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mmu_circArhgap12_1545
Basic information of circular RNA
PanCircBase ID:
mmu_circArhgap12_1545
mm39_Chr. Position ID:
chr18|6049276|6115850|-
Gene name:
Arhgap12
Transcript:
ENSMUST00000077128.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
9,8,7,6,5,4,3,2
Exon/intron offsets:
0,3585,12570,15064,16428,20554,62408,66537
Genomic length:
66574
Exon/intron sizes in nt:
82,62,126,81,141,261,755,37
Flanking exon/introns:
chr18:6039455-6049276|chr18:6115850-6135803
Splice length:
1545
Other database IDs:
circAtlas: mmu-Arhgap12_0034
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTTTAAATGAAACACCAGATGTTTACAGCCTTCCAAGTGTTATATTAATGCATCGAGGCACAAGGCATAATGTGGCATGCTATCTGTTTTGAGAGTGAGTATTACTGAGTAGAAATGGCCGAGAGAAGTGGAAAGATCACTGCAGGACAAGCGTATATTGAGGTGGAGTATGATTATGAGTATGACGCAAAGGACAGAAAGATTGTGATCAGACAAGGGGAGCGCTACCTCCTGGTGAAGAAGACCAATGATGACTGGTGGCAAGTCAGACCTGATGAGAACTCAAAAGCATTTTATGTGCCAGCACAGTATGTCAAGGAGGTCACTCGCAAAGCTCTGATGCCACCTGTGAAGCAGGCAACAGGACTGCCAAATAACTCTATGAAGACAATACAGAGTATGCATCTCCAGAGATCGACAGAAAATGTGAACAAAATGCCTGAGCTTTCAAGTTTTGGAAAGCCATCGTCATCTGTTCAAGGAACAGGTCTTATTCGTGATGCCAATCAGAATTTCGGATCCAATTATAATTCAGGCCAGACTCTCAACCTAAGCCTGGACCTGACCCATAATAATGGAAAGTTTAACAGTGACTCACATTCTCCTAAAGTTTCCAGCCAGAATAGGACACGCTTATTTGGTCATTTTCCCGGGCCAGAGTTCTTGGACATAGAGAAAACTAGCTTCTCTCAGGAACAGTCATGTGACTCAGCTGGAGAAGGCTCCGAAAGAATACAGCAGGATTCCGAGTCTGGAGATGAACTTAGCAGCAGCTCCACTGAGCAGATGAGGGCAACCACACCCCCTAATCAAGGAAGGCCAGATTCTCCAGTCTATGCTAACCTACAGGAACTGAAAATATCACAGTCTGCTCTTCCTCCTCTTCCTGGGAGCCCAGCAATTCAAGTTAATGGGGAATGGGAGACTCACAAAGACAGTTCAGGCCGTTGTTACTACTATAACCGCACAACCCAGGAGCGAACCTGGAAACCACCTCGATGGGCTCGAGATGTGAGCACAAGCCGAGATTTTCAGAGCCCAGGAGAGCAAGAGCCTCTTTCATCAGAAGAAAACTACCACAGCAGTTGTTTCAGCCAGTCAGATAGTCAGTGTGGCTCTCCTCCCAGGGGTTGGTCAGAAGAGCTGGATGAACGTGGGCATACCTTGTATACCAGTGACTATACTAAGGAAAAGTGGCTCAAGCATGTTGATGATCAAGGTAGACAGTATTACTACAGCGCAGATGGATCTCGGTCAGAGTGGGAATTGCCAAAGTATAATGCTTCATCTCAGCAGCAAAGAGAAATAATTAAAAGTAGGAGCTTGGACAGGCGGCTGCAAGAACCAATAGTGTTAACTAAATGGAGACATAGCACCATTGTGTTGGACTCCAACGACAAGGGTCAGGAGAAATATGGACTGTTAAATGTAACAAAAATTACTGAAAATGGGAAAAAAGTTCGAAAGAACTGGTTGTCTTCTTGGGCAGTGCTGCAGGGTTCGTCTTTACTTTTTACGAAAACTCAAGGAAGTAGTACAAGCTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGTCTTCTTGGGCAGTGCT
59.82
GCCACATTATGCCTTGTGCC
60.18
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTTGTCTTCTTGGGCAGTGC
59.69
GCCACATTATGCCTTGTGCC
60.18
149
PCR template sequence:
