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mmu_circUsh2a_2532
Basic information of circular RNA
PanCircBase ID:
mmu_circUsh2a_2532
mm39_Chr. Position ID:
chr1|188083233|188169167|+
Gene name:
Ush2a
Transcript:
ENSMUST00000124358.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
5,6,7,8,9,10,11,12,13,14,15,16
Exon/intron offsets:
0,5652,6819,7456,8778,27879,30380,44718,48704,64641,79670,85775
Genomic length:
85934
Exon/intron sizes in nt:
6,42,95,18,52,22,94,19,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr1:188051290-188083233|chr1:188169167-188175210
Splice length:
2532
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTCAGAGCAGTTTGTTGGAAGAATGCAAGATTTTCGATTGTACAATGTGTCACTTACAAACAGGGAGATTCTAGAGGTCTTTTCTGGAGATTTTCCTCACTTGCACATCCAGCCACATTGCCGATGTCCAGGTAGCCACCCCCGTGTCCACCCCTCCGTTCAGCAGTACTGCATTCCCAATGGTGCAGGAGACACGCCCGAGCATCGAATGTCACGGCTGAATCCCGAAGCCCACCCTCTCTCCTTCATCAATGATGACGACGTTGCTACTTCATGGATCTCTCATGTGTTTACAAACATTACGCAGCTCTATGAAGGAGTGGCTATTTCTATAGACTTAGAAAATGGACAGTACCAGGTGCTTAAAGTCATCACCCAGTTCTCCAGCCTACAGCCTGTGGCAATTCGGATCCAGAGGAAGAAGGCAGACAGCTCTCCCTGGGAGGACTGGCAGTATTTTGCCAGAAATTGCAGTGTTTGGGGAATGAAGGACAATGAAGATTTGGAAAATCCCAATTCTGTCAACTGTCTCCAGCTTCCTGATTTTATCCCGTTTTCCCATGGTAATGTCACCTTTGACCTCCTGACATCTGGACAGAAGCATCGTCCTGGGTACAACGACTTTTACAACAGCTCAGTGCTTCAAGAATTCATGAGAGCCACTCAAATAAGGCTGCACTTCCATGGGCAGTACTATCCGGCTGGACACACTGTTGACTGGAGACACCAATACTATGCAGTGGATGAGATCATTGTCAGTGGAAGATGCCAATGCCACGGCCATGCTGAGACCTGTGACAGGACCAGACGGCCTTACAGATGTCTCTGCTCTCCACACAGCTTCACTGAAGGGCCTCAGTGTGATCGATGCTCCCCTCTTTATAATGACAAGCCTTTCCGCAGTGGTGACAATGTTAATGCATTCAACTGTAAGCCTTGCCAGTGCCATGGCCATGCCAGCAGCTGCCACTACGATGCTTCTGTGGACCCATTTCCCCTGGAACACAACAGAGGCGGTGGAGGAGTCTGTGATGACTGTCAGCATCATACAACAGGGAGACACTGTGAGTCGTGCCAGGATTACTTTTACCGACCTGTTGGTGCTGATCCTGCTGCCCCGGATGCTTGCAAGCTCTGTGACTGTAACAGGGCCGGGACTAGAAATGGCAGCCTCCACTGTGACCCGATTGGAGGCCAATGTGATTGTAAGAGACGTGTGTCTGGCAGACAGTGCCTTCAGTGCCAGGATGGATTCTATGACCTGCAGGCGCTAGATCCTGACGGCTGCCGTCCCTGTAACTGTAATCCCTCTGGGACCGTGGATGGAGACATTACCTGTCACCAAAATTCAGGCCAGTGCTCGTGCAAAGCGAATGTTATTGGGCTTAGATGCAATCGCTGCAATTTCGGATTTAAATTCCTCCAGAGTTTTAATGGTGATGGATGTGAGCCTTGCCAATGTAACCTCCACGGCTCAGTGAACCAACTCTGTGATCCGCTTTCTGGGCAGTGTGCATGCAAGAAGGAAGCCAAAGGACTTAAGTGTGACTCTTGCAGAGAAAACTTTTATGGGTTGCCCTGGAGTGCTTGTGAGGTCTGTGACTGCAGCAAGGCTGGGTCCCAGCCTGGGACTGTCTGTGACACTGAGACAGGGCAGTGCGTTTGTAAGCCCAATGTTGGAGGGAGACAATGTAGTCAGTGTAAGGCAGGCTACTTCAACCTATATCAGAATGATTCCCACCTCTGTTTGACTTGTAACTGCGAGAAGATGGGAACGGTAAATGGCTCTCTAAGGTGTGACAAGTCAACCGGGCAGTGTCCTTGCAAACTAGGGGTAACTGGTCTGCGTTGCCACCAGTGCAAGCCTCACAGGTTCAATTTGACGATGGACAATCCTCAAGGTTGTCAGGCGTGCGACTGTGACTCGTTGGGGACATTACCTGGAAGCATGTGTGACCCCATCAGTGGCCAGTGTCTATGTCTACCTCATCGACAAGGAAGAAGGTGTGAGCAGTGTCAGCCAGGCTTTTACAGTTCTCCCAGCAATGCCACTGGCTGCCTGCCATGCTTATGCCACACAGCTGGTGCTGTGAGCCACATCTGTAATAGTGTCACGGGACAGTGCTCTTGCCATGACCCCTCAACCACTGGGCGTAGCTGTCACCAGTGTCAAGAAAGTTACTTTAGATTTGATCCCCTGACTGGAAGATGCAGGCCTTGTCACTGTCATGTAGCAGGAGCCTCGAATGGAACTTGTGATGCAGTCACAGGCCAGTGTTTCTGCAAAGAGTTTGTCACTGGCTCAAAATGTGACACTTGTGTTCCTGGTGCAAGCCACTTGGACGTCAACAATCTATTAGGCTGCAGCAAAACTCCATCTCAGCAACCTCCACCCAGAGGATGGGTTCAGAGTTCTTCTACCATCAATGTGTCCTGGAGTCCACCCGAGTGCCCAAATGCTCACTGGCTTACATACACTCTGTTCAGGAATGGCTCTGAGATCTACACAACTGAAGATGAACACCCGTACT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGTGCCCAAATGCTCACTG
59.48
TCTCCCTGTTTGTAAGTGACACA
59.55
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGTGCCCAAATGCTCACTG
59.48
CTCCCTGTTTGTAAGTGACACA
58.2
153
PCR template sequence:
TCCTGGAGTCCACCCGAGTGCCCAAATGCTCACTGGCTTACATACACTCTGTTCAGGAATGGCTCTGAGATCTACACAACTGAAGATGAACACCCGTACTGTTCAGAGCAGTTTGTTGGAAGAATGCAAGATTTTCGATTGTACAATGTGTCACTTACAAACAGGGAGATTCTAGAGGTCTTTTCTGGAGATTTTCCTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
29
