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mmu_circUsh2a_1203
Basic information of circular RNA
PanCircBase ID:
mmu_circUsh2a_1203
mm39_Chr. Position ID:
chr1|188529924|188558687|+
Gene name:
Ush2a
Transcript:
ENSMUST00000060479.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
49,50,51,52,53,54
Exon/intron offsets:
0,12445,16459,23951,24860,28564
Genomic length:
28763
Exon/intron sizes in nt:
2,22,22,42,05,19,81,55,000
Flanking exon/introns:
chr1:188517003-188529924|chr1:188558687-188573693
Splice length:
1203
Other database IDs:
circAtlas: mmu-Ush2a_0025
Human Ortholog IDs:
Mature spliced Sequence:
GAGAGATATGCTGCCCCGATGAGAGGCACAACCGGGTGTCCGTGGGCTTTGGTGATGCCTGCTGCGGCACAATGCCTTATGCCACCTCTGGGAGCCAGGTGTGCTGTGCCGGGAGGCTCCAGGACGGCTATAGACAGCAGTGCTGTGGGGGAGAGATGGTGAGCCAAGATTTCCAGTGCTGTGGTGGAGGAGAAGAGGGCATGGTATACAGTTACCTCCCAGGAATGCTGTGTTGTGGGCAGGATTATGTGAATATGTCAGAGACCATATGCTGTTCAGCTTCCAGTGGAGAGTCTAAAGCACATGTTAGAAAGGATGACCCCACACCAGTGAAATGCTGCGGCACTGAACTGAGTCCAGAGAGCCAGCGATGCTGTGATGGGGTTGGATATAATCCTTTGAAATATGTTTGTTCTGATGAGATTTCAGCTGGAATGGCGATGAAGGAAACCAGAGTATGTGCGACTATCTGCCCAGCAACCATGAAAGCCACAGCACACTGTGGGAGGTGTGACTTCAACGCCACCACCCATATCTGCACGGTGATGAGAGGGCCTCTCAATCCCACAGGGAAGAAAGCGGTGGAAGGACTGTGTTCTGCAGCAGAGGAAATAGTTCATTCTGGAGATGTAAACACACACTCTTTCATAGATAGAGACCTCAAGCCAAGCACTGTGTATGAATATAGAATTTCTGCATGGAACAGCTACGGGCGAGGATTCAGCCAATCCGTGAGAGCTAGCACAAGAGAAGATGTGCCTGAAGGAGTCAAGGCCCCTAGATGGGCCAGGACGGGCAAACATGAAGATGTTATTTTCTTACAGTGGGAAGAGCCCATGCAGTCAAATGGTCCTATCATTCACTATATTCTTTTTCGAGACGGAAGGGAGCGCTTTCAGGGAACAGCGCTGAGCTTCACGGACACGCAGGGAATTCAGCCACTCCAGGAATACTCATACCAGCTGAAGGCTTGCACAGCTGCTGGTTGTGCTGTCAGTTGCAAGGTAGTCGCTGCCACCACCCAAAGAAGCCCGGAGAATGTCCCACCACCAAACATCACAGCCCAGAGCTCAGAGACTCTACACCTCAGCTGGAGTGTCCCCGAGAAAATGAAAGATGCCATTAAAGCATACCAGCTCTGGCTGGATGGGAAAGGGCTCATCTACACCGACACAAGTGACAGGAGGCAGCATACGGTTACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCTGGCTGGATGGGAAAGG
60.11
GCTCCCAGAGGTGGCATAAG
60.18
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGCTCATCTACACCGACAC
60.18
GCTCCCAGAGGTGGCATAAG
60.18
144
PCR template sequence:
