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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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Institute of Life sciences, Bhubaneswar, India

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