTCAAAGCAGCGAGCCATGCTGGCAGGAGCCACAGCAGTTTACTCCCAGTTCATTACGCAGCTGACAGATGAAAACCAGTCCTGCTGCCCAGTCTGTCAGAGAGTATTTCAGACAGAGGCTGAGTTACAGGAAGTCATCAGCGACTTGCAGTCCAAGCTGAGGCTTGCTCCAGATAAACTCAAGTCAACAGAATCGGAACTGAAGAAAAAAGAGCGGCGCCGTGATGAAATGCTTGGGCTTGTGCCCGTGAGGCAAAGCATAATTGATTTGAAGGAAAAGGAAATACCAGAATTAAGAAACCGACTACAGAGTGTCAATAGAGACATACAGCGCCTAAAGAATGACATAGAAGAGCAGGAAACACTCTTGGGTACAATAATGCCTGAAGAAGAAAGTGCTAAAGTGTGCCTGACAGATGTTACAATCATGGAGAGGTTCCAGATGGAGCTGAAAGATGTTGAAAGGAAAATTGCACAGCAGGCAGCTAAGCTGCAGGGAGTAGACTTGGACCGGACTGTCCAGCAGGTTAACCAGGAAAAGCAGGAAAAGCAGCACAGGCTGGATACAGTTACCAGTAAGATTGAATTGAACCGTAAGCTTATACAGGACCAGCAGGAACAAATCCAACACCTGAAAAGTAAAACAAATGAGCTGAAGTCAGAGAAGCTGCAGATAGCCACCAATTTGCAACGGCGCCAGCAAATGGAGGAGCAGAGTGTGGAATTATCCACTGAAGTCCAGTCTTTAAACAGAGAAATAAAGGATGCTAAAGAACAAATAAGCCCTTTGGAGACAGCATTGGAAAAGTTGCAGCAGGAAAAAGAAGAATTAATCCACAGAAAACATACAAGTAACAAAATGGCTCAGGATAAAATTAATGATATCAAAGAGAAAGTTAAAAATATTCATGGTTACATGAAAGACATAGAGAATTATATTCAAGATGGAAAAGATGACTACAAGAAGCAAAAAGAAACTGAACTTAATGGAGTTGCTGTTCAACTAAATGAATGTGAGAAACACAGAGAAAAGATAAATAAAGACATGGGAACCATGAGGCAAGACATCGACACACAGAAGATACAGGAAAGGTGGCTACAGGATAACCTTACACTAAGAAAAAGGAGAGATGAACTAAAAGAAGTGGAAGAAGAACGAAAACAACACTTGAAGGAGATGGGACAAATGCAAGTTTTACAAATGAAAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAAGAAGAACGAAAACAACACT
59.3
AGGAAAGTACCCCAACAGTGA
58.59
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGGAAGAAGAACGAAAACAACA
59.3
AGGAAAGTACCCCAACAGTGA
58.59
144
PCR template sequence:
TTACACTAAGAAAAAGGAGAGATGAACTAAAAGAAGTGGAAGAAGAACGAAAACAACACTTGAAGGAGATGGGACAAATGCAAGTTTTACAAATGAAAAAACTGACAAAGATGAACAGATCAGAAAAATAAAGTCTAGGCACAGTGATGAACTAACTTCACTGTTGGGGTACTTTCCTAACAAAAAACAGCTTGAAGACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-297a-5p(2), mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-17-5p(1), mmu-miR-106b-5p(1), mmu-miR-181b-5p(1), mmu-miR-136-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-22-3p(1), mmu-miR-370-3p(1), mmu-miR-27a-5p(1), mmu-miR-3470b(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TACAAATGAAAAAACTGACAAAGATG
siRNA sets
ATCTTTGTCAGTTTTTTCA, CATCTTTGTCAGTTTTTTC, TTTGTCAGTTTTTTCATTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAD50_1529_ORF_1
1.1258
0.212382712
0.998468767
1224
ORF sequence:
ATGCTGGCAGGAGCCACAGCAGTTTACTCCCAGTTCATTACGCAGCTGACAGATGAAAACCAGTCCTGCTGCCCAGTCTGTCAGAGAGTATTTCAGACAGAGGCTGAGTTACAGGAAGTCATCAGCGACTTGCAGTCCAAGCTGAGGCTTGCTCCAGATAAACTCAAGTCAACAGAATCGGAACTGAAGAAAAAAGAGCGGCGCCGTGATGAAATGCTTGGGCTTGTGCCCGTGAGGCAAAGCATAATTGATTTGAAGGAAAAGGAAATACCAGAATTAAGAAACCGACTACAGAGTGTCAATAGAGACATACAGCGCCTAAAGAATGACATAGAAGAGCAGGAAACACTCTTGGGTACAATAATGCCTGAAGAAGAAAGTGCTAAAGTGTGCCTGACAGATGTTACAATCATGGAGAGGTTCCAGATGGAGCTGAAAGATGTTGAAAGGAAAATTGCACAGCAGGCAGCTAAGCTGCAGGGAGTAGACTTGGACCGGACTGTCCAGCAGGTTAACCAGGAAAAGCAGGAAAAGCAGCACAGGCTGGATACAGTTACCAGTAAGATTGAATTGAACCGTAAGCTTATACAGGACCAGCAGGAACAAATCCAACACCTGAAAAGTAAAACAAATGAGCTGAAGTCAGAGAAGCTGCAGATAGCCACCAATTTGCAACGGCGCCAGCAAATGGAGGAGCAGAGTGTGGAATTATCCACTGAAGTCCAGTCTTTAAACAGAGAAATAAAGGATGCTAAAGAACAAATAAGCCCTTTGGAGACAGCATTGGAAAAGTTGCAGCAGGAAAAAGAAGAATTAATCCACAGAAAACATACAAGTAACAAAATGGCTCAGGATAAAATTAATGATATCAAAGAGAAAGTTAAAAATATTCATGGTTACATGAAAGACATAGAGAATTATATTCAAGATGGAAAAGATGACTACAAGAAGCAAAAAGAAACTGAACTTAATGGAGTTGCTGTTCAACTAAATGAATGTGAGAAACACAGAGAAAAGATAAATAAAGACATGGGAACCATGAGGCAAGACATCGACACACAGAAGATACAGGAAAGGTGGCTACAGGATAACCTTACACTAAGAAAAAGGAGAGATGAACTAAAAGAAGTGGAAGAAGAACGAAAACAACACTTGAAGGAGATGGGACAAATGCAAGTTTTACAAATGAAAAAACTGACAAAGATGAACAGATCAGAAAAATAA
Peptide sequence:
MLAGATAVYSQFITQLTDENQSCCPVCQRVFQTEAELQEVISDLQSKLRLAPDKLKSTESELKKKERRRDEMLGLVPVRQSIIDLKEKEIPELRNRLQSVNRDIQRLKNDIEEQETLLGTIMPEEESAKVCLTDVTIMERFQMELKDVERKIAQQAAKLQGVDLDRTVQQVNQEKQEKQHRLDTVTSKIELNRKLIQDQQEQIQHLKSKTNELKSEKLQIATNLQRRQQMEEQSVELSTEVQSLNREIKDAKEQISPLETALEKLQQEKEELIHRKHTSNKMAQDKINDIKEKVKNIHGYMKDIENYIQDGKDDYKKQKETELNGVAVQLNECEKHREKINKDMGTMRQDIDTQKIQERWLQDNLTLRKRRDELKEVEEERKQHLKEMGQMQVLQMKKLTKMNRSEK
IRESfinder result
IRESfinder score
0.49240219
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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