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mmu_circKdm3b_2725
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm3b_2725
mm39_Chr. Position ID:
chr18|34928727|34946614|+
Gene name:
Kdm3b
Transcript:
ENSMUST00000043775.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
4,5,6,7,8,9,10,11
Exon/intron offsets:
0,1113,3610,7775,12566,14584,16697,17734
Genomic length:
17887
Exon/intron sizes in nt:
1,06,12,57,56,00,12,49,00,00,00,000
Flanking exon/introns:
chr18:34927616-34928727|chr18:34946614-34952833
Splice length:
2725
Other database IDs:
circAtlas: mmu-Kdm3b_0029
CIRCpedia: HSA_CIRCpedia_101784
Human Ortholog IDs:
Mature spliced Sequence:
ATGGGAACAGATGTTCAAAATCAGATTCTTTTAGAACATGCTGCATTAAGAGAGACAGTTAATGCTTTGATCAGTGACCAAAAGCTACAAGAGATTTTCAGCCGAGGTCCCTATAGTGTCCAGGGCCACAGAGTCAAGGTCTACCAACCCGAAGGAGAGGAAGTATGGCTCTGTGGTGTTGTGAGCCGTCAGGACTCAGTCACCCGTCTTATGGAAGTGTCTATAACTGAGACTGGTGAGGTCAAGTCAGTAGATCCCAGACTCACCCACGTGATGCTGATGGACAGCTCGACACCACAGAGTGAGGGGGGTACCATAAAAGCAGTAAAATCTTCCAAAGGAAAGAAGAAGAGAGAGAGCATAGAGGGGAGAGATGGCCGGAGGAGGAAAAGTGCTTCGGACTCTGGGTGTGACCCTGCTACAAAGAAATTAAAAGGAGACAGGGGTGAAGTAGACAGTAATGGGAGTGATGGAGGTGAGGCAAGCCGAGGGCCCTGGAAAGGAGGTAATGCCAGTGGAGAGCCAGGGCTGGAGCAGAGAGCCAAGCAGCCACCGTCTACATTTGTTCCCCAGATTAACCGCAACATTCGCTTTGCCACTTACACCAAAGAAAACGGCAGAACTCTGGTGGTACAGGATGAGCCTGTAGGTGGGGATACGCCCGTCCCTTTCACTCCGTATGCTTCAGCCACAGGTCAGACACCTTTGGCCCCAGAGGTAGGTGGAGCTGAAAACAAAGAGGCGGGAAAAACGCTGGAACAAGTTAGCCAGGGCATGGTGGCTTCAGCAGCTGTAGTCACTACCGCCAGCTCCACCCCAACCACGGTGAGGATCTCAGACACTGGCCTTGCATCAGGGACTGGGCCGGAAAAACAGAAAGGCAGCTGGTCGCAGGCCTCAGGAGAGAATTCAAGAAATTCTAGTCTGGCCTCTTCTGGATTTGGAGTGTCTCTCTCAAGTTTGTCACAACCATTGACTTTTGGAAGTGGACGGAGCCAGTCCAATGGAGTTTTAGCCACAGATAACAAGCCTTTGGGCTTCTCTTTCAGCTGCAGCTCTGCATCAGAGTCTCAGAAGGACTCCGATCTCTCCAAGAACTTGTTTTTTCAATGCATGTCCCAAAATGTACCCAGCACTAACTACCTGAGCAGGGTTTCAGAGAGCGTGGCCGATGACTCCTCGAGCAGGGATTCCTTCACACAAAGCCTCGAGAGCCTGACTTCAGGCCTGTGTAAAGGCAGATCTGTTCTCGGAGCAGATACTCAGCCAGGTCCCAAGGCCGGCAGCTCTGTGGACCGAAAAGTGCCTGCAGAGTCCATGCCCACCCTTACTCCAGCCTTCCCACGGAGTCTCCTAAATACCCGCACCCCAGAGAATCATGAAAATCTATTTTTACAGCCCCCGAAACTGTCCCGAGAAGAACCTTCTAACCCTTTCCTGGCGTTTGTGGAGAAAGTGGAACACAGCCCTTTCAGCAGCTTTGTGTCTCAGGCATCAGGTAGCTCTTCCTCTGCTACCTCTGTCACCTCAAAGGCAACAGCCAGCTGGCCTGAGTCTCACTCCTCTGCAGAGTCTGCACCTTTAGCAAAGAAAAAGCCCCTCTTTATTACAACTGACTCCTCCAAGCTGGTATCTGGTGTTCTGGGCTCCGCTCTCAGCACTGGGAGTCCGAGTCTCTCTGCAGTGGGGAATGGCCGCTCCAGCTCGCCCACCAACAGCCTCACCCAACCTATTGAGATGCCTACTCTCTCCTCCAGTCCCACAGAAGAGAGGCCAACTGTGGGGCCTGGCCAGCAGGACAATCCGCTCCTCAAAACCTTCAGTACCGTCTTTGGCAGGCACTCAGGCAGCTTTCTCTCCGCCCCAGCAGAGTTTGCACAGGAGAACAAAGCACCTTTTGAAGCTGTAAAAAGGTTCTCATTGGATGAGCGAAGCTTGGCTTGCAGACAGGATTCGGACTCCAGCACCAACAGTGACCTGTCAGATCTGAGCGACTCAGAGGAGCAGCTGCAGGCCAAGAGTGGCCTGAAGGGGATTCCAGAGCACCTGATGGGGAAGCTAGGCCCCAACGGGGAGCGTAGTGCTGAGCTGCTACTGGGCAAGGGCAAAGGGAAGCAGGCCCCAAAGGGCCGGCCCCGGACTGCTCCCCTGAAAGTTGGCCAGTCGGTGCTGAAGGACGTGAGTAAAGTAAGGAAGCTGAAGCAGTCTGGAGAGCCCTTCCTGCAGGACGGCTCCTGCATCAACGTGGCGCCTCACTTGCACAAGTGCCGAGAGTGCCGCCTGGAGAGGTACCGCAAGTTTAAGGAACAGGAGCAAGATGATTCTACTGTAGCCTGCCGCTTCTTTCACTTCCGGAGGTTGGTCTTCACTCGAAAGGGGGTGCTCCGTGTGGAGGGATTTCTGAGCCCCCAGCAGAGTGACCCGGATGCCATGAACCTGTGGATCCCCTCTTCCTCCCTAGCAGAAGGAATAGACCTAGAAACCTCAAAATACATCTTGGCCAATGTTGGGGACCAGTTCTGTCAGCTTGTAATGTCTGAGAAGGAGGCCATGATGATGGTGGAGCCACACCAGAAAGTGGCGTGGAAGCGAGCAGTGCGTGGAGTTCGGGAGATGTGTGATGTGTGTGAGACAACCCTCTTCAATATCCACTGGGTCTGTCGGAAATGTGGATTTGGGGTCTGCCTTGACTGTTACCGGCTCAGGAAAAGCCGTCCAAGGAGTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGTCTGTCGGAAATGTGG
59.96
AGCTTTTGGTCACTGATCAAAGC
59.99
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGATTTGGGGTCTGCCTTGA
59.96
AGCTTTTGGTCACTGATCAAAGC
59.99
141
PCR template sequence:
TGTGAGACAACCCTCTTCAATATCCACTGGGTCTGTCGGAAATGTGGATTTGGGGTCTGCCTTGACTGTTACCGGCTCAGGAAAAGCCGTCCAAGGAGTGATGGGAACAGATGTTCAAAATCAGATTCTTTTAGAACATGCTGCATTAAGAGAGACAGTTAATGCTTTGATCAGTGACCAAAAGCTACAAGAGATTTTCA
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-185-5p(3), mmu-miR-298-5p(2), mmu-miR-320-3p(2), mmu-miR-370-3p(2), mmu-let-7a-5p(1), mmu-miR-199a-5p(1), mmu-miR-103-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-19a-3p(1), mmu-miR-18a-5p(1), mmu-miR-196a-5p(1), mmu-miR-139-5p(1), mmu-let-7d-5p(1), mmu-miR-149-5p(1), mmu-miR-483-5p(1), mmu-miR-107-3p(1), mmu-miR-342-3p(1), mmu-miR-207(1), mmu-miR-300-3p(1), mmu-miR-335-3p(1), mmu-miR-484(1), mmu-miR-452-3p(1), mmu-miR-3470b(1), mmu-miR-1199-5p(1), mmu-miR-670-5p(1), mmu-miR-323-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CGTCCAAGGAGTGATGGGAACAGATG