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(2), mmu-miR-141-3p(2), mmu-miR-27b-3p(2), mmu-miR-27a-3p(2), mmu-miR-31-5p(2), mmu-miR-29a-3p(2), mmu-miR-680(2), mmu-miR-23b-3p(1), mmu-miR-134-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-221-3p(1), mmu-miR-200c-3p(1), mmu-miR-205-5p(1), mmu-miR-29b-3p(1), mmu-miR-29c-3p(1), mmu-miR-146a-5p(1), mmu-miR-217-5p(1), mmu-miR-23a-3p(1), mmu-miR-214-3p(1), mmu-miR-483-5p(1), mmu-miR-182-5p(1), mmu-miR-183-5p(1), mmu-miR-324-3p(1), mmu-miR-297a-5p(1), mmu-miR-98-5p(1), mmu-miR-673-5p(1), mmu-miR-3065-5p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAACACCCGTACTGTTCAGAGCAGTT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSH2A_2532_ORF_1
1.01
0.06193355
1
5040
ORF sequence:
ATGCAAGATTTTCGATTGTACAATGTGTCACTTACAAACAGGGAGATTCTAGAGGTCTTTTCTGGAGATTTTCCTCACTTGCACATCCAGCCACATTGCCGATGTCCAGGTAGCCACCCCCGTGTCCACCCCTCCGTTCAGCAGTACTGCATTCCCAATGGTGCAGGAGACACGCCCGAGCATCGAATGTCACGGCTGAATCCCGAAGCCCACCCTCTCTCCTTCATCAATGATGACGACGTTGCTACTTCATGGATCTCTCATGTGTTTACAAACATTACGCAGCTCTATGAAGGAGTGGCTATTTCTATAGACTTAGAAAATGGACAGTACCAGGTGCTTAAAGTCATCACCCAGTTCTCCAGCCTACAGCCTGTGGCAATTCGGATCCAGAGGAAGAAGGCAGACAGCTCTCCCTGGGAGGACTGGCAGTATTTTGCCAGAAATTGCAGTGTTTGGGGAATGAAGGACAATGAAGATTTGGAAAATCCCAATTCTGTCAACTGTCTCCAGCTTCCTGATTTTATCCCGTTTTCCCATGGTAATGTCACCTTTGACCTCCTGACATCTGGACAGAAGCATCGTCCTGGGTACAACGACTTTTACAACAGCTCAGTGCTTCAAGAATTCATGAGAGCCACTCAAATAAGGCTGCACTTCCATGGGCAGTACTATCCGGCTGGACACACTGTTGACTGGAGACACCAATACTATGCAGTGGATGAGATCATTGTCAGTGGAAGATGCCAATGCCACGGCCATGCTGAGACCTGTGACAGGACCAGACGGCCTTACAGATGTCTCTGCTCTCCACACAGCTTCACTGAAGGGCCTCAGTGTGATCGATGCTCCCCTCTTTATAATGACAAGCCTTTCCGCAGTGGTGACAATGTTAATGCATTCAACTGTAAGCCTTGCCAGTGCCATGGCCATGCCAGCAGCTGCCACTACGATGCTTCTGTGGACCCATTTCCCCTGGAACACAACAGAGGCGGTGGAGGAGTCTGTGATGACTGTCAGCATCATACAACAGGGAGACACTGTGAGTCGTGCCAGGATTACTTTTACCGACCTGTTGGTGCTGATCCTGCTGCCCCGGATGCTTGCAAGCTCTGTGACTGTAACAGGGCCGGGACTAGAAATGGCAGCCTCCACTGTGACCCGATTGGAGGCCAATGTGATTGTAAGAGACGTGTGTCTGGCAGACAGTGCCTTCAGTGCCAGGATGGATTCTATGACCTGCAGGCGCTAGATCCTGACGGCTGCCGTCCCTGTAACTGTAATCCCTCTGGGACCGTGGATGGAGACATTACCTGTCACCAAAATTCAGGCCAGTGCTCGTGCAAAGCGAATGTTATTGGGCTTAGATGCAATCGCTGCAATTTCGGATTTAAATTCCTCCAGAGTTTTAATGGTGATGGATGTGAGCCTTGCCAATGTAACCTCCACGGCTCAGTGAACCAACTCTGTGATCCGCTTTCTGGGCAGTGTGCATGCAAGAAGGAAGCCAAAGGACTTAAGTGTGACTCTTGCAGAGAAAACTTTTATGGGTTGCCCTGGAGTGCTTGTGAGGTCTGTGACTGCAGCAAGGCTGGGTCCCAGCCTGGGACTGTCTGTGACACTGAGACAGGGCAGTGCGTTTGTAAGCCCAATGTTGGAGGGAGACAATGTAGTCAGTGTAAGGCAGGCTACTTCAACCTATATCAGAATGATTCCCACCTCTGTTTGACTTGTAACTGCGAGAAGATGGGAACGGTAAATGGCTCTCTAAGGTGTGACAAGTCAACCGGGCAGTGTCCTTGCAAACTAGGGGTAACTGGTCTGCGTTGCCACCAGTGCAAGCCTCACAGGTTCAATTTGACGATGGACAATCCTCAAGGTTGTCAGGCGTGCGACTGTGACTCGTTGGGGACATTACCTGGAAGCATGTGTGACCCCATCAGTGGCCAGTGTCTATGTCTACCTCATCGACAAGGAAGAAGGTGTGAGCAGTGTCAGCCAGGCTTTTACAGTTCTCCCAGCAATGCCACTGGCTGCCTGCCATGCTTATGCCACACAGCTGGTGCTGTGAGCCACATCTGTAATAGTGTCACGGGACAGTGCTCTTGCCATGACCCCTCAACCACTGGGCGTAGCTGTCACCAGTGTCAAGAAAGTTACTTTAGATTTGATCCCCTGACTGGAAGATGCAGGCCTTGTCACTGTCATGTAGCAGGAGCCTCGAATGGAACTTGTGATGCAGTCACAGGCCAGTGTTTCTGCAAAGAGTTTGTCACTGGCTCAAAATGTGACACTTGTGTTCCTGGTGCAAGCCACTTGGACGTCAACAATCTATTAGGCTGCAGCAAAACTCCATCTCAGCAACCTCCACCCAGAGGATGGGTTCAGAGTTCTTCTACCATCAATGTGTCCTGGAGTCCACCCGAGTGCCCAAATGCTCACTGGCTTACATACACTCTGTTCAGGAATGGCTCTGAGATCTACACAACTGAAGATGAACACCCGTACTGTTCAGAGCAGTTTGTTGGAAGAATGCAAGATTTTCGATTGTACAATGTGTCACTTACAAACAGGGAGATTCTAGAGGTCTTTTCTGGAGATTTTCCTCACTTGCACATCCAGCCACATTGCCGATGTCCAGGTAGCCACCCCCGTGTCCACCCCTCCGTTCAGCAGTACTGCATTCCCAATGGTGCAGGAGACACGCCCGAGCATCGAATGTCACGGCTGAATCCCGAAGCCCACCCTCTCTCCTTCATCAATGATGACGACGTTGCTACTTCATGGATCTCTCATGTGTTTACAAACATTACGCAGCTCTATGAAGGAGTGGCTATTTCTATAGACTTAGAAAATGGACAGTACCAGGTGCTTAAAGTCATCACCCAGTTCTCCAGCCTACAGCCTGTGGCAATTCGGATCCAGAGGAAGAAGGCAGACAGCTCTCCCTGGGAGGACTGGCAGTATTTTGCCAGAAATTGCAGTGTTTGGGGAATGAAGGACAATGAAGATTTGGAAAATCCCAATTCTGTCAACTGTCTCCAGCTTCCTGATTTTATCCCGTTTTCCCATGGTAATGTCACCTTTGACCTCCTGACATCTGGACAGAAGCATCGTCCTGGGTACAACGACTTTTACAACAGCTCAGTGCTTCAAGAATTCATGAGAGCCACTCAAATAAGGCTGCACTTCCATGGGCAGTACTATCCGGCTGGACACACTGTTGACTGGAGACACCAATACTATGCAGTGGATGAGATCATTGTCAGTGGAAGATGCCAATGCCACGGCCATGCTGAGACCTGTGACAGGACCAGACGGCCTTACAGATGTCTCTGCTCTCCACACAGCTTCACTGAAGGGCCTCAGTGTGATCGATGCTCCCCTCTTTATAATGACAAGCCTTTCCGCAGTGGTGACAATGTTAATGCATTCAACTGTAAGCCTTGCCAGTGCCATGGCCATGCCAGCAGCTGCCACTACGATGCTTCTGTGGACCCATTTCCCCTGGAACACAACAGAGGCGGTGGAGGAGTCTGTGATGACTGTCAGCATCATACAACAGGGAGACACTGTGAGTCGTGCCAGGATTACTTTTACCGACCTGTTGGTGCTGATCCTGCTGCCCCGGATGCTTGCAAGCTCTGTGACTGTAACAGGGCCGGGACTAGAAATGGCAGCCTCCACTGTGACCCGATTGGAGGCCAATGTGATTGTAAGAGACGTGTGTCTGGCAGACAGTGCCTTCAGTGCCAGGATGGATTCTATGACCTGCAGGCGCTAGATCCTGACGGCTGCCGTCCCTGTAACTGTAATCCCTCTGGGACCGTGGATGGAGACATTACCTGTCACCAAAATTCAGGCCAGTGCTCGTGCAAAGCGAATGTTATTGGGCTTAGATGCAATCGCTGCAATTTCGGATTTAAATTCCTCCAGAGTTTTAATGGTGATGGATGTGAGCCTTGCCAATGTAACCTCCACGGCTCAGTGAACCAACTCTGTGATCCGCTTTCTGGGCAGTGTGCATGCAAGAAGGAAGCCAAAGGACTTAAGTGTGACTCTTGCAGAGAAAACTTTTATGGGTTGCCCTGGAGTGCTTGTGAGGTCTGTGACTGCAGCAAGGCTGGGTCCCAGCCTGGGACTGTCTGTGACACTGAGACAGGGCAGTGCGTTTGTAAGCCCAATGTTGGAGGGAGACAATGTAGTCAGTGTAAGGCAGGCTACTTCAACCTATATCAGAATGATTCCCACCTCTGTTTGACTTGTAACTGCGAGAAGATGGGAACGGTAAATGGCTCTCTAAGGTGTGACAAGTCAACCGGGCAGTGTCCTTGCAAACTAGGGGTAACTGGTCTGCGTTGCCACCAGTGCAAGCCTCACAGGTTCAATTTGACGATGGACAATCCTCAAGGTTGTCAGGCGTGCGACTGTGACTCGTTGGGGACATTACCTGGAAGCATGTGTGACCCCATCAGTGGCCAGTGTCTATGTCTACCTCATCGACAAGGAAGAAGGTGTGAGCAGTGTCAGCCAGGCTTTTACAGTTCTCCCAGCAATGCCACTGGCTGCCTGCCATGCTTATGCCACACAGCTGGTGCTGTGAGCCACATCTGTAATAGTGTCACGGGACAGTGCTCTTGCCATGACCCCTCAACCACTGGGCGTAGCTGTCACCAGTGTCAAGAAAGTTACTTTAGATTTGATCCCCTGACTGGAAGATGCAGGCCTTGTCACTGTCATGTAGCAGGAGCCTCGAATGGAACTTGTGATGCAGTCACAGGCCAGTGTTTCTGCAAAGAGTTTGTCACTGGCTCAAAATGTGACACTTGTGTTCCTGGTGCAAGCCACTTGGACGTCAACAATCTATTAGGCTGCAGCAAAACTCCATCTCAGCAACCTCCACCCAGAGGATGGGTTCAGAGTTCTTCTACCATCAATGTGTCCTGGAGTCCACCCGAGTGCCCAAATGCTCACTGGCTTACATACACTCTGTTCAGGAATGGCTCTGAGATCTACACAACTGAAGATGAACACCCGTAC
