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mmu_circUsh2a_2442
Basic information of circular RNA
PanCircBase ID:
mmu_circUsh2a_2442
mm39_Chr. Position ID:
chr1|188131937|188198537|+
Gene name:
Ush2a
Transcript:
ENSMUST00000060479.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
12,13,14,15,16,17,18,19,20
Exon/intron offsets:
0,15937,30966,37071,43273,44702,46956,51993,66378
Genomic length:
66600
Exon/intron sizes in nt:
64,21,84,16,41,59,49,50,00,00,00,00,000
Flanking exon/introns:
chr1:188128147-188131937|chr1:188198537-188255524
Splice length:
2442
Other database IDs:
circAtlas: mmu-Ush2a_0049
Human Ortholog IDs:
Mature spliced Sequence:
GGCTTAGATGCAATCGCTGCAATTTCGGATTTAAATTCCTCCAGAGTTTTAATGGTGATGGATGTGAGCCTTGCCAATGTAACCTCCACGGCTCAGTGAACCAACTCTGTGATCCGCTTTCTGGGCAGTGTGCATGCAAGAAGGAAGCCAAAGGACTTAAGTGTGACTCTTGCAGAGAAAACTTTTATGGGTTGCCCTGGAGTGCTTGTGAGGTCTGTGACTGCAGCAAGGCTGGGTCCCAGCCTGGGACTGTCTGTGACACTGAGACAGGGCAGTGCGTTTGTAAGCCCAATGTTGGAGGGAGACAATGTAGTCAGTGTAAGGCAGGCTACTTCAACCTATATCAGAATGATTCCCACCTCTGTTTGACTTGTAACTGCGAGAAGATGGGAACGGTAAATGGCTCTCTAAGGTGTGACAAGTCAACCGGGCAGTGTCCTTGCAAACTAGGGGTAACTGGTCTGCGTTGCCACCAGTGCAAGCCTCACAGGTTCAATTTGACGATGGACAATCCTCAAGGTTGTCAGGCGTGCGACTGTGACTCGTTGGGGACATTACCTGGAAGCATGTGTGACCCCATCAGTGGCCAGTGTCTATGTCTACCTCATCGACAAGGAAGAAGGTGTGAGCAGTGTCAGCCAGGCTTTTACAGTTCTCCCAGCAATGCCACTGGCTGCCTGCCATGCTTATGCCACACAGCTGGTGCTGTGAGCCACATCTGTAATAGTGTCACGGGACAGTGCTCTTGCCATGACCCCTCAACCACTGGGCGTAGCTGTCACCAGTGTCAAGAAAGTTACTTTAGATTTGATCCCCTGACTGGAAGATGCAGGCCTTGTCACTGTCATGTAGCAGGAGCCTCGAATGGAACTTGTGATGCAGTCACAGGCCAGTGTTTCTGCAAAGAGTTTGTCACTGGCTCAAAATGTGACACTTGTGTTCCTGGTGCAAGCCACTTGGACGTCAACAATCTATTAGGCTGCAGCAAAACTCCATCTCAGCAACCTCCACCCAGAGGATGGGTTCAGAGTTCTTCTACCATCAATGTGTCCTGGAGTCCACCCGAGTGCCCAAATGCTCACTGGCTTACATACACTCTGTTCAGGAATGGCTCTGAGATCTACACAACTGAAGATGAACACCCGTACTATACTCAGTACTTCTTAGACACTAGTCTGTCACCACACACAGCATATTCATATTATATAGAGACCTCCAATGTGCACAGTTCGACAAGGAGCATACCTGTCATTTATGAGACAAAGCCAGAGGTCTCAGAAGGACACTTGAACTTGACTCACATCATTCCTGTGGGCTCGGACTCCATTACACTTACCTGGACTGGACTCTCCAACAGCTCTGATCCTGTGGCAAAATATGTTTTATCATGCACACCTGTGGACAGCACTGAGCCCTGTGTCTCCTATGAAGGTCCAGAAACCTCAGCTACCATCTGGAATCTGGTTCCATTCACCCAGTACTGTTTTTCTGTCCAGGGCTGTACTAATGAGAGCTGTTTCTACAGCTTGCCTATTATAGTAACCACAGCCCAAGCACCTCCTCAAACGCAGGGGCCACCTACAGTATGGAAAATCAGTCCCACAGAACTCAGAATAGAATGGTCTCCTCCAGTGGACTCAAATGGTATAATTATAAGCTATGAGTTATACATGAGGAGATGGCTGTCCACCGAAGAAAGCCTAGTGTTTGAGAGCCACGGTTTGGTCAGTTCTCACTCAGCTTTACAGTCGGTCAATCCGAGTAAGAACCTGCTCCAGCAGCCCCAAGCCAGCACGTTCATCTCTGGCTTGGAGCCACACACAGAGTATGCATTTAGGGTCTTGGCTGTGAATATGGCTGGCAGGGTGTCGTCTGCCTGGGCCTCAGAAAGAACGGGGGAATCAGTACCCGTATTCATGGCCCCTCCTTCAGTCTCTCCACTCTCACCACACTCCCTCAGTGTCTCCTGGGAGAAGCCAGCAGAAAACTTTACAAGAGGAGAAATTATAGGGTACAAGATCAGCATGGTTTCTGAACATTTCCCTCTACACGATGTTCCAGTCATGTGCTCAAAGATGGTGCATTTTGCTAAGTCCCAAGACCAGTCTTACATCGTAAGGGGACTCGAGCCTTATAGGACCTACAGCTTCACAGTGTCCCTCTGCGATTCCGTGGGCTGTGTAACCAGTGCTTTGGGATCAGGACAAACCTTAGCAGCAGCTCCTGCTCAGCTCCGGCCTCCCATGGTGACAGGAGTCAACAGTACTACAGTCCATATCAGGTGGCTTCCTCCTGCAGGAGTCAATGGACCACCTCCTTTGTACCATCTAGAAAGGAAGAAGTCTTCCCTCCCAGCTGCCACAGCTGCTGTGACAAAGGGAACCCGCTTCGTGGGACACGGTTACTGCAGGTTTCCCAGAACAGCTCACGCAGATTTTATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTGCTGTGACAAAGGGAA
59.82
AGCCGTGGAGGTTACATTGG
60.04
173
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTGCTGTGACAAAGGGAA
59.82
TTGGCAAGGCTCACATCCAT
59.96
157
PCR template sequence:
TCTTCCCTCCCAGCTGCCACAGCTGCTGTGACAAAGGGAACCCGCTTCGTGGGACACGGTTACTGCAGGTTTCCCAGAACAGCTCACGCAGATTTTATAGGGCTTAGATGCAATCGCTGCAATTTCGGATTTAAATTCCTCCAGAGTTTTAATGGTGATGGATGTGAGCCTTGCCAATGTAACCTCCACGGCTCAGTGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
30
Interacting miRNAs (#binding sites)
mmu-miR-673-5p(3), mmu-miR-146a-5p(2), mmu-miR-574-5p(2), mmu-miR-23b-3p(1), mmu-miR-134-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-7b-5p(1), mmu-miR-221-3p(1), mmu-miR-31-5p(1), mmu-miR-101a-3p(1), mmu-miR-122-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-29a-3p(1), mmu-miR-298-5p(1), mmu-miR-217-5p(1), mmu-miR-7a-5p(1), mmu-miR-203-3p(1), mmu-miR-320-3p(1), mmu-miR-23a-3p(1), mmu-miR-143-3p(1), mmu-miR-24-3p(1), mmu-miR-382-3p(1), mmu-miR-182-5p(1), mmu-miR-324-3p(1), mmu-miR-297a-5p(1), mmu-miR-484(1), mmu-miR-1904(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCAGATTTTATAGGGCTTAGATGCAA