AAATGGGAAAAAAGTTCGAAAGAACTGGTTGTCTTCTTGGGCAGTGCTGCAGGGTTCGTCTTTACTTTTTACGAAAACTCAAGGAAGTAGTACAAGCTGGGTTTAAATGAAACACCAGATGTTTACAGCCTTCCAAGTGTTATATTAATGCATCGAGGCACAAGGCATAATGTGGCATGCTATCTGTTTTGAGAGTGAGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-135a-5p(1), mmu-miR-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-30c-5p(1), mmu-miR-23a-3p(1), mmu-miR-143-3p(1), mmu-miR-381-3p(1), mmu-miR-30d-5p(1), mmu-miR-30b-5p(1), mmu-miR-136-5p(1), mmu-miR-182-5p(1), mmu-miR-324-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-410-3p(1), mmu-miR-344d-3p(1), mmu-miR-207(1), mmu-miR-532-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TAGTACAAGCTGGGTTTAAATGAAAC
siRNA sets
ATTTAAACCCAGCTTGTAC, GTTTCATTTAAACCCAGCT, TCATTTAAACCCAGCTTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARHGAP12_1545_ORF_1
0.7438
0.132631595
0.99907056
1437
ORF sequence:
ATGGCCGAGAGAAGTGGAAAGATCACTGCAGGACAAGCGTATATTGAGGTGGAGTATGATTATGAGTATGACGCAAAGGACAGAAAGATTGTGATCAGACAAGGGGAGCGCTACCTCCTGGTGAAGAAGACCAATGATGACTGGTGGCAAGTCAGACCTGATGAGAACTCAAAAGCATTTTATGTGCCAGCACAGTATGTCAAGGAGGTCACTCGCAAAGCTCTGATGCCACCTGTGAAGCAGGCAACAGGACTGCCAAATAACTCTATGAAGACAATACAGAGTATGCATCTCCAGAGATCGACAGAAAATGTGAACAAAATGCCTGAGCTTTCAAGTTTTGGAAAGCCATCGTCATCTGTTCAAGGAACAGGTCTTATTCGTGATGCCAATCAGAATTTCGGATCCAATTATAATTCAGGCCAGACTCTCAACCTAAGCCTGGACCTGACCCATAATAATGGAAAGTTTAACAGTGACTCACATTCTCCTAAAGTTTCCAGCCAGAATAGGACACGCTTATTTGGTCATTTTCCCGGGCCAGAGTTCTTGGACATAGAGAAAACTAGCTTCTCTCAGGAACAGTCATGTGACTCAGCTGGAGAAGGCTCCGAAAGAATACAGCAGGATTCCGAGTCTGGAGATGAACTTAGCAGCAGCTCCACTGAGCAGATGAGGGCAACCACACCCCCTAATCAAGGAAGGCCAGATTCTCCAGTCTATGCTAACCTACAGGAACTGAAAATATCACAGTCTGCTCTTCCTCCTCTTCCTGGGAGCCCAGCAATTCAAGTTAATGGGGAATGGGAGACTCACAAAGACAGTTCAGGCCGTTGTTACTACTATAACCGCACAACCCAGGAGCGAACCTGGAAACCACCTCGATGGGCTCGAGATGTGAGCACAAGCCGAGATTTTCAGAGCCCAGGAGAGCAAGAGCCTCTTTCATCAGAAGAAAACTACCACAGCAGTTGTTTCAGCCAGTCAGATAGTCAGTGTGGCTCTCCTCCCAGGGGTTGGTCAGAAGAGCTGGATGAACGTGGGCATACCTTGTATACCAGTGACTATACTAAGGAAAAGTGGCTCAAGCATGTTGATGATCAAGGTAGACAGTATTACTACAGCGCAGATGGATCTCGGTCAGAGTGGGAATTGCCAAAGTATAATGCTTCATCTCAGCAGCAAAGAGAAATAATTAAAAGTAGGAGCTTGGACAGGCGGCTGCAAGAACCAATAGTGTTAACTAAATGGAGACATAGCACCATTGTGTTGGACTCCAACGACAAGGGTCAGGAGAAATATGGACTGTTAAATGTAACAAAAATTACTGAAAATGGGAAAAAAGTTCGAAAGAACTGGTTGTCTTCTTGGGCAGTGCTGCAGGGTTCGTCTTTACTTTTTACGAAAACTCAAGGAAGTAGTACAAGCTGGGTTTAA
Peptide sequence:
MAERSGKITAGQAYIEVEYDYEYDAKDRKIVIRQGERYLLVKKTNDDWWQVRPDENSKAFYVPAQYVKEVTRKALMPPVKQATGLPNNSMKTIQSMHLQRSTENVNKMPELSSFGKPSSSVQGTGLIRDANQNFGSNYNSGQTLNLSLDLTHNNGKFNSDSHSPKVSSQNRTRLFGHFPGPEFLDIEKTSFSQEQSCDSAGEGSERIQQDSESGDELSSSSTEQMRATTPPNQGRPDSPVYANLQELKISQSALPPLPGSPAIQVNGEWETHKDSSGRCYYYNRTTQERTWKPPRWARDVSTSRDFQSPGEQEPLSSEENYHSSCFSQSDSQCGSPPRGWSEELDERGHTLYTSDYTKEKWLKHVDDQGRQYYYSADGSRSEWELPKYNASSQQQREIIKSRSLDRRLQEPIVLTKWRHSTIVLDSNDKGQEKYGLLNVTKITENGKKVRKNWLSSWAVLQGSSLLFTKTQGSSTSWV
IRESfinder result
IRESfinder score
0.530669842
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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