Peptide sequence:
MQDFRLYNVSLTNREILEVFSGDFPHLHIQPHCRCPGSHPRVHPSVQQYCIPNGAGDTPEHRMSRLNPEAHPLSFINDDDVATSWISHVFTNITQLYEGVAISIDLENGQYQVLKVITQFSSLQPVAIRIQRKKADSSPWEDWQYFARNCSVWGMKDNEDLENPNSVNCLQLPDFIPFSHGNVTFDLLTSGQKHRPGYNDFYNSSVLQEFMRATQIRLHFHGQYYPAGHTVDWRHQYYAVDEIIVSGRCQCHGHAETCDRTRRPYRCLCSPHSFTEGPQCDRCSPLYNDKPFRSGDNVNAFNCKPCQCHGHASSCHYDASVDPFPLEHNRGGGGVCDDCQHHTTGRHCESCQDYFYRPVGADPAAPDACKLCDCNRAGTRNGSLHCDPIGGQCDCKRRVSGRQCLQCQDGFYDLQALDPDGCRPCNCNPSGTVDGDITCHQNSGQCSCKANVIGLRCNRCNFGFKFLQSFNGDGCEPCQCNLHGSVNQLCDPLSGQCACKKEAKGLKCDSCRENFYGLPWSACEVCDCSKAGSQPGTVCDTETGQCVCKPNVGGRQCSQCKAGYFNLYQNDSHLCLTCNCEKMGTVNGSLRCDKSTGQCPCKLGVTGLRCHQCKPHRFNLTMDNPQGCQACDCDSLGTLPGSMCDPISGQCLCLPHRQGRRCEQCQPGFYSSPSNATGCLPCLCHTAGAVSHICNSVTGQCSCHDPSTTGRSCHQCQESYFRFDPLTGRCRPCHCHVAGASNGTCDAVTGQCFCKEFVTGSKCDTCVPGASHLDVNNLLGCSKTPSQQPPPRGWVQSSSTINVSWSPPECPNAHWLTYTLFRNGSEIYTTEDEHPYCSEQFVGRMQDFRLYNVSLTNREILEVFSGDFPHLHIQPHCRCPGSHPRVHPSVQQYCIPNGAGDTPEHRMSRLNPEAHPLSFINDDDVATSWISHVFTNITQLYEGVAISIDLENGQYQVLKVITQFSSLQPVAIRIQRKKADSSPWEDWQYFARNCSVWGMKDNEDLENPNSVNCLQLPDFIPFSHGNVTFDLLTSGQKHRPGYNDFYNSSVLQEFMRATQIRLHFHGQYYPAGHTVDWRHQYYAVDEIIVSGRCQCHGHAETCDRTRRPYRCLCSPHSFTEGPQCDRCSPLYNDKPFRSGDNVNAFNCKPCQCHGHASSCHYDASVDPFPLEHNRGGGGVCDDCQHHTTGRHCESCQDYFYRPVGADPAAPDACKLCDCNRAGTRNGSLHCDPIGGQCDCKRRVSGRQCLQCQDGFYDLQALDPDGCRPCNCNPSGTVDGDITCHQNSGQCSCKANVIGLRCNRCNFGFKFLQSFNGDGCEPCQCNLHGSVNQLCDPLSGQCACKKEAKGLKCDSCRENFYGLPWSACEVCDCSKAGSQPGTVCDTETGQCVCKPNVGGRQCSQCKAGYFNLYQNDSHLCLTCNCEKMGTVNGSLRCDKSTGQCPCKLGVTGLRCHQCKPHRFNLTMDNPQGCQACDCDSLGTLPGSMCDPISGQCLCLPHRQGRRCEQCQPGFYSSPSNATGCLPCLCHTAGAVSHICNSVTGQCSCHDPSTTGRSCHQCQESYFRFDPLTGRCRPCHCHVAGASNGTCDAVTGQCFCKEFVTGSKCDTCVPGASHLDVNNLLGCSKTPSQQPPPRGWVQSSSTINVSWSPPECPNAHWLTYTLFRNGSEIYTTEDEHPY
IRESfinder result
IRESfinder score
0.528978084
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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