siRNA sets
TAAGCCCTATAAAATCTGC, CTAAGCCCTATAAAATCTG, ATCTAAGCCCTATAAAATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSH2A_2442_ORF_1
0.7251
0.012226337
1
4497
ORF sequence:
ATGGGAACGGTAAATGGCTCTCTAAGGTGTGACAAGTCAACCGGGCAGTGTCCTTGCAAACTAGGGGTAACTGGTCTGCGTTGCCACCAGTGCAAGCCTCACAGGTTCAATTTGACGATGGACAATCCTCAAGGTTGTCAGGCGTGCGACTGTGACTCGTTGGGGACATTACCTGGAAGCATGTGTGACCCCATCAGTGGCCAGTGTCTATGTCTACCTCATCGACAAGGAAGAAGGTGTGAGCAGTGTCAGCCAGGCTTTTACAGTTCTCCCAGCAATGCCACTGGCTGCCTGCCATGCTTATGCCACACAGCTGGTGCTGTGAGCCACATCTGTAATAGTGTCACGGGACAGTGCTCTTGCCATGACCCCTCAACCACTGGGCGTAGCTGTCACCAGTGTCAAGAAAGTTACTTTAGATTTGATCCCCTGACTGGAAGATGCAGGCCTTGTCACTGTCATGTAGCAGGAGCCTCGAATGGAACTTGTGATGCAGTCACAGGCCAGTGTTTCTGCAAAGAGTTTGTCACTGGCTCAAAATGTGACACTTGTGTTCCTGGTGCAAGCCACTTGGACGTCAACAATCTATTAGGCTGCAGCAAAACTCCATCTCAGCAACCTCCACCCAGAGGATGGGTTCAGAGTTCTTCTACCATCAATGTGTCCTGGAGTCCACCCGAGTGCCCAAATGCTCACTGGCTTACATACACTCTGTTCAGGAATGGCTCTGAGATCTACACAACTGAAGATGAACACCCGTACTATACTCAGTACTTCTTAGACACTAGTCTGTCACCACACACAGCATATTCATATTATATAGAGACCTCCAATGTGCACAGTTCGACAAGGAGCATACCTGTCATTTATGAGACAAAGCCAGAGGTCTCAGAAGGACACTTGAACTTGACTCACATCATTCCTGTGGGCTCGGACTCCATTACACTTACCTGGACTGGACTCTCCAACAGCTCTGATCCTGTGGCAAAATATGTTTTATCATGCACACCTGTGGACAGCACTGAGCCCTGTGTCTCCTATGAAGGTCCAGAAACCTCAGCTACCATCTGGAATCTGGTTCCATTCACCCAGTACTGTTTTTCTGTCCAGGGCTGTACTAATGAGAGCTGTTTCTACAGCTTGCCTATTATAGTAACCACAGCCCAAGCACCTCCTCAAACGCAGGGGCCACCTACAGTATGGAAAATCAGTCCCACAGAACTCAGAATAGAATGGTCTCCTCCAGTGGACTCAAATGGTATAATTATAAGCTATGAGTTATACATGAGGAGATGGCTGTCCACCGAAGAAAGCCTAGTGTTTGAGAGCCACGGTTTGGTCAGTTCTCACTCAGCTTTACAGTCGGTCAATCCGAGTAAGAACCTGCTCCAGCAGCCCCAAGCCAGCACGTTCATCTCTGGCTTGGAGCCACACACAGAGTATGCATTTAGGGTCTTGGCTGTGAATATGGCTGGCAGGGTGTCGTCTGCCTGGGCCTCAGAAAGAACGGGGGAATCAGTACCCGTATTCATGGCCCCTCCTTCAGTCTCTCCACTCTCACCACACTCCCTCAGTGTCTCCTGGGAGAAGCCAGCAGAAAACTTTACAAGAGGAGAAATTATAGGGTACAAGATCAGCATGGTTTCTGAACATTTCCCTCTACACGATGTTCCAGTCATGTGCTCAAAGATGGTGCATTTTGCTAAGTCCCAAGACCAGTCTTACATCGTAAGGGGACTCGAGCCTTATAGGACCTACAGCTTCACAGTGTCCCTCTGCGATTCCGTGGGCTGTGTAACCAGTGCTTTGGGATCAGGACAAACCTTAGCAGCAGCTCCTGCTCAGCTCCGGCCTCCCATGGTGACAGGAGTCAACAGTACTACAGTCCATATCAGGTGGCTTCCTCCTGCAGGAGTCAATGGACCACCTCCTTTGTACCATCTAGAAAGGAAGAAGTCTTCCCTCCCAGCTGCCACAGCTGCTGTGACAAAGGGAACCCGCTTCGTGGGACACGGTTACTGCAGGTTTCCCAGAACAGCTCACGCAGATTTTATAGGGCTTAGATGCAATCGCTGCAATTTCGGATTTAAATTCCTCCAGAGTTTTAATGGTGATGGATGTGAGCCTTGCCAATGTAACCTCCACGGCTCAGTGAACCAACTCTGTGATCCGCTTTCTGGGCAGTGTGCATGCAAGAAGGAAGCCAAAGGACTTAAGTGTGACTCTTGCAGAGAAAACTTTTATGGGTTGCCCTGGAGTGCTTGTGAGGTCTGTGACTGCAGCAAGGCTGGGTCCCAGCCTGGGACTGTCTGTGACACTGAGACAGGGCAGTGCGTTTGTAAGCCCAATGTTGGAGGGAGACAATGTAGTCAGTGTAAGGCAGGCTACTTCAACCTATATCAGAATGATTCCCACCTCTGTTTGACTTGTAACTGCGAGAAGATGGGAACGGTAAATGGCTCTCTAAGGTGTGACAAGTCAACCGGGCAGTGTCCTTGCAAACTAGGGGTAACTGGTCTGCGTTGCCACCAGTGCAAGCCTCACAGGTTCAATTTGACGATGGACAATCCTCAAGGTTGTCAGGCGTGCGACTGTGACTCGTTGGGGACATTACCTGGAAGCATGTGTGACCCCATCAGTGGCCAGTGTCTATGTCTACCTCATCGACAAGGAAGAAGGTGTGAGCAGTGTCAGCCAGGCTTTTACAGTTCTCCCAGCAATGCCACTGGCTGCCTGCCATGCTTATGCCACACAGCTGGTGCTGTGAGCCACATCTGTAATAGTGTCACGGGACAGTGCTCTTGCCATGACCCCTCAACCACTGGGCGTAGCTGTCACCAGTGTCAAGAAAGTTACTTTAGATTTGATCCCCTGACTGGAAGATGCAGGCCTTGTCACTGTCATGTAGCAGGAGCCTCGAATGGAACTTGTGATGCAGTCACAGGCCAGTGTTTCTGCAAAGAGTTTGTCACTGGCTCAAAATGTGACACTTGTGTTCCTGGTGCAAGCCACTTGGACGTCAACAATCTATTAGGCTGCAGCAAAACTCCATCTCAGCAACCTCCACCCAGAGGATGGGTTCAGAGTTCTTCTACCATCAATGTGTCCTGGAGTCCACCCGAGTGCCCAAATGCTCACTGGCTTACATACACTCTGTTCAGGAATGGCTCTGAGATCTACACAACTGAAGATGAACACCCGTACTATACTCAGTACTTCTTAGACACTAGTCTGTCACCACACACAGCATATTCATATTATATAGAGACCTCCAATGTGCACAGTTCGACAAGGAGCATACCTGTCATTTATGAGACAAAGCCAGAGGTCTCAGAAGGACACTTGAACTTGACTCACATCATTCCTGTGGGCTCGGACTCCATTACACTTACCTGGACTGGACTCTCCAACAGCTCTGATCCTGTGGCAAAATATGTTTTATCATGCACACCTGTGGACAGCACTGAGCCCTGTGTCTCCTATGAAGGTCCAGAAACCTCAGCTACCATCTGGAATCTGGTTCCATTCACCCAGTACTGTTTTTCTGTCCAGGGCTGTACTAATGAGAGCTGTTTCTACAGCTTGCCTATTATAGTAACCACAGCCCAAGCACCTCCTCAAACGCAGGGGCCACCTACAGTATGGAAAATCAGTCCCACAGAACTCAGAATAGAATGGTCTCCTCCAGTGGACTCAAATGGTATAATTATAAGCTATGAGTTATACATGAGGAGATGGCTGTCCACCGAAGAAAGCCTAGTGTTTGAGAGCCACGGTTTGGTCAGTTCTCACTCAGCTTTACAGTCGGTCAATCCGAGTAAGAACCTGCTCCAGCAGCCCCAAGCCAGCACGTTCATCTCTGGCTTGGAGCCACACACAGAGTATGCATTTAGGGTCTTGGCTGTGAATATGGCTGGCAGGGTGTCGTCTGCCTGGGCCTCAGAAAGAACGGGGGAATCAGTACCCGTATTCATGGCCCCTCCTTCAGTCTCTCCACTCTCACCACACTCCCTCAGTGTCTCCTGGGAGAAGCCAGCAGAAAACTTTACAAGAGGAGAAATTATAGGGTACAAGATCAGCATGGTTTCTGAACATTTCCCTCTACACGATGTTCCAGTCATGTGCTCAAAGATGGTGCATTTTGCTAAGTCCCAAGACCAGTCTTACATCGTAAGGGGACTCGAGCCTTATAGGACCTACAGCTTCACAGTGTCCCTCTGCGATTCCGTGGGCTGTGTAACCAGTGCTTTGGGATCAGGACAAACCTTAGCAGCAGCTCCTGCTCAGCTCCGGCCTCCCATGGTGACAGGAGTCAACAGTACTACAGTCCATATCAGGTGGCTTCCTCCTGCAGGAGTCAATGGACCACCTCCTTTGTACCATCTAGAAAGGAAGAAGTCTTCCCTCCCAGCTGCCACAGCTGCTGTGACAAAGGGAACCCGCTTCGTGGGACACGGTTACTGCAGGTTTCCCAGAACAGCTCACGCAGATTTTATA
Peptide sequence:
MGTVNGSLRCDKSTGQCPCKLGVTGLRCHQCKPHRFNLTMDNPQGCQACDCDSLGTLPGSMCDPISGQCLCLPHRQGRRCEQCQPGFYSSPSNATGCLPCLCHTAGAVSHICNSVTGQCSCHDPSTTGRSCHQCQESYFRFDPLTGRCRPCHCHVAGASNGTCDAVTGQCFCKEFVTGSKCDTCVPGASHLDVNNLLGCSKTPSQQPPPRGWVQSSSTINVSWSPPECPNAHWLTYTLFRNGSEIYTTEDEHPYYTQYFLDTSLSPHTAYSYYIETSNVHSSTRSIPVIYETKPEVSEGHLNLTHIIPVGSDSITLTWTGLSNSSDPVAKYVLSCTPVDSTEPCVSYEGPETSATIWNLVPFTQYCFSVQGCTNESCFYSLPIIVTTAQAPPQTQGPPTVWKISPTELRIEWSPPVDSNGIIISYELYMRRWLSTEESLVFESHGLVSSHSALQSVNPSKNLLQQPQASTFISGLEPHTEYAFRVLAVNMAGRVSSAWASERTGESVPVFMAPPSVSPLSPHSLSVSWEKPAENFTRGEIIGYKISMVSEHFPLHDVPVMCSKMVHFAKSQDQSYIVRGLEPYRTYSFTVSLCDSVGCVTSALGSGQTLAAAPAQLRPPMVTGVNSTTVHIRWLPPAGVNGPPPLYHLERKKSSLPAATAAVTKGTRFVGHGYCRFPRTAHADFIGLRCNRCNFGFKFLQSFNGDGCEPCQCNLHGSVNQLCDPLSGQCACKKEAKGLKCDSCRENFYGLPWSACEVCDCSKAGSQPGTVCDTETGQCVCKPNVGGRQCSQCKAGYFNLYQNDSHLCLTCNCEKMGTVNGSLRCDKSTGQCPCKLGVTGLRCHQCKPHRFNLTMDNPQGCQACDCDSLGTLPGSMCDPISGQCLCLPHRQGRRCEQCQPGFYSSPSNATGCLPCLCHTAGAVSHICNSVTGQCSCHDPSTTGRSCHQCQESYFRFDPLTGRCRPCHCHVAGASNGTCDAVTGQCFCKEFVTGSKCDTCVPGASHLDVNNLLGCSKTPSQQPPPRGWVQSSSTINVSWSPPECPNAHWLTYTLFRNGSEIYTTEDEHPYYTQYFLDTSLSPHTAYSYYIETSNVHSSTRSIPVIYETKPEVSEGHLNLTHIIPVGSDSITLTWTGLSNSSDPVAKYVLSCTPVDSTEPCVSYEGPETSATIWNLVPFTQYCFSVQGCTNESCFYSLPIIVTTAQAPPQTQGPPTVWKISPTELRIEWSPPVDSNGIIISYELYMRRWLSTEESLVFESHGLVSSHSALQSVNPSKNLLQQPQASTFISGLEPHTEYAFRVLAVNMAGRVSSAWASERTGESVPVFMAPPSVSPLSPHSLSVSWEKPAENFTRGEIIGYKISMVSEHFPLHDVPVMCSKMVHFAKSQDQSYIVRGLEPYRTYSFTVSLCDSVGCVTSALGSGQTLAAAPAQLRPPMVTGVNSTTVHIRWLPPAGVNGPPPLYHLERKKSSLPAATAAVTKGTRFVGHGYCRFPRTAHADFI
IRESfinder result
IRESfinder score
0.613377003
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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