GAGAAAATGAAAGATGCCATTAAAGCATACCAGCTCTGGCTGGATGGGAAAGGGCTCATCTACACCGACACAAGTGACAGGAGGCAGCATACGGTTACAGGAGAGATATGCTGCCCCGATGAGAGGCACAACCGGGTGTCCGTGGGCTTTGGTGATGCCTGCTGCGGCACAATGCCTTATGCCACCTCTGGGAGCCAGGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(1), mmu-miR-205-5p(1), mmu-miR-216a-5p(1), mmu-miR-495-3p(1), mmu-miR-214-3p(1), mmu-miR-149-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-127-5p(1), mmu-miR-218-5p(1), mmu-miR-107-3p(1), mmu-miR-466a-5p(1), mmu-miR-466p-5p(1), mmu-miR-673-5p(1), mmu-miR-669d-5p(1), mmu-miR-188-3p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATACGGTTACAGGAGAGATATGCTG
siRNA sets
ATATCTCTCCTGTAACCGT, CATATCTCTCCTGTAACCG, TATCTCTCCTGTAACCGTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSH2A_1203_ORF_1
0.6292
0.141439894
0.999998312
2334
ORF sequence:
ATGCCTTATGCCACCTCTGGGAGCCAGGTGTGCTGTGCCGGGAGGCTCCAGGACGGCTATAGACAGCAGTGCTGTGGGGGAGAGATGGTGAGCCAAGATTTCCAGTGCTGTGGTGGAGGAGAAGAGGGCATGGTATACAGTTACCTCCCAGGAATGCTGTGTTGTGGGCAGGATTATGTGAATATGTCAGAGACCATATGCTGTTCAGCTTCCAGTGGAGAGTCTAAAGCACATGTTAGAAAGGATGACCCCACACCAGTGAAATGCTGCGGCACTGAACTGAGTCCAGAGAGCCAGCGATGCTGTGATGGGGTTGGATATAATCCTTTGAAATATGTTTGTTCTGATGAGATTTCAGCTGGAATGGCGATGAAGGAAACCAGAGTATGTGCGACTATCTGCCCAGCAACCATGAAAGCCACAGCACACTGTGGGAGGTGTGACTTCAACGCCACCACCCATATCTGCACGGTGATGAGAGGGCCTCTCAATCCCACAGGGAAGAAAGCGGTGGAAGGACTGTGTTCTGCAGCAGAGGAAATAGTTCATTCTGGAGATGTAAACACACACTCTTTCATAGATAGAGACCTCAAGCCAAGCACTGTGTATGAATATAGAATTTCTGCATGGAACAGCTACGGGCGAGGATTCAGCCAATCCGTGAGAGCTAGCACAAGAGAAGATGTGCCTGAAGGAGTCAAGGCCCCTAGATGGGCCAGGACGGGCAAACATGAAGATGTTATTTTCTTACAGTGGGAAGAGCCCATGCAGTCAAATGGTCCTATCATTCACTATATTCTTTTTCGAGACGGAAGGGAGCGCTTTCAGGGAACAGCGCTGAGCTTCACGGACACGCAGGGAATTCAGCCACTCCAGGAATACTCATACCAGCTGAAGGCTTGCACAGCTGCTGGTTGTGCTGTCAGTTGCAAGGTAGTCGCTGCCACCACCCAAAGAAGCCCGGAGAATGTCCCACCACCAAACATCACAGCCCAGAGCTCAGAGACTCTACACCTCAGCTGGAGTGTCCCCGAGAAAATGAAAGATGCCATTAAAGCATACCAGCTCTGGCTGGATGGGAAAGGGCTCATCTACACCGACACAAGTGACAGGAGGCAGCATACGGTTACAGGAGAGATATGCTGCCCCGATGAGAGGCACAACCGGGTGTCCGTGGGCTTTGGTGATGCCTGCTGCGGCACAATGCCTTATGCCACCTCTGGGAGCCAGGTGTGCTGTGCCGGGAGGCTCCAGGACGGCTATAGACAGCAGTGCTGTGGGGGAGAGATGGTGAGCCAAGATTTCCAGTGCTGTGGTGGAGGAGAAGAGGGCATGGTATACAGTTACCTCCCAGGAATGCTGTGTTGTGGGCAGGATTATGTGAATATGTCAGAGACCATATGCTGTTCAGCTTCCAGTGGAGAGTCTAAAGCACATGTTAGAAAGGATGACCCCACACCAGTGAAATGCTGCGGCACTGAACTGAGTCCAGAGAGCCAGCGATGCTGTGATGGGGTTGGATATAATCCTTTGAAATATGTTTGTTCTGATGAGATTTCAGCTGGAATGGCGATGAAGGAAACCAGAGTATGTGCGACTATCTGCCCAGCAACCATGAAAGCCACAGCACACTGTGGGAGGTGTGACTTCAACGCCACCACCCATATCTGCACGGTGATGAGAGGGCCTCTCAATCCCACAGGGAAGAAAGCGGTGGAAGGACTGTGTTCTGCAGCAGAGGAAATAGTTCATTCTGGAGATGTAAACACACACTCTTTCATAGATAGAGACCTCAAGCCAAGCACTGTGTATGAATATAGAATTTCTGCATGGAACAGCTACGGGCGAGGATTCAGCCAATCCGTGAGAGCTAGCACAAGAGAAGATGTGCCTGAAGGAGTCAAGGCCCCTAGATGGGCCAGGACGGGCAAACATGAAGATGTTATTTTCTTACAGTGGGAAGAGCCCATGCAGTCAAATGGTCCTATCATTCACTATATTCTTTTTCGAGACGGAAGGGAGCGCTTTCAGGGAACAGCGCTGAGCTTCACGGACACGCAGGGAATTCAGCCACTCCAGGAATACTCATACCAGCTGAAGGCTTGCACAGCTGCTGGTTGTGCTGTCAGTTGCAAGGTAGTCGCTGCCACCACCCAAAGAAGCCCGGAGAATGTCCCACCACCAAACATCACAGCCCAGAGCTCAGAGACTCTACACCTCAGCTGGAGTGTCCCCGAGAAAATGAAAGATGCCATTAAAGCATACCAGCTCTGGCTGGATGGGAAAGGGCTCATCTACACCGACACAAGTGACAGGAGGCAGCATACGGTTACA
Peptide sequence:
MPYATSGSQVCCAGRLQDGYRQQCCGGEMVSQDFQCCGGGEEGMVYSYLPGMLCCGQDYVNMSETICCSASSGESKAHVRKDDPTPVKCCGTELSPESQRCCDGVGYNPLKYVCSDEISAGMAMKETRVCATICPATMKATAHCGRCDFNATTHICTVMRGPLNPTGKKAVEGLCSAAEEIVHSGDVNTHSFIDRDLKPSTVYEYRISAWNSYGRGFSQSVRASTREDVPEGVKAPRWARTGKHEDVIFLQWEEPMQSNGPIIHYILFRDGRERFQGTALSFTDTQGIQPLQEYSYQLKACTAAGCAVSCKVVAATTQRSPENVPPPNITAQSSETLHLSWSVPEKMKDAIKAYQLWLDGKGLIYTDTSDRRQHTVTGEICCPDERHNRVSVGFGDACCGTMPYATSGSQVCCAGRLQDGYRQQCCGGEMVSQDFQCCGGGEEGMVYSYLPGMLCCGQDYVNMSETICCSASSGESKAHVRKDDPTPVKCCGTELSPESQRCCDGVGYNPLKYVCSDEISAGMAMKETRVCATICPATMKATAHCGRCDFNATTHICTVMRGPLNPTGKKAVEGLCSAAEEIVHSGDVNTHSFIDRDLKPSTVYEYRISAWNSYGRGFSQSVRASTREDVPEGVKAPRWARTGKHEDVIFLQWEEPMQSNGPIIHYILFRDGRERFQGTALSFTDTQGIQPLQEYSYQLKACTAAGCAVSCKVVAATTQRSPENVPPPNITAQSSETLHLSWSVPEKMKDAIKAYQLWLDGKGLIYTDTSDRRQHTVT
IRESfinder result
IRESfinder score
0.275862095
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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