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mmu_circUsh2a_2673
Basic information of circular RNA
PanCircBase ID:
mmu_circUsh2a_2673
mm39_Chr. Position ID:
chr1|188255524|188410626|+
Gene name:
Ush2a
Transcript:
ENSMUST00000060479.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
17
Exon/intron indexes:
21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37
Exon/intron offsets:
0,8331,9811,12981,14370,19275,26507,26837,29771,52850,55037,103249,105215,110253,124946,131232,154922
Genomic length:
155102
Exon/intron sizes in nt:
1,31,12,71,02,18,01,31,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr1:188198537-188255524|chr1:188410626-188446500
Splice length:
2673
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GAATCAAGGCCAGCTTCCGGACAAGGGTGCCTGAAGGGCTGATCCTCCTGGCACTGTCCCCTGGCGACCAGGAAGAGTATTTCACCCTGCAGTTGAAGAATGGCCGTCCTTACTTTCTTTACAATTCCCAGGGAACACTAGTGGAAGTTACCCCAACTGATGATCCTAGTCAAGGATACAGGGATGGAGAGTGGCATGAAATCATAGCAGTCAGACATCAGGCTTTTGGCCAGATTACTCTTGATGGACAGTACACAGGCTCCTCTTCTTCTCTGAATGGAAGCTCCGTGACAGGAGGCTACACTGGACTGTTTGTGGGTGGAGTGCCACAAGGTCATAGCGTCCTCCAGAAGAGGCTTGAGATAATCCAAAGAGGTTTTGTGGGCTGCCTCAAGGATGTGTTCATCATGAAGGGTTACAGCCCCTCTGGGACGTGGCTACCTTTGGATTGGCAGAGCTCTGAGGAGCAGGTGAATGTTCATCCCAGCTGGGAAGGTTGTCCCACCAACCTAGAAGAAGGAGTTCAGTTCCTAGGAGCAGGATTTCTGGAGCTTCCTTCAGATACGTTTCATGCTGCAAAGGACTTTGAGATCTCCCTGAAGTTTCAAACAGACCAACTAAATGGATTGCTTCTTTTCATTCACAATACAGAGGGACCGGATTTTCTTGCGGTGGAGCTGAAGAGAGGGCTGCTGAGCTTCAAGTTCAATTCCAGTCTCGTCTTTACACGCGTGGATCTCAGGCTGGGGCTGGCCGATTGTGATGGAAAGTGGAATACAGTCAGTATCAAAAAGGAAGGCTCTGTGGTATCTGTCCGTGTGAATGCACTTAAGAAGAGCACCTCCCAGGCTGGAGGCCAGCCTCTGCTGGTGAATTCTCCTGTCTATCTGGGCGGGATCCCACGGGAGCTGCAGGACGCCTACAGACATTTGACTCTGGAGCCAGGGTTCCGTGGTTGCGTGAAGGAAGTTGCATTTGCACGGGGTGTTGTCGTTAACTTGGCATCTGTGTCCAGCCGTGCTGTCAGAGTCAATCAGGATGGATGCCTATCAAGTGACAGTACTGTTAACTGTGGGGGAAATGACTCCATCCTGGTTTATCGGGGAAGCCAGCAGAGTGTTTATGAGAGCGGTCTCCAGCCCTTTACAGAATACCTGTATCGGGTCACAGCCTCACACGAAGGAGGAGCGGTGTCCAGTGATTGGAGTCGGGGACGCACATTGGGCACAGCTCCGCAGAGTGTGCCAACTCCCTCAAGAGCCCAGAGCATAAACGGATCCAGCGTTGAGGTGGCCTGGAATGAGCCTGCTGTGGTTAAAGGTGTCCTGGAGAAGTACGTTCTGAAAGCCTACAGTGAGGACAGCTCCCAGCCCCGCGTGCCCTCTGCCAGCACTGAGCTTCATGACACCAGCACCCACTCAGGCGTGTTGATAGGACTTCATCCCTTCCACAGCTACACGGTAACCCTGACTGCTTGTTCTCGGGCAGGCTGCACCGAGAGCTCACAGGCATTGAGCATCTCCACTCCACAAGAAGCGCCCCAGGAGGTGCAGGCACCAGTCGCCGTGGCCCTTCCCAACTCCTTGTCATTCTTTTGGAGTCTACCCAGACAAGCAAATGGGATTATTACGCAGTACTCCTTATACGTGGATGGGAGGCTGGTCTACACAGGCAAGGGACAGAACTACACAGTCACAGATTTAAGAGTATTCGCAGCCTACGAGATTATAGTTGGTGCATGCACACAAGCAGGGTGCACAAACAGCTCCCAAGTCATCTTGCACACAGCACAGCTGCCGCCAGAGCAAGTGGATCCCCCGGGTTTGACTGTCCTGGATTCTAGGACTATCCATGTACGGTGGAAACAACCAAGGCAACTAAATGGAATTCTGGAGCGCTACATATTATATATTTTGAATCCTATACATAACTCCACAATGTGGAGTGTTGTCTATAACAGCACAGAAAAACTCCAGGCTCACGTGCTCCACCACCTTTCCCCTGGGGGTCTATACCTCATCAGGCTGAGAGTGTGTACCGGTGGGGGCTGCACAACAAGTGAGCCCAGCCAGGCCCTAATGGAGGAGACGATTCCAGAAGGTGTGCCAGCCCCCAGAGCTCACTCCTACTCACCAGACTCCTTTAACATCTCCTGGACAGAGCCTGAGTATCCGAATGGAGTGATCACCACATATGAGTTATATCTAGATGACACTCTGATTCACAATTCATCAGGACTCAGCTGCCATGCCTATGGATTTGATCCTGGGAGCTTACACACCTTCCAAGTTCAAGCATGCACGGCAAAGGGTTGTGCTCTGGGCCCACTGGTAGGAAACCGGACTCTAGAAGCTCCTCCGGAAGGCGTGGTCAACGTGCTTGTCAAACCTGAGGGATCCCGGGAAGCCCACGTGAGGTGGGATGCGCCTGCGCACCCTAACGGGCGCTTAACCTACTCAGTCCATTTCACCGGAAGTTTCTATGCAGATCAAGCAGGTGACAACTACACCCTTCTCAGTGGTACAAAAACTATCCGCGGCATCGAAGGAAGCCGGCTCTGGGTGCTGGTGGACGGACTGGTTCCTTGCTCACACTACATGGTACAAGTGAATGCTTCTAACAGCAGAGGGAGCGTGCTCAGTGACCCTGTTTCCGTTGAAATGCCTCCCGGGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGACTGGTTCCTTGCTCACA
59.89
GACAGTGCCAGGAGGATCAG
59.82
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGACTGGTTCCTTGCTCACA
59.89
CAGGAGGATCAGCCCTTCAG
59.53
150
PCR template sequence:
