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mmu_circDmxl1_1883
Basic information of circular RNA
PanCircBase ID:
mmu_circDmxl1_1883
mm39_Chr. Position ID:
chr18|50013801|50027364|+
Gene name:
Dmxl1
Transcript:
ENSMUST00000180611.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
19,20,21,22,23,24
Exon/intron offsets:
0,7981,8728,9881,10656,12484
Genomic length:
13563
Exon/intron sizes in nt:
1,08,17,09,81,66,26,21,000
Flanking exon/introns:
chr18:50012432-50013801|chr18:50027364-50028048
Splice length:
1883
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGGGGAAACTCTAGACGAGTGCGGATTAAAGTTTCTTTTGGCTGTTCGACTCCATACCTTTCTTACAACTTCCCTTCCAGCCTACCGAGCTCAACTCCTTCACCAAGGCCTTTCTACTGGTCATTTTGCTTGGGCTTTTCATTCAGTAGCAGAGGAAGAACTACTGAATATGTTGCCGGCCATGCAGAAAGATGATCCAACTTGGTCTGAACTGAGAGCAATGGGTGTGGGGTGGTGGGTTCGCAATGCTCGCATCCTGCGCAGATGCATAGAAAAAGTAGCCAAAGCAGCCTTTCATAGAAATAATGATCCTTTAGATGCTGCAATTTTTTACCTTGCAATGAAAAAAAAAGCTGTGATTTGGGGATTATATAGATCTCAAAAAGACACCAAAATGACACAGTTTTTTGGGCACAATTTTGAGGAAGAGAGGTGGCGTAAAGCAGCTTTGAAAAATGCCTTTTCTTTATTAGGCAAGCAAAGGTTTGAACATTCTGCAGCATTTTTTCTTCTAGGTGGTTGCCTCAAAGATGCAATTGAGGTATGTCTTGAGAAACTGAATGACATTCAGTTGGCTCTTGTAATAGCAAGACTATTTGAATCTGAATTTGATAAGTCAGCAACATACAAGTCTATTTTACGCAAAAAAGTTTTGGGAATTGGTTCTCCAGCCAGTGAGCTCAGTTCGTCAAGCATAAATGCACATCATGACCCCTTTCTTCGGAGTATGGCACATTGGATTTTAGAAGATTATAGTGCTGCTCTGGAAACATTAATAAAGCAACCAGTTACAGAGGATGAAGATCAAGTCATGATGTCAGCCTGTAATCCTATAGTTTTTAATTTCTACAATTACCTAAGAACACATCCTCTTTTGCTAAGAAGACATTTTGGATCATCATCGGAAACATTTTCAACACACATGACTTTAGCAGGAAAAAGTGGACTGGCAGGAACAATTAATCTAAGTGAAAGAAGATTATTTTTTACTACTGCTAGTGCTCACCTAAAAGCTGGCTGCCCAATGTTGGCTTTGGAAGTATTGTCAAAGATGCCCAAAGTCAGTAAGAAAGCAAAACCGTGTTGTAGAGGATCTAGTTTTTTAACTAGTAAAGATTCTTCACTAAAATTGGATGTAAGAGAAGACAAGTGTTGTGCTGCTGACTGGTCACCGTCGCTGACAAATGGTCTTGAATCTTCTTCAGAGGGTTCCTCAGAGAGGCACTCACATTCTACCCTTTCTTTTGATTGGAGCCAACCGAGTGTGGTATTTCAAGATGACTCTTTGGAGTTGAAATGGGATAGTGATAATGATGAAGAAAATGAAGATCCCCCTATTTCAATGAAAGAAATAAGACCTTTGCAGAGAAAGACAGTTAAAGAAATAGATGAATTGAGCAGTTACACAGACTCTTTAAGCACACTAGATGAAAATGACATTTTAAATCCATCAGAAGATATAATTGCTGTTCAACTAAAATTTAGAGCATGTTTGAAGATTCTCACCGTAGAACTTCGTACTTTATCTACTGGCTATGAAATAGATGGTGGGAAATTGCGTTACCAACTCTACCACTGGCTTGAGAAAGAGGTAGTAGCTCTTCAGAGGACTTGTGACTTTTGCTCAGACGCAGACCAGCTGCAGACCACATTTAGCCAGAGTGCAGATGAATCTGGATCAACTGAGGATGCTGATGATTTGCATCACCAAACAAAAGTGAAACAACTGAGAGAAAGTTTCCAGGAAAAAAGGCAGTGGCTCTTGAAATATCAGTCACTCTTAAGAATGTTTCTTAGTTACTGTGTGCTTCATGGCTCTCATGGTGGGGGTCTTGCATCAGTGAGAATGGAATTAATTTTACTTTTGCAAGAATCTCAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCTCATGGTGGGGGTCTTG
59.75
GAGTTGAGCTCGGTAGGCTG
60.18
165
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGGGTCTTGCATCAGTGAG
60.39
GAGTTGAGCTCGGTAGGCTG
60.18
155
PCR template sequence:
AAGAATGTTTCTTAGTTACTGTGTGCTTCATGGCTCTCATGGTGGGGGTCTTGCATCAGTGAGAATGGAATTAATTTTACTTTTGCAAGAATCTCAGCAGGTGGGGAAACTCTAGACGAGTGCGGATTAAAGTTTCTTTTGGCTGTTCGACTCCATACCTTTCTTACAACTTCCCTTCCAGCCTACCGAGCTCAACTCCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
23
Interacting miRNAs (#binding sites)
mmu-miR-322-5p(3), mmu-miR-16-5p(2), mmu-miR-15a-5p(2), mmu-miR-15b-5p(2), mmu-miR-134-5p(1), mmu-miR-103-3p(1), mmu-miR-223-3p(1), mmu-miR-181b-5p(1), mmu-miR-433-3p(1), mmu-miR-433-5p(1), mmu-miR-351-5p(1), mmu-miR-107-3p(1), mmu-miR-224-5p(1), mmu-miR-680(1), mmu-miR-802-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-1198-5p(1), mmu-miR-466p-5p(1), mmu-miR-129-5p(1), mmu-miR-5101(1), mmu-miR-335-3p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAATCTCAGCAGGTGGGGAAACTCT
siRNA sets
AGAGTTTCCCCACCTGCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDMXL1_1883_ORF_1
0.7458
-0.093513096
0.999709403
1728
ORF sequence:
ATGTTGCCGGCCATGCAGAAAGATGATCCAACTTGGTCTGAACTGAGAGCAATGGGTGTGGGGTGGTGGGTTCGCAATGCTCGCATCCTGCGCAGATGCATAGAAAAAGTAGCCAAAGCAGCCTTTCATAGAAATAATGATCCTTTAGATGCTGCAATTTTTTACCTTGCAATGAAAAAAAAAGCTGTGATTTGGGGATTATATAGATCTCAAAAAGACACCAAAATGACACAGTTTTTTGGGCACAATTTTGAGGAAGAGAGGTGGCGTAAAGCAGCTTTGAAAAATGCCTTTTCTTTATTAGGCAAGCAAAGGTTTGAACATTCTGCAGCATTTTTTCTTCTAGGTGGTTGCCTCAAAGATGCAATTGAGGTATGTCTTGAGAAACTGAATGACATTCAGTTGGCTCTTGTAATAGCAAGACTATTTGAATCTGAATTTGATAAGTCAGCAACATACAAGTCTATTTTACGCAAAAAAGTTTTGGGAATTGGTTCTCCAGCCAGTGAGCTCAGTTCGTCAAGCATAAATGCACATCATGACCCCTTTCTTCGGAGTATGGCACATTGGATTTTAGAAGATTATAGTGCTGCTCTGGAAACATTAATAAAGCAACCAGTTACAGAGGATGAAGATCAAGTCATGATGTCAGCCTGTAATCCTATAGTTTTTAATTTCTACAATTACCTAAGAACACATCCTCTTTTGCTAAGAAGACATTTTGGATCATCATCGGAAACATTTTCAACACACATGACTTTAGCAGGAAAAAGTGGACTGGCAGGAACAATTAATCTAAGTGAAAGAAGATTATTTTTTACTACTGCTAGTGCTCACCTAAAAGCTGGCTGCCCAATGTTGGCTTTGGAAGTATTGTCAAAGATGCCCAAAGTCAGTAAGAAAGCAAAACCGTGTTGTAGAGGATCTAGTTTTTTAACTAGTAAAGATTCTTCACTAAAATTGGATGTAAGAGAAGACAAGTGTTGTGCTGCTGACTGGTCACCGTCGCTGACAAATGGTCTTGAATCTTCTTCAGAGGGTTCCTCAGAGAGGCACTCACATTCTACCCTTTCTTTTGATTGGAGCCAACCGAGTGTGGTATTTCAAGATGACTCTTTGGAGTTGAAATGGGATAGTGATAATGATGAAGAAAATGAAGATCCCCCTATTTCAATGAAAGAAATAAGACCTTTGCAGAGAAAGACAGTTAAAGAAATAGATGAATTGAGCAGTTACACAGACTCTTTAAGCACACTAGATGAAAATGACATTTTAAATCCATCAGAAGATATAATTGCTGTTCAACTAAAATTTAGAGCATGTTTGAAGATTCTCACCGTAGAACTTCGTACTTTATCTACTGGCTATGAAATAGATGGTGGGAAATTGCGTTACCAACTCTACCACTGGCTTGAGAAAGAGGTAGTAGCTCTTCAGAGGACTTGTGACTTTTGCTCAGACGCAGACCAGCTGCAGACCACATTTAGCCAGAGTGCAGATGAATCTGGATCAACTGAGGATGCTGATGATTTGCATCACCAAACAAAAGTGAAACAACTGAGAGAAAGTTTCCAGGAAAAAAGGCAGTGGCTCTTGAAATATCAGTCACTCTTAAGAATGTTTCTTAGTTACTGTGTGCTTCATGGCTCTCATGGTGGGGGTCTTGCATCAGTGAGAATGGAATTAATTTTACTTTTGCAAGAATCTCAGCAGGTGGGGAAACTCTAG
Peptide sequence:
MLPAMQKDDPTWSELRAMGVGWWVRNARILRRCIEKVAKAAFHRNNDPLDAAIFYLAMKKKAVIWGLYRSQKDTKMTQFFGHNFEEERWRKAALKNAFSLLGKQRFEHSAAFFLLGGCLKDAIEVCLEKLNDIQLALVIARLFESEFDKSATYKSILRKKVLGIGSPASELSSSSINAHHDPFLRSMAHWILEDYSAALETLIKQPVTEDEDQVMMSACNPIVFNFYNYLRTHPLLLRRHFGSSSETFSTHMTLAGKSGLAGTINLSERRLFFTTASAHLKAGCPMLALEVLSKMPKVSKKAKPCCRGSSFLTSKDSSLKLDVREDKCCAADWSPSLTNGLESSSEGSSERHSHSTLSFDWSQPSVVFQDDSLELKWDSDNDEENEDPPISMKEIRPLQRKTVKEIDELSSYTDSLSTLDENDILNPSEDIIAVQLKFRACLKILTVELRTLSTGYEIDGGKLRYQLYHWLEKEVVALQRTCDFCSDADQLQTTFSQSADESGSTEDADDLHHQTKVKQLRESFQEKRQWLLKYQSLLRMFLSYCVLHGSHGGGLASVRMELILLLQESQQVGKL
IRESfinder result
IRESfinder score
0.697252831
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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