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mmu_circRad50_1182
Basic information of circular RNA
PanCircBase ID:
mmu_circRad50_1182
mm39_Chr. Position ID:
chr11|53558848|53571049|-
Gene name:
Rad50
Transcript:
ENSMUST00000020649.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
21,20,19,18,17,16,15,14
Exon/intron offsets:
0,1608,6676,6881,7880,10843,11368,12011
Genomic length:
12201
Exon/intron sizes in nt:
22,51,28,11,49,31,11,10,00,00,000
Flanking exon/introns:
chr11:53546445-53558848|chr11:53571049-53574028
Splice length:
1182
Other database IDs:
circBase: hsa_circ_0127928, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_169502
Human Ortholog IDs:
Mature spliced Sequence:
GCAAAGCATAATTGATTTGAAGGAAAAGGAAATACCAGAATTAAGAAACCGACTACAGAGTGTCAATAGAGACATACAGCGCCTAAAGAATGACATAGAAGAGCAGGAAACACTCTTGGGTACAATAATGCCTGAAGAAGAAAGTGCTAAAGTGTGCCTGACAGATGTTACAATCATGGAGAGGTTCCAGATGGAGCTGAAAGATGTTGAAAGGAAAATTGCACAGCAGGCAGCTAAGCTGCAGGGAGTAGACTTGGACCGGACTGTCCAGCAGGTTAACCAGGAAAAGCAGGAAAAGCAGCACAGGCTGGATACAGTTACCAGTAAGATTGAATTGAACCGTAAGCTTATACAGGACCAGCAGGAACAAATCCAACACCTGAAAAGTAAAACAAATGAGCTGAAGTCAGAGAAGCTGCAGATAGCCACCAATTTGCAACGGCGCCAGCAAATGGAGGAGCAGAGTGTGGAATTATCCACTGAAGTCCAGTCTTTAAACAGAGAAATAAAGGATGCTAAAGAACAAATAAGCCCTTTGGAGACAGCATTGGAAAAGTTGCAGCAGGAAAAAGAAGAATTAATCCACAGAAAACATACAAGTAACAAAATGGCTCAGGATAAAATTAATGATATCAAAGAGAAAGTTAAAAATATTCATGGTTACATGAAAGACATAGAGAATTATATTCAAGATGGAAAAGATGACTACAAGAAGCAAAAAGAAACTGAACTTAATGGAGTTGCTGTTCAACTAAATGAATGTGAGAAACACAGAGAAAAGATAAATAAAGACATGGGAACCATGAGGCAAGACATCGACACACAGAAGATACAGGAAAGGTGGCTACAGGATAACCTTACACTAAGAAAAAGGAGAGATGAACTAAAAGAAGTGGAAGAAGAACGAAAACAACACTTGAAGGAGATGGGACAAATGCAAGTTTTACAAATGAAAAATGAGCATCAGAAGTTGGAAGAGAACATAGACACTATAAAGAGAAATCACAGTTTGGCATTGGGGCGTCAGAAAGGCTATGAAGACGAAATTCTTCACTTTAAAAAGGAGCTCCGAGAACCTCAGTTCCGGGATGCCGAGGAAAAGTACAGAGAAATGATGATCGTCATGAGGACCACAGAGCTGGTGAACAAGGACCTCGACATCTACTACAAGACTCTTGACCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACCACAGAGCTGGTGAACA
59.89
TGTCATTCTTTAGGCGCTGT
57.53
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATGAGGACCACAGAGCTGG
60.11
TGTCATTCTTTAGGCGCTGT
57.53
155
PCR template sequence:
TCCGGGATGCCGAGGAAAAGTACAGAGAAATGATGATCGTCATGAGGACCACAGAGCTGGTGAACAAGGACCTCGACATCTACTACAAGACTCTTGACCAGCAAAGCATAATTGATTTGAAGGAAAAGGAAATACCAGAATTAAGAAACCGACTACAGAGTGTCAATAGAGACATACAGCGCCTAAAGAATGACATAGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-297a-5p(2), mmu-miR-181b-5p(1), mmu-miR-136-5p(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
AGACTCTTGACCAGCAAAGCATAATT
siRNA sets
AATTATGCTTTGCTGGTCA, ATTATGCTTTGCTGGTCAA, TTATGCTTTGCTGGTCAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAD50_1182_ORF_1
1.1776
0.268906054
0.999999262
2235
ORF sequence:
