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mmu_circSmc6_1662
Basic information of circular RNA
PanCircBase ID:
mmu_circSmc6_1662
mm39_Chr. Position ID:
chr12|11329605|11345084|+
Gene name:
Smc6
Transcript:
ENSMUST00000020931.6
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:
0,736,2755,3466,5493,5706,9523,10032,10287,11108,11921,14880,15318
Genomic length:
15479
Exon/intron sizes in nt:
137,62,81,102,120,99,147,89,165,179,205,115,161
Flanking exon/introns:
chr12:11326366-11329605|chr12:11345084-11347150
Splice length:
1662
Other database IDs:
CIRCpedia: MMU_CIRCpedia_222001, circAtlas: mmu-Smc6_0017
Human Ortholog IDs:
Mature spliced Sequence:
CTCAGCAGATATCTCAATAACATTAAGGAACAGAGGAGATGATGCCTTCAGAGCAAATGTGTATGGTGACTCTATAGTTGTGCAGCAACACATTAGCGTGGATGGAAGTCGATCTTACAAACTAAAAAGTGAAAAAGGCACCGTGGTTTCTACTAGGAAAGAAGAGCTGATTGCAATTCTTGACCATTTTAACATCCAGGTGGATAATCCGGTTTCTGTTTTAACACAAGAGATGAGCAAGCAGTTCTTACAGTCCAAAAATGAGGGAGACAAATACAAATTCTTCATGAAAGCAACCCAGCTCGAACAGATGAAGGAAGATTATTCATATATTATGGAAACAAAAGAAAGAACAAAGGAACAAATAAATCAGGGAGAAGAGCGACTTACTGAACTAAAACGCCAGTGTTTGGAGAAAGAGGAACGTTTTCAAAATATTGCTGGTTTAAGTACAATGAAGACTAATTTAGAGTACTTGAAACATGAAATGGCTTGGGCAGTGGTCAATGAAATTGAAAAACAATTGAATGCTATTCGAGACAATATCAAAATTGGAGAAGAACGTGCTGCAAAACTTGACAGGAAAATGGAAGAGCAGCAGGTCAGACTTAATGATGCAGAAAAAAAGTACAAAGATATACAAGATAAACTAGAAAAAATTAGTGAAGAGACAAATGCACGAGCACCAGAATGTATGGCATTGAAAACAGATGTCATTGCAAGGACAAGAGCCTTTAATGACGCTGAGGTTTTATATAACCGTTCCCTAAATGAATATAAAGCATTAAAAAAAGATGGTGAACAGCTTTGTAAAAGAATTGAAGAACTGAAGAAAAGTACTGATCAGTCATTAGAACCAGAGCGATTGGAAAGGCAAAAAAGGATCTGCTGGTTAAAAGAGAAAGTCAAGGCCTTACAGGATCAGGAACATACAGTCAATCAGGAGGCTGAGCAGTTTGAGCAAGCCATAGAAAAGGACAAGCAAGAGCATGGCCGAGTTAGGAAAGAAGATATAGAAGTGAGACATGCACTCAACTATAATCAGAGACAATTGAAAGAACTGAAAGATAGTAAAACTGATCGACTAAAAAGATTTGGTCCTCATGTTCCAGCTCTTCTGGAAGCAATAGATGATGCTTACAGACGGAGACAATTTACCCATAAACCTATCGGCCCTTTAGGTGCTTGCATTCATCTACGGGACCCTGAACTTGCTTTGGCCATTGAATCTTGCTTAAAAGGACTTCTGCAAGCCTATTGTTGCCATAATCATGCTGATGAGAGAGTACTTCAGTCTTTGATGAAAAAATTTTATCCACCAGGGACCTCTCGGCCACAGATAATTGTGTCTGAGTTTCGGGATGAGGTATATGATGTGAGACTCAGAGCTGCTTACCATCCAGAGTTTCCAACTGTTCTGACAGCTTTAGAAATAGACAATGCTGTTGTGGCAAACAGCCTGATTGACATGCGGAGCATAGAGACAGTGCTGCTGATCAAAAATAATTCTGTGGCTCGTGCAGTCATGCAATCCCAAAAGCCACCCAAAAATTGTAGAGAAGCTTTTACTGCTGATGGTGATCAAGTGTTTGCAGGACGTTATTATTCATCTGAAAGTACAAGACCCAAGTTTCTAAGCAGAGATGTGGATTCTGAAATAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCAAGTGTTTGCAGGACGTT
58.25
ACGCTAATGTGTTGCTGCAC
59.76
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTGATCAAGTGTTTGCAGG
59.04
TGCTCTGAAGGCATCATCTCC
59.86
142
PCR template sequence:
CTTTTACTGCTGATGGTGATCAAGTGTTTGCAGGACGTTATTATTCATCTGAAAGTACAAGACCCAAGTTTCTAAGCAGAGATGTGGATTCTGAAATAAGCTCAGCAGATATCTCAATAACATTAAGGAACAGAGGAGATGATGCCTTCAGAGCAAATGTGTATGGTGACTCTATAGTTGTGCAGCAACACATTAGCGTG
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-137-3p(1), mmu-miR-155-5p(1), mmu-miR-16-5p(1), mmu-miR-26a-5p(1), mmu-miR-322-5p(1), mmu-miR-130a-3p(1), mmu-miR-26b-5p(1), mmu-miR-676-3p(1), mmu-miR-324-3p(1), mmu-miR-325-3p(1), mmu-miR-1198-5p(1), mmu-miR-670-5p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTCTGAAATAAGCTCAGCAGATATC
siRNA sets
TATCTGCTGAGCTTATTTC, ATCTGCTGAGCTTATTTCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMC6_1662_ORF_1
1.106
0.096080444
0.999999996
3090
ORF sequence:
ATGAGCAAGCAGTTCTTACAGTCCAAAAATGAGGGAGACAAATACAAATTCTTCATGAAAGCAACCCAGCTCGAACAGATGAAGGAAGATTATTCATATATTATGGAAACAAAAGAAAGAACAAAGGAACAAATAAATCAGGGAGAAGAGCGACTTACTGAACTAAAACGCCAGTGTTTGGAGAAAGAGGAACGTTTTCAAAATATTGCTGGTTTAAGTACAATGAAGACTAATTTAGAGTACTTGAAACATGAAATGGCTTGGGCAGTGGTCAATGAAATTGAAAAACAATTGAATGCTATTCGAGACAATATCAAAATTGGAGAAGAACGTGCTGCAAAACTTGACAGGAAAATGGAAGAGCAGCAGGTCAGACTTAATGATGCAGAAAAAAAGTACAAAGATATACAAGATAAACTAGAAAAAATTAGTGAAGAGACAAATGCACGAGCACCAGAATGTATGGCATTGAAAACAGATGTCATTGCAAGGACAAGAGCCTTTAATGACGCTGAGGTTTTATATAACCGTTCCCTAAATGAATATAAAGCATTAAAAAAAGATGGTGAACAGCTTTGTAAAAGAATTGAAGAACTGAAGAAAAGTACTGATCAGTCATTAGAACCAGAGCGATTGGAAAGGCAAAAAAGGATCTGCTGGTTAAAAGAGAAAGTCAAGGCCTTACAGGATCAGGAACATACAGTCAATCAGGAGGCTGAGCAGTTTGAGCAAGCCATAGAAAAGGACAAGCAAGAGCATGGCCGAGTTAGGAAAGAAGATATAGAAGTGAGACATGCACTCAACTATAATCAGAGACAATTGAAAGAACTGAAAGATAGTAAAACTGATCGACTAAAAAGATTTGGTCCTCATGTTCCAGCTCTTCTGGAAGCAATAGATGATGCTTACAGACGGAGACAATTTACCCATAAACCTATCGGCCCTTTAGGTGCTTGCATTCATCTACGGGACCCTGAACTTGCTTTGGCCATTGAATCTTGCTTAAAAGGACTTCTGCAAGCCTATTGTTGCCATAATCATGCTGATGAGAGAGTACTTCAGTCTTTGATGAAAAAATTTTATCCACCAGGGACCTCTCGGCCACAGATAATTGTGTCTGAGTTTCGGGATGAGGTATATGATGTGAGACTCAGAGCTGCTTACCATCCAGAGTTTCCAACTGTTCTGACAGCTTTAGAAATAGACAATGCTGTTGTGGCAAACAGCCTGATTGACATGCGGAGCATAGAGACAGTGCTGCTGATCAAAAATAATTCTGTGGCTCGTGCAGTCATGCAATCCCAAAAGCCACCCAAAAATTGTAGAGAAGCTTTTACTGCTGATGGTGATCAAGTGTTTGCAGGACGTTATTATTCATCTGAAAGTACAAGACCCAAGTTTCTAAGCAGAGATGTGGATTCTGAAATAAGCTCAGCAGATATCTCAATAACATTAAGGAACAGAGGAGATGATGCCTTCAGAGCAAATGTGTATGGTGACTCTATAGTTGTGCAGCAACACATTAGCGTGGATGGAAGTCGATCTTACAAACTAAAAAGTGAAAAAGGCACCGTGGTTTCTACTAGGAAAGAAGAGCTGATTGCAATTCTTGACCATTTTAACATCCAGGTGGATAATCCGGTTTCTGTTTTAACACAAGAGATGAGCAAGCAGTTCTTACAGTCCAAAAATGAGGGAGACAAATACAAATTCTTCATGAAAGCAACCCAGCTCGAACAGATGAAGGAAGATTATTCATATATTATGGAAACAAAAGAAAGAACAAAGGAACAAATAAATCAGGGAGAAGAGCGACTTACTGAACTAAAACGCCAGTGTTTGGAGAAAGAGGAACGTTTTCAAAATATTGCTGGTTTAAGTACAATGAAGACTAATTTAGAGTACTTGAAACATGAAATGGCTTGGGCAGTGGTCAATGAAATTGAAAAACAATTGAATGCTATTCGAGACAATATCAAAATTGGAGAAGAACGTGCTGCAAAACTTGACAGGAAAATGGAAGAGCAGCAGGTCAGACTTAATGATGCAGAAAAAAAGTACAAAGATATACAAGATAAACTAGAAAAAATTAGTGAAGAGACAAATGCACGAGCACCAGAATGTATGGCATTGAAAACAGATGTCATTGCAAGGACAAGAGCCTTTAATGACGCTGAGGTTTTATATAACCGTTCCCTAAATGAATATAAAGCATTAAAAAAAGATGGTGAACAGCTTTGTAAAAGAATTGAAGAACTGAAGAAAAGTACTGATCAGTCATTAGAACCAGAGCGATTGGAAAGGCAAAAAAGGATCTGCTGGTTAAAAGAGAAAGTCAAGGCCTTACAGGATCAGGAACATACAGTCAATCAGGAGGCTGAGCAGTTTGAGCAAGCCATAGAAAAGGACAAGCAAGAGCATGGCCGAGTTAGGAAAGAAGATATAGAAGTGAGACATGCACTCAACTATAATCAGAGACAATTGAAAGAACTGAAAGATAGTAAAACTGATCGACTAAAAAGATTTGGTCCTCATGTTCCAGCTCTTCTGGAAGCAATAGATGATGCTTACAGACGGAGACAATTTACCCATAAACCTATCGGCCCTTTAGGTGCTTGCATTCATCTACGGGACCCTGAACTTGCTTTGGCCATTGAATCTTGCTTAAAAGGACTTCTGCAAGCCTATTGTTGCCATAATCATGCTGATGAGAGAGTACTTCAGTCTTTGATGAAAAAATTTTATCCACCAGGGACCTCTCGGCCACAGATAATTGTGTCTGAGTTTCGGGATGAGGTATATGATGTGAGACTCAGAGCTGCTTACCATCCAGAGTTTCCAACTGTTCTGACAGCTTTAGAAATAGACAATGCTGTTGTGGCAAACAGCCTGATTGACATGCGGAGCATAGAGACAGTGCTGCTGATCAAAAATAATTCTGTGGCTCGTGCAGTCATGCAATCCCAAAAGCCACCCAAAAATTGTAGAGAAGCTTTTACTGCTGATGGTGATCAAGTGTTTGCAGGACGTTATTATTCATCTGAAAGTACAAGACCCAAGTTTCTAAGCAGAGATGTGGATTCTGAAATA
Peptide sequence:
MSKQFLQSKNEGDKYKFFMKATQLEQMKEDYSYIMETKERTKEQINQGEERLTELKRQCLEKEERFQNIAGLSTMKTNLEYLKHEMAWAVVNEIEKQLNAIRDNIKIGEERAAKLDRKMEEQQVRLNDAEKKYKDIQDKLEKISEETNARAPECMALKTDVIARTRAFNDAEVLYNRSLNEYKALKKDGEQLCKRIEELKKSTDQSLEPERLERQKRICWLKEKVKALQDQEHTVNQEAEQFEQAIEKDKQEHGRVRKEDIEVRHALNYNQRQLKELKDSKTDRLKRFGPHVPALLEAIDDAYRRRQFTHKPIGPLGACIHLRDPELALAIESCLKGLLQAYCCHNHADERVLQSLMKKFYPPGTSRPQIIVSEFRDEVYDVRLRAAYHPEFPTVLTALEIDNAVVANSLIDMRSIETVLLIKNNSVARAVMQSQKPPKNCREAFTADGDQVFAGRYYSSESTRPKFLSRDVDSEISSADISITLRNRGDDAFRANVYGDSIVVQQHISVDGSRSYKLKSEKGTVVSTRKEELIAILDHFNIQVDNPVSVLTQEMSKQFLQSKNEGDKYKFFMKATQLEQMKEDYSYIMETKERTKEQINQGEERLTELKRQCLEKEERFQNIAGLSTMKTNLEYLKHEMAWAVVNEIEKQLNAIRDNIKIGEERAAKLDRKMEEQQVRLNDAEKKYKDIQDKLEKISEETNARAPECMALKTDVIARTRAFNDAEVLYNRSLNEYKALKKDGEQLCKRIEELKKSTDQSLEPERLERQKRICWLKEKVKALQDQEHTVNQEAEQFEQAIEKDKQEHGRVRKEDIEVRHALNYNQRQLKELKDSKTDRLKRFGPHVPALLEAIDDAYRRRQFTHKPIGPLGACIHLRDPELALAIESCLKGLLQAYCCHNHADERVLQSLMKKFYPPGTSRPQIIVSEFRDEVYDVRLRAAYHPEFPTVLTALEIDNAVVANSLIDMRSIETVLLIKNNSVARAVMQSQKPPKNCREAFTADGDQVFAGRYYSSESTRPKFLSRDVDSEI
IRESfinder result
IRESfinder score
0.566149966
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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