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mmu_circKdm3b_1927
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm3b_1927
mm39_Chr. Position ID:
chr18|34941293|34952941|+
Gene name:
Kdm3b
Transcript:
ENSMUST00000043775.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,9,10,11,12
Exon/intron offsets:
0,2018,4131,5168,11540
Genomic length:
11648
Exon/intron sizes in nt:
1,24,92,02,21,51,53,100
Flanking exon/introns:
chr18:34937102-34941293|chr18:34952941-34955424
Splice length:
1927
Other database IDs:
circAtlas: mmu-Kdm3b_0005
circBase: hsa_circ_0074116, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_351914
Human Ortholog IDs:
Mature spliced Sequence:
AATTCAAGAAATTCTAGTCTGGCCTCTTCTGGATTTGGAGTGTCTCTCTCAAGTTTGTCACAACCATTGACTTTTGGAAGTGGACGGAGCCAGTCCAATGGAGTTTTAGCCACAGATAACAAGCCTTTGGGCTTCTCTTTCAGCTGCAGCTCTGCATCAGAGTCTCAGAAGGACTCCGATCTCTCCAAGAACTTGTTTTTTCAATGCATGTCCCAAAATGTACCCAGCACTAACTACCTGAGCAGGGTTTCAGAGAGCGTGGCCGATGACTCCTCGAGCAGGGATTCCTTCACACAAAGCCTCGAGAGCCTGACTTCAGGCCTGTGTAAAGGCAGATCTGTTCTCGGAGCAGATACTCAGCCAGGTCCCAAGGCCGGCAGCTCTGTGGACCGAAAAGTGCCTGCAGAGTCCATGCCCACCCTTACTCCAGCCTTCCCACGGAGTCTCCTAAATACCCGCACCCCAGAGAATCATGAAAATCTATTTTTACAGCCCCCGAAACTGTCCCGAGAAGAACCTTCTAACCCTTTCCTGGCGTTTGTGGAGAAAGTGGAACACAGCCCTTTCAGCAGCTTTGTGTCTCAGGCATCAGGTAGCTCTTCCTCTGCTACCTCTGTCACCTCAAAGGCAACAGCCAGCTGGCCTGAGTCTCACTCCTCTGCAGAGTCTGCACCTTTAGCAAAGAAAAAGCCCCTCTTTATTACAACTGACTCCTCCAAGCTGGTATCTGGTGTTCTGGGCTCCGCTCTCAGCACTGGGAGTCCGAGTCTCTCTGCAGTGGGGAATGGCCGCTCCAGCTCGCCCACCAACAGCCTCACCCAACCTATTGAGATGCCTACTCTCTCCTCCAGTCCCACAGAAGAGAGGCCAACTGTGGGGCCTGGCCAGCAGGACAATCCGCTCCTCAAAACCTTCAGTACCGTCTTTGGCAGGCACTCAGGCAGCTTTCTCTCCGCCCCAGCAGAGTTTGCACAGGAGAACAAAGCACCTTTTGAAGCTGTAAAAAGGTTCTCATTGGATGAGCGAAGCTTGGCTTGCAGACAGGATTCGGACTCCAGCACCAACAGTGACCTGTCAGATCTGAGCGACTCAGAGGAGCAGCTGCAGGCCAAGAGTGGCCTGAAGGGGATTCCAGAGCACCTGATGGGGAAGCTAGGCCCCAACGGGGAGCGTAGTGCTGAGCTGCTACTGGGCAAGGGCAAAGGGAAGCAGGCCCCAAAGGGCCGGCCCCGGACTGCTCCCCTGAAAGTTGGCCAGTCGGTGCTGAAGGACGTGAGTAAAGTAAGGAAGCTGAAGCAGTCTGGAGAGCCCTTCCTGCAGGACGGCTCCTGCATCAACGTGGCGCCTCACTTGCACAAGTGCCGAGAGTGCCGCCTGGAGAGGTACCGCAAGTTTAAGGAACAGGAGCAAGATGATTCTACTGTAGCCTGCCGCTTCTTTCACTTCCGGAGGTTGGTCTTCACTCGAAAGGGGGTGCTCCGTGTGGAGGGATTTCTGAGCCCCCAGCAGAGTGACCCGGATGCCATGAACCTGTGGATCCCCTCTTCCTCCCTAGCAGAAGGAATAGACCTAGAAACCTCAAAATACATCTTGGCCAATGTTGGGGACCAGTTCTGTCAGCTTGTAATGTCTGAGAAGGAGGCCATGATGATGGTGGAGCCACACCAGAAAGTGGCGTGGAAGCGAGCAGTGCGTGGAGTTCGGGAGATGTGTGATGTGTGTGAGACAACCCTCTTCAATATCCACTGGGTCTGTCGGAAATGTGGATTTGGGGTCTGCCTTGACTGTTACCGGCTCAGGAAAAGCCGTCCAAGGAGTGAGACAGAAGAAATGGGGGATGAGGAAGTTTTCTCCTGGCTGAAGTGTGCAAAGGGGCAGTCCCACGAACCAGAAAACCTCATGCCCACCCAGATCATCCCTGGCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGGCTGAAGTGTGCAAA
60.11
GGCTCCGTCCACTTCCAAAA
60.54
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTCCTGGCTGAAGTGTGC
60.25
GGCTCCGTCCACTTCCAAAA
60.54
170
PCR template sequence:
GAAATGGGGGATGAGGAAGTTTTCTCCTGGCTGAAGTGTGCAAAGGGGCAGTCCCACGAACCAGAAAACCTCATGCCCACCCAGATCATCCCTGGCACAGAATTCAAGAAATTCTAGTCTGGCCTCTTCTGGATTTGGAGTGTCTCTCTCAAGTTTGTCACAACCATTGACTTTTGGAAGTGGACGGAGCCAGTCCAATG
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-185-5p(3), mmu-miR-298-5p(2), mmu-miR-320-3p(2), mmu-miR-370-3p(2), mmu-let-7a-5p(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-342-3p(1), mmu-miR-335-3p(1), mmu-miR-323-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCCCTGGCACAGAATTCAAGAAATT
siRNA sets
AATTTCTTGAATTCTGTGC, ATTTCTTGAATTCTGTGCC, TTTCTTGAATTCTGTGCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM3B_1927_ORF_1
0.7483
0.286672243
0.999942589
1737
ORF sequence:
ATGTCCCAAAATGTACCCAGCACTAACTACCTGAGCAGGGTTTCAGAGAGCGTGGCCGATGACTCCTCGAGCAGGGATTCCTTCACACAAAGCCTCGAGAGCCTGACTTCAGGCCTGTGTAAAGGCAGATCTGTTCTCGGAGCAGATACTCAGCCAGGTCCCAAGGCCGGCAGCTCTGTGGACCGAAAAGTGCCTGCAGAGTCCATGCCCACCCTTACTCCAGCCTTCCCACGGAGTCTCCTAAATACCCGCACCCCAGAGAATCATGAAAATCTATTTTTACAGCCCCCGAAACTGTCCCGAGAAGAACCTTCTAACCCTTTCCTGGCGTTTGTGGAGAAAGTGGAACACAGCCCTTTCAGCAGCTTTGTGTCTCAGGCATCAGGTAGCTCTTCCTCTGCTACCTCTGTCACCTCAAAGGCAACAGCCAGCTGGCCTGAGTCTCACTCCTCTGCAGAGTCTGCACCTTTAGCAAAGAAAAAGCCCCTCTTTATTACAACTGACTCCTCCAAGCTGGTATCTGGTGTTCTGGGCTCCGCTCTCAGCACTGGGAGTCCGAGTCTCTCTGCAGTGGGGAATGGCCGCTCCAGCTCGCCCACCAACAGCCTCACCCAACCTATTGAGATGCCTACTCTCTCCTCCAGTCCCACAGAAGAGAGGCCAACTGTGGGGCCTGGCCAGCAGGACAATCCGCTCCTCAAAACCTTCAGTACCGTCTTTGGCAGGCACTCAGGCAGCTTTCTCTCCGCCCCAGCAGAGTTTGCACAGGAGAACAAAGCACCTTTTGAAGCTGTAAAAAGGTTCTCATTGGATGAGCGAAGCTTGGCTTGCAGACAGGATTCGGACTCCAGCACCAACAGTGACCTGTCAGATCTGAGCGACTCAGAGGAGCAGCTGCAGGCCAAGAGTGGCCTGAAGGGGATTCCAGAGCACCTGATGGGGAAGCTAGGCCCCAACGGGGAGCGTAGTGCTGAGCTGCTACTGGGCAAGGGCAAAGGGAAGCAGGCCCCAAAGGGCCGGCCCCGGACTGCTCCCCTGAAAGTTGGCCAGTCGGTGCTGAAGGACGTGAGTAAAGTAAGGAAGCTGAAGCAGTCTGGAGAGCCCTTCCTGCAGGACGGCTCCTGCATCAACGTGGCGCCTCACTTGCACAAGTGCCGAGAGTGCCGCCTGGAGAGGTACCGCAAGTTTAAGGAACAGGAGCAAGATGATTCTACTGTAGCCTGCCGCTTCTTTCACTTCCGGAGGTTGGTCTTCACTCGAAAGGGGGTGCTCCGTGTGGAGGGATTTCTGAGCCCCCAGCAGAGTGACCCGGATGCCATGAACCTGTGGATCCCCTCTTCCTCCCTAGCAGAAGGAATAGACCTAGAAACCTCAAAATACATCTTGGCCAATGTTGGGGACCAGTTCTGTCAGCTTGTAATGTCTGAGAAGGAGGCCATGATGATGGTGGAGCCACACCAGAAAGTGGCGTGGAAGCGAGCAGTGCGTGGAGTTCGGGAGATGTGTGATGTGTGTGAGACAACCCTCTTCAATATCCACTGGGTCTGTCGGAAATGTGGATTTGGGGTCTGCCTTGACTGTTACCGGCTCAGGAAAAGCCGTCCAAGGAGTGAGACAGAAGAAATGGGGGATGAGGAAGTTTTCTCCTGGCTGAAGTGTGCAAAGGGGCAGTCCCACGAACCAGAAAACCTCATGCCCACCCAGATCATCCCTGGCACAGAATTCAAGAAATTCTAG
Peptide sequence:
MSQNVPSTNYLSRVSESVADDSSSRDSFTQSLESLTSGLCKGRSVLGADTQPGPKAGSSVDRKVPAESMPTLTPAFPRSLLNTRTPENHENLFLQPPKLSREEPSNPFLAFVEKVEHSPFSSFVSQASGSSSSATSVTSKATASWPESHSSAESAPLAKKKPLFITTDSSKLVSGVLGSALSTGSPSLSAVGNGRSSSPTNSLTQPIEMPTLSSSPTEERPTVGPGQQDNPLLKTFSTVFGRHSGSFLSAPAEFAQENKAPFEAVKRFSLDERSLACRQDSDSSTNSDLSDLSDSEEQLQAKSGLKGIPEHLMGKLGPNGERSAELLLGKGKGKQAPKGRPRTAPLKVGQSVLKDVSKVRKLKQSGEPFLQDGSCINVAPHLHKCRECRLERYRKFKEQEQDDSTVACRFFHFRRLVFTRKGVLRVEGFLSPQQSDPDAMNLWIPSSSLAEGIDLETSKYILANVGDQFCQLVMSEKEAMMMVEPHQKVAWKRAVRGVREMCDVCETTLFNIHWVCRKCGFGVCLDCYRLRKSRPRSETEEMGDEEVFSWLKCAKGQSHEPENLMPTQIIPGTEFKKF
IRESfinder result
IRESfinder score
0.570335032
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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