GGACTGGTTCCTTGCTCACACTACATGGTACAAGTGAATGCTTCTAACAGCAGAGGGAGCGTGCTCAGTGACCCTGTTTCCGTTGAAATGCCTCCCGGGGGAATCAAGGCCAGCTTCCGGACAAGGGTGCCTGAAGGGCTGATCCTCCTGGCACTGTCCCCTGGCGACCAGGAAGAGTATTTCACCCTGCAGTTGAAGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
24
Interacting miRNAs (#binding sites)
mmu-miR-127-5p(3), mmu-miR-484(2), mmu-miR-199a-5p(1), mmu-miR-181a-5p(1), mmu-miR-19b-3p(1), mmu-miR-101a-3p(1), mmu-miR-298-5p(1), mmu-miR-326-3p(1), mmu-miR-138-5p(1), mmu-miR-181b-5p(1), mmu-miR-214-3p(1), mmu-miR-149-5p(1), mmu-miR-127-3p(1), mmu-miR-433-3p(1), mmu-miR-676-3p(1), mmu-miR-382-3p(1), mmu-miR-467b-5p(1), mmu-miR-410-3p(1), mmu-miR-207(1), mmu-miR-669d-5p(1), mmu-miR-3470b(1), mmu-miR-1199-5p(1), mmu-miR-202-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGCCTCCCGGGGGAATCAAGGCCAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSH2A_2673_ORF_1
0.751
0.171589688
1
4938
ORF sequence:
ATGAAGGGTTACAGCCCCTCTGGGACGTGGCTACCTTTGGATTGGCAGAGCTCTGAGGAGCAGGTGAATGTTCATCCCAGCTGGGAAGGTTGTCCCACCAACCTAGAAGAAGGAGTTCAGTTCCTAGGAGCAGGATTTCTGGAGCTTCCTTCAGATACGTTTCATGCTGCAAAGGACTTTGAGATCTCCCTGAAGTTTCAAACAGACCAACTAAATGGATTGCTTCTTTTCATTCACAATACAGAGGGACCGGATTTTCTTGCGGTGGAGCTGAAGAGAGGGCTGCTGAGCTTCAAGTTCAATTCCAGTCTCGTCTTTACACGCGTGGATCTCAGGCTGGGGCTGGCCGATTGTGATGGAAAGTGGAATACAGTCAGTATCAAAAAGGAAGGCTCTGTGGTATCTGTCCGTGTGAATGCACTTAAGAAGAGCACCTCCCAGGCTGGAGGCCAGCCTCTGCTGGTGAATTCTCCTGTCTATCTGGGCGGGATCCCACGGGAGCTGCAGGACGCCTACAGACATTTGACTCTGGAGCCAGGGTTCCGTGGTTGCGTGAAGGAAGTTGCATTTGCACGGGGTGTTGTCGTTAACTTGGCATCTGTGTCCAGCCGTGCTGTCAGAGTCAATCAGGATGGATGCCTATCAAGTGACAGTACTGTTAACTGTGGGGGAAATGACTCCATCCTGGTTTATCGGGGAAGCCAGCAGAGTGTTTATGAGAGCGGTCTCCAGCCCTTTACAGAATACCTGTATCGGGTCACAGCCTCACACGAAGGAGGAGCGGTGTCCAGTGATTGGAGTCGGGGACGCACATTGGGCACAGCTCCGCAGAGTGTGCCAACTCCCTCAAGAGCCCAGAGCATAAACGGATCCAGCGTTGAGGTGGCCTGGAATGAGCCTGCTGTGGTTAAAGGTGTCCTGGAGAAGTACGTTCTGAAAGCCTACAGTGAGGACAGCTCCCAGCCCCGCGTGCCCTCTGCCAGCACTGAGCTTCATGACACCAGCACCCACTCAGGCGTGTTGATAGGACTTCATCCCTTCCACAGCTACACGGTAACCCTGACTGCTTGTTCTCGGGCAGGCTGCACCGAGAGCTCACAGGCATTGAGCATCTCCACTCCACAAGAAGCGCCCCAGGAGGTGCAGGCACCAGTCGCCGTGGCCCTTCCCAACTCCTTGTCATTCTTTTGGAGTCTACCCAGACAAGCAAATGGGATTATTACGCAGTACTCCTTATACGTGGATGGGAGGCTGGTCTACACAGGCAAGGGACAGAACTACACAGTCACAGATTTAAGAGTATTCGCAGCCTACGAGATTATAGTTGGTGCATGCACACAAGCAGGGTGCACAAACAGCTCCCAAGTCATCTTGCACACAGCACAGCTGCCGCCAGAGCAAGTGGATCCCCCGGGTTTGACTGTCCTGGATTCTAGGACTATCCATGTACGGTGGAAACAACCAAGGCAACTAAATGGAATTCTGGAGCGCTACATATTATATATTTTGAATCCTATACATAACTCCACAATGTGGAGTGTTGTCTATAACAGCACAGAAAAACTCCAGGCTCACGTGCTCCACCACCTTTCCCCTGGGGGTCTATACCTCATCAGGCTGAGAGTGTGTACCGGTGGGGGCTGCACAACAAGTGAGCCCAGCCAGGCCCTAATGGAGGAGACGATTCCAGAAGGTGTGCCAGCCCCCAGAGCTCACTCCTACTCACCAGACTCCTTTAACATCTCCTGGACAGAGCCTGAGTATCCGAATGGAGTGATCACCACATATGAGTTATATCTAGATGACACTCTGATTCACAATTCATCAGGACTCAGCTGCCATGCCTATGGATTTGATCCTGGGAGCTTACACACCTTCCAAGTTCAAGCATGCACGGCAAAGGGTTGTGCTCTGGGCCCACTGGTAGGAAACCGGACTCTAGAAGCTCCTCCGGAAGGCGTGGTCAACGTGCTTGTCAAACCTGAGGGATCCCGGGAAGCCCACGTGAGGTGGGATGCGCCTGCGCACCCTAACGGGCGCTTAACCTACTCAGTCCATTTCACCGGAAGTTTCTATGCAGATCAAGCAGGTGACAACTACACCCTTCTCAGTGGTACAAAAACTATCCGCGGCATCGAAGGAAGCCGGCTCTGGGTGCTGGTGGACGGACTGGTTCCTTGCTCACACTACATGGTACAAGTGAATGCTTCTAACAGCAGAGGGAGCGTGCTCAGTGACCCTGTTTCCGTTGAAATGCCTCCCGGGGGAATCAAGGCCAGCTTCCGGACAAGGGTGCCTGAAGGGCTGATCCTCCTGGCACTGTCCCCTGGCGACCAGGAAGAGTATTTCACCCTGCAGTTGAAGAATGGCCGTCCTTACTTTCTTTACAATTCCCAGGGAACACTAGTGGAAGTTACCCCAACTGATGATCCTAGTCAAGGATACAGGGATGGAGAGTGGCATGAAATCATAGCAGTCAGACATCAGGCTTTTGGCCAGATTACTCTTGATGGACAGTACACAGGCTCCTCTTCTTCTCTGAATGGAAGCTCCGTGACAGGAGGCTACACTGGACTGTTTGTGGGTGGAGTGCCACAAGGTCATAGCGTCCTCCAGAAGAGGCTTGAGATAATCCAAAGAGGTTTTGTGGGCTGCCTCAAGGATGTGTTCATCATGAAGGGTTACAGCCCCTCTGGGACGTGGCTACCTTTGGATTGGCAGAGCTCTGAGGAGCAGGTGAATGTTCATCCCAGCTGGGAAGGTTGTCCCACCAACCTAGAAGAAGGAGTTCAGTTCCTAGGAGCAGGATTTCTGGAGCTTCCTTCAGATACGTTTCATGCTGCAAAGGACTTTGAGATCTCCCTGAAGTTTCAAACAGACCAACTAAATGGATTGCTTCTTTTCATTCACAATACAGAGGGACCGGATTTTCTTGCGGTGGAGCTGAAGAGAGGGCTGCTGAGCTTCAAGTTCAATTCCAGTCTCGTCTTTACACGCGTGGATCTCAGGCTGGGGCTGGCCGATTGTGATGGAAAGTGGAATACAGTCAGTATCAAAAAGGAAGGCTCTGTGGTATCTGTCCGTGTGAATGCACTTAAGAAGAGCACCTCCCAGGCTGGAGGCCAGCCTCTGCTGGTGAATTCTCCTGTCTATCTGGGCGGGATCCCACGGGAGCTGCAGGACGCCTACAGACATTTGACTCTGGAGCCAGGGTTCCGTGGTTGCGTGAAGGAAGTTGCATTTGCACGGGGTGTTGTCGTTAACTTGGCATCTGTGTCCAGCCGTGCTGTCAGAGTCAATCAGGATGGATGCCTATCAAGTGACAGTACTGTTAACTGTGGGGGAAATGACTCCATCCTGGTTTATCGGGGAAGCCAGCAGAGTGTTTATGAGAGCGGTCTCCAGCCCTTTACAGAATACCTGTATCGGGTCACAGCCTCACACGAAGGAGGAGCGGTGTCCAGTGATTGGAGTCGGGGACGCACATTGGGCACAGCTCCGCAGAGTGTGCCAACTCCCTCAAGAGCCCAGAGCATAAACGGATCCAGCGTTGAGGTGGCCTGGAATGAGCCTGCTGTGGTTAAAGGTGTCCTGGAGAAGTACGTTCTGAAAGCCTACAGTGAGGACAGCTCCCAGCCCCGCGTGCCCTCTGCCAGCACTGAGCTTCATGACACCAGCACCCACTCAGGCGTGTTGATAGGACTTCATCCCTTCCACAGCTACACGGTAACCCTGACTGCTTGTTCTCGGGCAGGCTGCACCGAGAGCTCACAGGCATTGAGCATCTCCACTCCACAAGAAGCGCCCCAGGAGGTGCAGGCACCAGTCGCCGTGGCCCTTCCCAACTCCTTGTCATTCTTTTGGAGTCTACCCAGACAAGCAAATGGGATTATTACGCAGTACTCCTTATACGTGGATGGGAGGCTGGTCTACACAGGCAAGGGACAGAACTACACAGTCACAGATTTAAGAGTATTCGCAGCCTACGAGATTATAGTTGGTGCATGCACACAAGCAGGGTGCACAAACAGCTCCCAAGTCATCTTGCACACAGCACAGCTGCCGCCAGAGCAAGTGGATCCCCCGGGTTTGACTGTCCTGGATTCTAGGACTATCCATGTACGGTGGAAACAACCAAGGCAACTAAATGGAATTCTGGAGCGCTACATATTATATATTTTGAATCCTATACATAACTCCACAATGTGGAGTGTTGTCTATAACAGCACAGAAAAACTCCAGGCTCACGTGCTCCACCACCTTTCCCCTGGGGGTCTATACCTCATCAGGCTGAGAGTGTGTACCGGTGGGGGCTGCACAACAAGTGAGCCCAGCCAGGCCCTAATGGAGGAGACGATTCCAGAAGGTGTGCCAGCCCCCAGAGCTCACTCCTACTCACCAGACTCCTTTAACATCTCCTGGACAGAGCCTGAGTATCCGAATGGAGTGATCACCACATATGAGTTATATCTAGATGACACTCTGATTCACAATTCATCAGGACTCAGCTGCCATGCCTATGGATTTGATCCTGGGAGCTTACACACCTTCCAAGTTCAAGCATGCACGGCAAAGGGTTGTGCTCTGGGCCCACTGGTAGGAAACCGGACTCTAGAAGCTCCTCCGGAAGGCGTGGTCAACGTGCTTGTCAAACCTGAGGGATCCCGGGAAGCCCACGTGAGGTGGGATGCGCCTGCGCACCCTAACGGGCGCTTAACCTACTCAGTCCATTTCACCGGAAGTTTCTATGCAGATCAAGCAGGTGACAACTACACCCTTCTCAGTGGTACAAAAACTATCCGCGGCATCGAAGGAAGCCGGCTCTGGGTGCTGGTGGACGGACTGGTTCCTTGCTCACACTACATGGTACAAGTGAATGCTTCTAACAGCAGAGGGAGCGTGCTCAGTGACCCTGTTTCCGTTGAAATGCCTCCCGGG