siRNA sets
CATCTGTTCCCATCACTCC, ATCTGTTCCCATCACTCCT, TGTTCCCATCACTCCTTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM3B_2725_ORF_1
0.676
0.220694049
0.999999966
2829
ORF sequence:
ATGTGTGTGAGACAACCCTCTTCAATATCCACTGGGTCTGTCGGAAATGTGGATTTGGGGTCTGCCTTGACTGTTACCGGCTCAGGAAAAGCCGTCCAAGGAGTGATGGGAACAGATGTTCAAAATCAGATTCTTTTAGAACATGCTGCATTAAGAGAGACAGTTAATGCTTTGATCAGTGACCAAAAGCTACAAGAGATTTTCAGCCGAGGTCCCTATAGTGTCCAGGGCCACAGAGTCAAGGTCTACCAACCCGAAGGAGAGGAAGTATGGCTCTGTGGTGTTGTGAGCCGTCAGGACTCAGTCACCCGTCTTATGGAAGTGTCTATAACTGAGACTGGTGAGGTCAAGTCAGTAGATCCCAGACTCACCCACGTGATGCTGATGGACAGCTCGACACCACAGAGTGAGGGGGGTACCATAAAAGCAGTAAAATCTTCCAAAGGAAAGAAGAAGAGAGAGAGCATAGAGGGGAGAGATGGCCGGAGGAGGAAAAGTGCTTCGGACTCTGGGTGTGACCCTGCTACAAAGAAATTAAAAGGAGACAGGGGTGAAGTAGACAGTAATGGGAGTGATGGAGGTGAGGCAAGCCGAGGGCCCTGGAAAGGAGGTAATGCCAGTGGAGAGCCAGGGCTGGAGCAGAGAGCCAAGCAGCCACCGTCTACATTTGTTCCCCAGATTAACCGCAACATTCGCTTTGCCACTTACACCAAAGAAAACGGCAGAACTCTGGTGGTACAGGATGAGCCTGTAGGTGGGGATACGCCCGTCCCTTTCACTCCGTATGCTTCAGCCACAGGTCAGACACCTTTGGCCCCAGAGGTAGGTGGAGCTGAAAACAAAGAGGCGGGAAAAACGCTGGAACAAGTTAGCCAGGGCATGGTGGCTTCAGCAGCTGTAGTCACTACCGCCAGCTCCACCCCAACCACGGTGAGGATCTCAGACACTGGCCTTGCATCAGGGACTGGGCCGGAAAAACAGAAAGGCAGCTGGTCGCAGGCCTCAGGAGAGAATTCAAGAAATTCTAGTCTGGCCTCTTCTGGATTTGGAGTGTCTCTCTCAAGTTTGTCACAACCATTGACTTTTGGAAGTGGACGGAGCCAGTCCAATGGAGTTTTAGCCACAGATAACAAGCCTTTGGGCTTCTCTTTCAGCTGCAGCTCTGCATCAGAGTCTCAGAAGGACTCCGATCTCTCCAAGAACTTGTTTTTTCAATGCATGTCCCAAAATGTACCCAGCACTAACTACCTGAGCAGGGTTTCAGAGAGCGTGGCCGATGACTCCTCGAGCAGGGATTCCTTCACACAAAGCCTCGAGAGCCTGACTTCAGGCCTGTGTAAAGGCAGATCTGTTCTCGGAGCAGATACTCAGCCAGGTCCCAAGGCCGGCAGCTCTGTGGACCGAAAAGTGCCTGCAGAGTCCATGCCCACCCTTACTCCAGCCTTCCCACGGAGTCTCCTAAATACCCGCACCCCAGAGAATCATGAAAATCTATTTTTACAGCCCCCGAAACTGTCCCGAGAAGAACCTTCTAACCCTTTCCTGGCGTTTGTGGAGAAAGTGGAACACAGCCCTTTCAGCAGCTTTGTGTCTCAGGCATCAGGTAGCTCTTCCTCTGCTACCTCTGTCACCTCAAAGGCAACAGCCAGCTGGCCTGAGTCTCACTCCTCTGCAGAGTCTGCACCTTTAGCAAAGAAAAAGCCCCTCTTTATTACAACTGACTCCTCCAAGCTGGTATCTGGTGTTCTGGGCTCCGCTCTCAGCACTGGGAGTCCGAGTCTCTCTGCAGTGGGGAATGGCCGCTCCAGCTCGCCCACCAACAGCCTCACCCAACCTATTGAGATGCCTACTCTCTCCTCCAGTCCCACAGAAGAGAGGCCAACTGTGGGGCCTGGCCAGCAGGACAATCCGCTCCTCAAAACCTTCAGTACCGTCTTTGGCAGGCACTCAGGCAGCTTTCTCTCCGCCCCAGCAGAGTTTGCACAGGAGAACAAAGCACCTTTTGAAGCTGTAAAAAGGTTCTCATTGGATGAGCGAAGCTTGGCTTGCAGACAGGATTCGGACTCCAGCACCAACAGTGACCTGTCAGATCTGAGCGACTCAGAGGAGCAGCTGCAGGCCAAGAGTGGCCTGAAGGGGATTCCAGAGCACCTGATGGGGAAGCTAGGCCCCAACGGGGAGCGTAGTGCTGAGCTGCTACTGGGCAAGGGCAAAGGGAAGCAGGCCCCAAAGGGCCGGCCCCGGACTGCTCCCCTGAAAGTTGGCCAGTCGGTGCTGAAGGACGTGAGTAAAGTAAGGAAGCTGAAGCAGTCTGGAGAGCCCTTCCTGCAGGACGGCTCCTGCATCAACGTGGCGCCTCACTTGCACAAGTGCCGAGAGTGCCGCCTGGAGAGGTACCGCAAGTTTAAGGAACAGGAGCAAGATGATTCTACTGTAGCCTGCCGCTTCTTTCACTTCCGGAGGTTGGTCTTCACTCGAAAGGGGGTGCTCCGTGTGGAGGGATTTCTGAGCCCCCAGCAGAGTGACCCGGATGCCATGAACCTGTGGATCCCCTCTTCCTCCCTAGCAGAAGGAATAGACCTAGAAACCTCAAAATACATCTTGGCCAATGTTGGGGACCAGTTCTGTCAGCTTGTAATGTCTGAGAAGGAGGCCATGATGATGGTGGAGCCACACCAGAAAGTGGCGTGGAAGCGAGCAGTGCGTGGAGTTCGGGAGATGTGTGATGTGTGTGAGACAACCCTCTTCAATATCCACTGGGTCTGTCGGAAATGTGGATTTGGGGTCTGCCTTGACTGTTACCGGCTCAGGAAAAGCCGTCCAAGGAGT
Peptide sequence:
MCVRQPSSISTGSVGNVDLGSALTVTGSGKAVQGVMGTDVQNQILLEHAALRETVNALISDQKLQEIFSRGPYSVQGHRVKVYQPEGEEVWLCGVVSRQDSVTRLMEVSITETGEVKSVDPRLTHVMLMDSSTPQSEGGTIKAVKSSKGKKKRESIEGRDGRRRKSASDSGCDPATKKLKGDRGEVDSNGSDGGEASRGPWKGGNASGEPGLEQRAKQPPSTFVPQINRNIRFATYTKENGRTLVVQDEPVGGDTPVPFTPYASATGQTPLAPEVGGAENKEAGKTLEQVSQGMVASAAVVTTASSTPTTVRISDTGLASGTGPEKQKGSWSQASGENSRNSSLASSGFGVSLSSLSQPLTFGSGRSQSNGVLATDNKPLGFSFSCSSASESQKDSDLSKNLFFQCMSQNVPSTNYLSRVSESVADDSSSRDSFTQSLESLTSGLCKGRSVLGADTQPGPKAGSSVDRKVPAESMPTLTPAFPRSLLNTRTPENHENLFLQPPKLSREEPSNPFLAFVEKVEHSPFSSFVSQASGSSSSATSVTSKATASWPESHSSAESAPLAKKKPLFITTDSSKLVSGVLGSALSTGSPSLSAVGNGRSSSPTNSLTQPIEMPTLSSSPTEERPTVGPGQQDNPLLKTFSTVFGRHSGSFLSAPAEFAQENKAPFEAVKRFSLDERSLACRQDSDSSTNSDLSDLSDSEEQLQAKSGLKGIPEHLMGKLGPNGERSAELLLGKGKGKQAPKGRPRTAPLKVGQSVLKDVSKVRKLKQSGEPFLQDGSCINVAPHLHKCRECRLERYRKFKEQEQDDSTVACRFFHFRRLVFTRKGVLRVEGFLSPQQSDPDAMNLWIPSSSLAEGIDLETSKYILANVGDQFCQLVMSEKEAMMMVEPHQKVAWKRAVRGVREMCDVCETTLFNIHWVCRKCGFGVCLDCYRLRKSRPRS
IRESfinder result
IRESfinder score
0.519039291
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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