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mmu_circUsh2a_2869
Basic information of circular RNA
PanCircBase ID:
mmu_circUsh2a_2869
mm39_Chr. Position ID:
chr1|188485709|188596948|+
Gene name:
Ush2a
Transcript:
ENSMUST00000060479.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
16
Exon/intron indexes:
44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59
Exon/intron offsets:
0,1552,6234,28807,31125,44215,56660,60674,68166,69075,72779,87984,95435,96436,109225,111076
Genomic length:
111239
Exon/intron sizes in nt:
2,10,20,31,13,19,91,69,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr1:188475882-188485709|chr1:188596948-188606793
Splice length:
2869
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CATTTCAAGATCTACAAGGTGATGTGGAATATTACACACTGTTTTGGAGTTCTGGGACCTCAGAGGAATCTCTGAAAATCTTCCCGGATGTAGACTTTCACGTCATTGGCCAGTTATCTCCAAACGTGGAGTACCAGGTTTTCCTCTTGGTTTTCAATGGAGTCCACGCAATCAACAGCACAGTTGTGCATGTGACCATGTGGGAGGAGGAGCCTCAGGGCATGCTTCCCCCAGAGGTTGTCATCATCAACAGTACAGCTGTACGTGTCATCTGGACATCGCCTTCAAACCCAAATGCCGTTGTCACCGAGTCTTCTGTCTATGTAAATAATAAGCTCTACAAGACTGGAACGGATGCGCCCGGGTCGTTTGTTCTGGAAGACCTGTCTCCCTTCACTATCTATGACATTCAGGTGGAAGTCTGTACAAAAGACGCCTGCGTGAAAAGCAATGGAACGCAAGTCAGCACAGCGGAAGATACTCCAAGTGACATTTCAATACCTGTAATCCGAGGTATTACTTCAAGATCCCTTCAAATAGATTGGACAACACCAGCAAATCCAAATGGTATCATTCTTGGGTATGACGTTTTGCGGAAAACATGGCGCCCATGCTCTGAAACCCAGAAGTTAACAGACAAACCGCGTGATGAGCTTTGCAAAGCAGTCAAGTGCCAATACCCTGGAAAAGTCTGTGGGCACACGTGCTACTCTCCAGGAACTAAGGTATGTTGTGACGGACTTCTGTATGACCCTCAGCCTGGATACAGCTGCTGTGAGGACAAATACATCGCACTCTCTCCGAATGCCACTGGGGTTTGCTGTGGAGGGCGAATGTGGGAGGCACAGCCAGACCACCAGTGCTGCTCTGGGCATTACGCTAGAATCCTTCCAGGAGAGATATGCTGCCCCGATGAGAGGCACAACCGGGTGTCCGTGGGCTTTGGTGATGCCTGCTGCGGCACAATGCCTTATGCCACCTCTGGGAGCCAGGTGTGCTGTGCCGGGAGGCTCCAGGACGGCTATAGACAGCAGTGCTGTGGGGGAGAGATGGTGAGCCAAGATTTCCAGTGCTGTGGTGGAGGAGAAGAGGGCATGGTATACAGTTACCTCCCAGGAATGCTGTGTTGTGGGCAGGATTATGTGAATATGTCAGAGACCATATGCTGTTCAGCTTCCAGTGGAGAGTCTAAAGCACATGTTAGAAAGGATGACCCCACACCAGTGAAATGCTGCGGCACTGAACTGAGTCCAGAGAGCCAGCGATGCTGTGATGGGGTTGGATATAATCCTTTGAAATATGTTTGTTCTGATGAGATTTCAGCTGGAATGGCGATGAAGGAAACCAGAGTATGTGCGACTATCTGCCCAGCAACCATGAAAGCCACAGCACACTGTGGGAGGTGTGACTTCAACGCCACCACCCATATCTGCACGGTGATGAGAGGGCCTCTCAATCCCACAGGGAAGAAAGCGGTGGAAGGACTGTGTTCTGCAGCAGAGGAAATAGTTCATTCTGGAGATGTAAACACACACTCTTTCATAGATAGAGACCTCAAGCCAAGCACTGTGTATGAATATAGAATTTCTGCATGGAACAGCTACGGGCGAGGATTCAGCCAATCCGTGAGAGCTAGCACAAGAGAAGATGTGCCTGAAGGAGTCAAGGCCCCTAGATGGGCCAGGACGGGCAAACATGAAGATGTTATTTTCTTACAGTGGGAAGAGCCCATGCAGTCAAATGGTCCTATCATTCACTATATTCTTTTTCGAGACGGAAGGGAGCGCTTTCAGGGAACAGCGCTGAGCTTCACGGACACGCAGGGAATTCAGCCACTCCAGGAATACTCATACCAGCTGAAGGCTTGCACAGCTGCTGGTTGTGCTGTCAGTTGCAAGGTAGTCGCTGCCACCACCCAAAGAAGCCCGGAGAATGTCCCACCACCAAACATCACAGCCCAGAGCTCAGAGACTCTACACCTCAGCTGGAGTGTCCCCGAGAAAATGAAAGATGCCATTAAAGCATACCAGCTCTGGCTGGATGGGAAAGGGCTCATCTACACCGACACAAGTGACAGGAGGCAGCATACGGTTACAGGTCTCCAGCCATACACAAACTACAGCTTCACACTCGCGGTTTGTACATCTGTCGGATGCACTTCCAGTGAGCCCTGTGTAGGTCAGACTCTGCAGGCTGCCCCTCAAGGAGTTTGGGTGACACCGCGACACATTATCATCAATTCTACAACCGTGGAGCTATATTGGAATCCTCCAGAAAGGCCCAACGGCCTCATTTCTCAATATCAGCTGAGGCGTAATGGAAGCTTGCTTCTCGTGGGGGGCAGAGATAATCAGAGTTTCACTGATAGCAACCTGGAGCCCGGCAGCAGGTACATTTACAAGTTGGAAGCGAGAACTGGAGGTGGTAGCAGTTGGAGTGAGGACTACCTTGTCCAGATGCCTCTGTGGACCCCAGAAGACATTCATCCCCCATGTAATGTCACTGTGCTGGGCTCTGATTCCATATTTGTAGCATGGCCAACACCAGGGAACCTGCTTCCCAAAATTCCAGTCGAGTACAGCATCTTACTCAGTGGCGGGAGTGTGACGCTCTTAGTCTTCTCTGTCAGACACCGGCAATCTGCACACCTGAAAAACCTGTCTCCGTTCACACAGTATGAAATACGGATCCAAGCCTGCCAAAATGGGGGCTGTGGAGTCAGCCCTGGGACATACGTCAGAACGCTTGAAGCAGCACCCGTGGGTCTGATGCCCCCTCTTCTGAAGGCTCTGGGGTCATCTTGCATAGAGGTTAAGTGGATGCCACCAACGAGACCCAATGGAATCATCACTAGCTATGTCGTTCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCTGGGGTCATCTTGCAT
60.11
TCTGAGGTCCCAGAACTCCA
59.51
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTTCTGAAGGCTCTGGGGT
60.18
TCTGAGGTCCCAGAACTCCA
59.51
157
PCR template sequence:
TGCCCCCTCTTCTGAAGGCTCTGGGGTCATCTTGCATAGAGGTTAAGTGGATGCCACCAACGAGACCCAATGGAATCATCACTAGCTATGTCGTTCACAGCATTTCAAGATCTACAAGGTGATGTGGAATATTACACACTGTTTTGGAGTTCTGGGACCTCAGAGGAATCTCTGAAAATCTTCCCGGATGTAGACTTTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
33
Interacting miRNAs (#binding sites)
mmu-miR-673-5p(2), mmu-miR-188-3p(2), mmu-miR-574-5p(2), mmu-miR-15a-5p(1), mmu-miR-103-3p(1), mmu-miR-205-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-216a-5p(1), mmu-miR-196a-5p(1), mmu-miR-203-3p(1), mmu-miR-125b-5p(1), mmu-miR-138-5p(1), mmu-miR-495-3p(1), mmu-miR-214-3p(1), mmu-miR-149-5p(1), mmu-miR-351-5p(1), mmu-miR-125a-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-127-5p(1), mmu-miR-96-5p(1), mmu-miR-218-5p(1), mmu-miR-541-5p(1), mmu-miR-425-5p(1), mmu-miR-107-3p(1), mmu-miR-680(1), mmu-miR-466a-5p(1), mmu-miR-466p-5p(1), mmu-miR-539-5p(1), mmu-miR-669d-5p(1), mmu-miR-490-3p(1), mmu-miR-323-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGTCGTTCACAGCATTTCAAGATCT