Peptide sequence:
MKGYSPSGTWLPLDWQSSEEQVNVHPSWEGCPTNLEEGVQFLGAGFLELPSDTFHAAKDFEISLKFQTDQLNGLLLFIHNTEGPDFLAVELKRGLLSFKFNSSLVFTRVDLRLGLADCDGKWNTVSIKKEGSVVSVRVNALKKSTSQAGGQPLLVNSPVYLGGIPRELQDAYRHLTLEPGFRGCVKEVAFARGVVVNLASVSSRAVRVNQDGCLSSDSTVNCGGNDSILVYRGSQQSVYESGLQPFTEYLYRVTASHEGGAVSSDWSRGRTLGTAPQSVPTPSRAQSINGSSVEVAWNEPAVVKGVLEKYVLKAYSEDSSQPRVPSASTELHDTSTHSGVLIGLHPFHSYTVTLTACSRAGCTESSQALSISTPQEAPQEVQAPVAVALPNSLSFFWSLPRQANGIITQYSLYVDGRLVYTGKGQNYTVTDLRVFAAYEIIVGACTQAGCTNSSQVILHTAQLPPEQVDPPGLTVLDSRTIHVRWKQPRQLNGILERYILYILNPIHNSTMWSVVYNSTEKLQAHVLHHLSPGGLYLIRLRVCTGGGCTTSEPSQALMEETIPEGVPAPRAHSYSPDSFNISWTEPEYPNGVITTYELYLDDTLIHNSSGLSCHAYGFDPGSLHTFQVQACTAKGCALGPLVGNRTLEAPPEGVVNVLVKPEGSREAHVRWDAPAHPNGRLTYSVHFTGSFYADQAGDNYTLLSGTKTIRGIEGSRLWVLVDGLVPCSHYMVQVNASNSRGSVLSDPVSVEMPPGGIKASFRTRVPEGLILLALSPGDQEEYFTLQLKNGRPYFLYNSQGTLVEVTPTDDPSQGYRDGEWHEIIAVRHQAFGQITLDGQYTGSSSSLNGSSVTGGYTGLFVGGVPQGHSVLQKRLEIIQRGFVGCLKDVFIMKGYSPSGTWLPLDWQSSEEQVNVHPSWEGCPTNLEEGVQFLGAGFLELPSDTFHAAKDFEISLKFQTDQLNGLLLFIHNTEGPDFLAVELKRGLLSFKFNSSLVFTRVDLRLGLADCDGKWNTVSIKKEGSVVSVRVNALKKSTSQAGGQPLLVNSPVYLGGIPRELQDAYRHLTLEPGFRGCVKEVAFARGVVVNLASVSSRAVRVNQDGCLSSDSTVNCGGNDSILVYRGSQQSVYESGLQPFTEYLYRVTASHEGGAVSSDWSRGRTLGTAPQSVPTPSRAQSINGSSVEVAWNEPAVVKGVLEKYVLKAYSEDSSQPRVPSASTELHDTSTHSGVLIGLHPFHSYTVTLTACSRAGCTESSQALSISTPQEAPQEVQAPVAVALPNSLSFFWSLPRQANGIITQYSLYVDGRLVYTGKGQNYTVTDLRVFAAYEIIVGACTQAGCTNSSQVILHTAQLPPEQVDPPGLTVLDSRTIHVRWKQPRQLNGILERYILYILNPIHNSTMWSVVYNSTEKLQAHVLHHLSPGGLYLIRLRVCTGGGCTTSEPSQALMEETIPEGVPAPRAHSYSPDSFNISWTEPEYPNGVITTYELYLDDTLIHNSSGLSCHAYGFDPGSLHTFQVQACTAKGCALGPLVGNRTLEAPPEGVVNVLVKPEGSREAHVRWDAPAHPNGRLTYSVHFTGSFYADQAGDNYTLLSGTKTIRGIEGSRLWVLVDGLVPCSHYMVQVNASNSRGSVLSDPVSVEMPPG
IRESfinder result
IRESfinder score
0.589486236
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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