ATGCCTGAAGAAGAAAGTGCTAAAGTGTGCCTGACAGATGTTACAATCATGGAGAGGTTCCAGATGGAGCTGAAAGATGTTGAAAGGAAAATTGCACAGCAGGCAGCTAAGCTGCAGGGAGTAGACTTGGACCGGACTGTCCAGCAGGTTAACCAGGAAAAGCAGGAAAAGCAGCACAGGCTGGATACAGTTACCAGTAAGATTGAATTGAACCGTAAGCTTATACAGGACCAGCAGGAACAAATCCAACACCTGAAAAGTAAAACAAATGAGCTGAAGTCAGAGAAGCTGCAGATAGCCACCAATTTGCAACGGCGCCAGCAAATGGAGGAGCAGAGTGTGGAATTATCCACTGAAGTCCAGTCTTTAAACAGAGAAATAAAGGATGCTAAAGAACAAATAAGCCCTTTGGAGACAGCATTGGAAAAGTTGCAGCAGGAAAAAGAAGAATTAATCCACAGAAAACATACAAGTAACAAAATGGCTCAGGATAAAATTAATGATATCAAAGAGAAAGTTAAAAATATTCATGGTTACATGAAAGACATAGAGAATTATATTCAAGATGGAAAAGATGACTACAAGAAGCAAAAAGAAACTGAACTTAATGGAGTTGCTGTTCAACTAAATGAATGTGAGAAACACAGAGAAAAGATAAATAAAGACATGGGAACCATGAGGCAAGACATCGACACACAGAAGATACAGGAAAGGTGGCTACAGGATAACCTTACACTAAGAAAAAGGAGAGATGAACTAAAAGAAGTGGAAGAAGAACGAAAACAACACTTGAAGGAGATGGGACAAATGCAAGTTTTACAAATGAAAAATGAGCATCAGAAGTTGGAAGAGAACATAGACACTATAAAGAGAAATCACAGTTTGGCATTGGGGCGTCAGAAAGGCTATGAAGACGAAATTCTTCACTTTAAAAAGGAGCTCCGAGAACCTCAGTTCCGGGATGCCGAGGAAAAGTACAGAGAAATGATGATCGTCATGAGGACCACAGAGCTGGTGAACAAGGACCTCGACATCTACTACAAGACTCTTGACCAGCAAAGCATAATTGATTTGAAGGAAAAGGAAATACCAGAATTAAGAAACCGACTACAGAGTGTCAATAGAGACATACAGCGCCTAAAGAATGACATAGAAGAGCAGGAAACACTCTTGGGTACAATAATGCCTGAAGAAGAAAGTGCTAAAGTGTGCCTGACAGATGTTACAATCATGGAGAGGTTCCAGATGGAGCTGAAAGATGTTGAAAGGAAAATTGCACAGCAGGCAGCTAAGCTGCAGGGAGTAGACTTGGACCGGACTGTCCAGCAGGTTAACCAGGAAAAGCAGGAAAAGCAGCACAGGCTGGATACAGTTACCAGTAAGATTGAATTGAACCGTAAGCTTATACAGGACCAGCAGGAACAAATCCAACACCTGAAAAGTAAAACAAATGAGCTGAAGTCAGAGAAGCTGCAGATAGCCACCAATTTGCAACGGCGCCAGCAAATGGAGGAGCAGAGTGTGGAATTATCCACTGAAGTCCAGTCTTTAAACAGAGAAATAAAGGATGCTAAAGAACAAATAAGCCCTTTGGAGACAGCATTGGAAAAGTTGCAGCAGGAAAAAGAAGAATTAATCCACAGAAAACATACAAGTAACAAAATGGCTCAGGATAAAATTAATGATATCAAAGAGAAAGTTAAAAATATTCATGGTTACATGAAAGACATAGAGAATTATATTCAAGATGGAAAAGATGACTACAAGAAGCAAAAAGAAACTGAACTTAATGGAGTTGCTGTTCAACTAAATGAATGTGAGAAACACAGAGAAAAGATAAATAAAGACATGGGAACCATGAGGCAAGACATCGACACACAGAAGATACAGGAAAGGTGGCTACAGGATAACCTTACACTAAGAAAAAGGAGAGATGAACTAAAAGAAGTGGAAGAAGAACGAAAACAACACTTGAAGGAGATGGGACAAATGCAAGTTTTACAAATGAAAAATGAGCATCAGAAGTTGGAAGAGAACATAGACACTATAAAGAGAAATCACAGTTTGGCATTGGGGCGTCAGAAAGGCTATGAAGACGAAATTCTTCACTTTAAAAAGGAGCTCCGAGAACCTCAGTTCCGGGATGCCGAGGAAAAGTACAGAGAAATGATGATCGTCATGAGGACCACAGAGCTGGTGAACAAGGACCTCGACATCTACTACAAGACTCTTGAC
Peptide sequence:
MPEEESAKVCLTDVTIMERFQMELKDVERKIAQQAAKLQGVDLDRTVQQVNQEKQEKQHRLDTVTSKIELNRKLIQDQQEQIQHLKSKTNELKSEKLQIATNLQRRQQMEEQSVELSTEVQSLNREIKDAKEQISPLETALEKLQQEKEELIHRKHTSNKMAQDKINDIKEKVKNIHGYMKDIENYIQDGKDDYKKQKETELNGVAVQLNECEKHREKINKDMGTMRQDIDTQKIQERWLQDNLTLRKRRDELKEVEEERKQHLKEMGQMQVLQMKNEHQKLEENIDTIKRNHSLALGRQKGYEDEILHFKKELREPQFRDAEEKYREMMIVMRTTELVNKDLDIYYKTLDQQSIIDLKEKEIPELRNRLQSVNRDIQRLKNDIEEQETLLGTIMPEEESAKVCLTDVTIMERFQMELKDVERKIAQQAAKLQGVDLDRTVQQVNQEKQEKQHRLDTVTSKIELNRKLIQDQQEQIQHLKSKTNELKSEKLQIATNLQRRQQMEEQSVELSTEVQSLNREIKDAKEQISPLETALEKLQQEKEELIHRKHTSNKMAQDKINDIKEKVKNIHGYMKDIENYIQDGKDDYKKQKETELNGVAVQLNECEKHREKINKDMGTMRQDIDTQKIQERWLQDNLTLRKRRDELKEVEEERKQHLKEMGQMQVLQMKNEHQKLEENIDTIKRNHSLALGRQKGYEDEILHFKKELREPQFRDAEEKYREMMIVMRTTELVNKDLDIYYKTLD
IRESfinder result
IRESfinder score
0.424891263
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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