siRNA sets
TTGAAATGCTGTGAACGAC, AGATCTTGAAATGCTGTGA, TCTTGAAATGCTGTGAACG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSH2A_2869_ORF_1
0.7231
0.127054885
0.999999972
2898
ORF sequence:
ATGGAATCATCACTAGCTATGTCGTTCACAGCATTTCAAGATCTACAAGGTGATGTGGAATATTACACACTGTTTTGGAGTTCTGGGACCTCAGAGGAATCTCTGAAAATCTTCCCGGATGTAGACTTTCACGTCATTGGCCAGTTATCTCCAAACGTGGAGTACCAGGTTTTCCTCTTGGTTTTCAATGGAGTCCACGCAATCAACAGCACAGTTGTGCATGTGACCATGTGGGAGGAGGAGCCTCAGGGCATGCTTCCCCCAGAGGTTGTCATCATCAACAGTACAGCTGTACGTGTCATCTGGACATCGCCTTCAAACCCAAATGCCGTTGTCACCGAGTCTTCTGTCTATGTAAATAATAAGCTCTACAAGACTGGAACGGATGCGCCCGGGTCGTTTGTTCTGGAAGACCTGTCTCCCTTCACTATCTATGACATTCAGGTGGAAGTCTGTACAAAAGACGCCTGCGTGAAAAGCAATGGAACGCAAGTCAGCACAGCGGAAGATACTCCAAGTGACATTTCAATACCTGTAATCCGAGGTATTACTTCAAGATCCCTTCAAATAGATTGGACAACACCAGCAAATCCAAATGGTATCATTCTTGGGTATGACGTTTTGCGGAAAACATGGCGCCCATGCTCTGAAACCCAGAAGTTAACAGACAAACCGCGTGATGAGCTTTGCAAAGCAGTCAAGTGCCAATACCCTGGAAAAGTCTGTGGGCACACGTGCTACTCTCCAGGAACTAAGGTATGTTGTGACGGACTTCTGTATGACCCTCAGCCTGGATACAGCTGCTGTGAGGACAAATACATCGCACTCTCTCCGAATGCCACTGGGGTTTGCTGTGGAGGGCGAATGTGGGAGGCACAGCCAGACCACCAGTGCTGCTCTGGGCATTACGCTAGAATCCTTCCAGGAGAGATATGCTGCCCCGATGAGAGGCACAACCGGGTGTCCGTGGGCTTTGGTGATGCCTGCTGCGGCACAATGCCTTATGCCACCTCTGGGAGCCAGGTGTGCTGTGCCGGGAGGCTCCAGGACGGCTATAGACAGCAGTGCTGTGGGGGAGAGATGGTGAGCCAAGATTTCCAGTGCTGTGGTGGAGGAGAAGAGGGCATGGTATACAGTTACCTCCCAGGAATGCTGTGTTGTGGGCAGGATTATGTGAATATGTCAGAGACCATATGCTGTTCAGCTTCCAGTGGAGAGTCTAAAGCACATGTTAGAAAGGATGACCCCACACCAGTGAAATGCTGCGGCACTGAACTGAGTCCAGAGAGCCAGCGATGCTGTGATGGGGTTGGATATAATCCTTTGAAATATGTTTGTTCTGATGAGATTTCAGCTGGAATGGCGATGAAGGAAACCAGAGTATGTGCGACTATCTGCCCAGCAACCATGAAAGCCACAGCACACTGTGGGAGGTGTGACTTCAACGCCACCACCCATATCTGCACGGTGATGAGAGGGCCTCTCAATCCCACAGGGAAGAAAGCGGTGGAAGGACTGTGTTCTGCAGCAGAGGAAATAGTTCATTCTGGAGATGTAAACACACACTCTTTCATAGATAGAGACCTCAAGCCAAGCACTGTGTATGAATATAGAATTTCTGCATGGAACAGCTACGGGCGAGGATTCAGCCAATCCGTGAGAGCTAGCACAAGAGAAGATGTGCCTGAAGGAGTCAAGGCCCCTAGATGGGCCAGGACGGGCAAACATGAAGATGTTATTTTCTTACAGTGGGAAGAGCCCATGCAGTCAAATGGTCCTATCATTCACTATATTCTTTTTCGAGACGGAAGGGAGCGCTTTCAGGGAACAGCGCTGAGCTTCACGGACACGCAGGGAATTCAGCCACTCCAGGAATACTCATACCAGCTGAAGGCTTGCACAGCTGCTGGTTGTGCTGTCAGTTGCAAGGTAGTCGCTGCCACCACCCAAAGAAGCCCGGAGAATGTCCCACCACCAAACATCACAGCCCAGAGCTCAGAGACTCTACACCTCAGCTGGAGTGTCCCCGAGAAAATGAAAGATGCCATTAAAGCATACCAGCTCTGGCTGGATGGGAAAGGGCTCATCTACACCGACACAAGTGACAGGAGGCAGCATACGGTTACAGGTCTCCAGCCATACACAAACTACAGCTTCACACTCGCGGTTTGTACATCTGTCGGATGCACTTCCAGTGAGCCCTGTGTAGGTCAGACTCTGCAGGCTGCCCCTCAAGGAGTTTGGGTGACACCGCGACACATTATCATCAATTCTACAACCGTGGAGCTATATTGGAATCCTCCAGAAAGGCCCAACGGCCTCATTTCTCAATATCAGCTGAGGCGTAATGGAAGCTTGCTTCTCGTGGGGGGCAGAGATAATCAGAGTTTCACTGATAGCAACCTGGAGCCCGGCAGCAGGTACATTTACAAGTTGGAAGCGAGAACTGGAGGTGGTAGCAGTTGGAGTGAGGACTACCTTGTCCAGATGCCTCTGTGGACCCCAGAAGACATTCATCCCCCATGTAATGTCACTGTGCTGGGCTCTGATTCCATATTTGTAGCATGGCCAACACCAGGGAACCTGCTTCCCAAAATTCCAGTCGAGTACAGCATCTTACTCAGTGGCGGGAGTGTGACGCTCTTAGTCTTCTCTGTCAGACACCGGCAATCTGCACACCTGAAAAACCTGTCTCCGTTCACACAGTATGAAATACGGATCCAAGCCTGCCAAAATGGGGGCTGTGGAGTCAGCCCTGGGACATACGTCAGAACGCTTGAAGCAGCACCCGTGGGTCTGATGCCCCCTCTTCTGAAGGCTCTGGGGTCATCTTGCATAGAGGTTAAGTGGATGCCACCAACGAGACCCAATGGAATCATCACTAGCTATGTCGTTCAC
Peptide sequence:
MESSLAMSFTAFQDLQGDVEYYTLFWSSGTSEESLKIFPDVDFHVIGQLSPNVEYQVFLLVFNGVHAINSTVVHVTMWEEEPQGMLPPEVVIINSTAVRVIWTSPSNPNAVVTESSVYVNNKLYKTGTDAPGSFVLEDLSPFTIYDIQVEVCTKDACVKSNGTQVSTAEDTPSDISIPVIRGITSRSLQIDWTTPANPNGIILGYDVLRKTWRPCSETQKLTDKPRDELCKAVKCQYPGKVCGHTCYSPGTKVCCDGLLYDPQPGYSCCEDKYIALSPNATGVCCGGRMWEAQPDHQCCSGHYARILPGEICCPDERHNRVSVGFGDACCGTMPYATSGSQVCCAGRLQDGYRQQCCGGEMVSQDFQCCGGGEEGMVYSYLPGMLCCGQDYVNMSETICCSASSGESKAHVRKDDPTPVKCCGTELSPESQRCCDGVGYNPLKYVCSDEISAGMAMKETRVCATICPATMKATAHCGRCDFNATTHICTVMRGPLNPTGKKAVEGLCSAAEEIVHSGDVNTHSFIDRDLKPSTVYEYRISAWNSYGRGFSQSVRASTREDVPEGVKAPRWARTGKHEDVIFLQWEEPMQSNGPIIHYILFRDGRERFQGTALSFTDTQGIQPLQEYSYQLKACTAAGCAVSCKVVAATTQRSPENVPPPNITAQSSETLHLSWSVPEKMKDAIKAYQLWLDGKGLIYTDTSDRRQHTVTGLQPYTNYSFTLAVCTSVGCTSSEPCVGQTLQAAPQGVWVTPRHIIINSTTVELYWNPPERPNGLISQYQLRRNGSLLLVGGRDNQSFTDSNLEPGSRYIYKLEARTGGGSSWSEDYLVQMPLWTPEDIHPPCNVTVLGSDSIFVAWPTPGNLLPKIPVEYSILLSGGSVTLLVFSVRHRQSAHLKNLSPFTQYEIRIQACQNGGCGVSPGTYVRTLEAAPVGLMPPLLKALGSSCIEVKWMPPTRPNGIITSYVVH
IRESfinder result
IRESfinder score
0.389428347
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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