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mmu_circKdm5d_1553
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm5d_1553
mm39_Chr. Position ID:
chrY|914024|928384|+
Gene name:
Kdm5d
Transcript:
ENSMUST00000055032.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
8,9,10,11,12,13,14,15,16,17
Exon/intron offsets:
0,2616,2821,7377,7649,12982,13220,13685,13945,14212
Genomic length:
14360
Exon/intron sizes in nt:
1,59,12,01,59,18,21,63,00,00,00,00,00,00,000
Flanking exon/introns:
chrY:910849-914024|chrY:928384-936875
Splice length:
1553
Other database IDs:
circAtlas: mmu-Kdm5d_0022
Human Ortholog IDs:
Mature spliced Sequence:
ATGAATTCATATGTTTGCCGAATATGCTCTCGTGGGGATGAAGTCGATAAGTTTCTGCTCTGTGATGGCTGCAGTGATAATTACCACATCTTTTGCCTATTGCCACCGCTTTCTGAAGTCCCCAAGGGAGTATGGAGATGCCCGAAGTGTATCTTAGCAGAGTGTAAGAGTCCCCCTGAAGCTTTTGGCTTTGAGCAGGCTACACAGGAGTATACTTTGCAGAGTTTTGGTGAGATGGCTGACTCCTTCAAGGCTGACTACTTCAACATGCCTGTGCATATGGTACCTACAGAAGTTGTGGAAAAGGAATTCTGGAGGCTGGTGAGCAGCATTGAGGAGGATGTGACAGTTGAATATGGAGCAGACATTCACTCCAAAGAATTTGGCAGTGGGTTTCCTGTCAACAATAGCAAATGGGACTTATCTCCTGAAGAAAAGGAATATGCTGCTTGTGGTTGGAATCTCAATGTGATGCCAGTGCTGGATCAGTCTGTTCTCTGCCACATCAATGCAGACATCTCAGGCATGAAAGTGCCCTGGTTATATGTGGGCATGGTGTTTTCAGCATTTTGTTGGCATATTGAGGATCACTGGAGTTATTCCATTAACTACCTGCACTGGGGTGAACCAAAGACCTGGTATGGAGTACCTTCGCTAGCAGCAGAACACTTAGAGGATGTAATGAAGAGACTTACACCAGAGTTGTTTGACAGCCAACCTGACCTCCTGCACCAACTTGTCACTCTGATGAATCCTAACACTCTCATGTCACATGGAGTGCCAGTTGTTCGTACAAACCAGTGTGCAGGGGAATTTGTCATTACTTTTCCCCGTGCTTACCACAGTGGCTTTAACCAAGGCTATAACTTTGCTGAGGCAGTGAACTTTTGCACTGCCGATTGGCTACCTGTTGGACGCCAGTGTATTGAACACTACCGCCGACTCCGGCGCTATTGTGTCTTCTCCCATGAAGAACTTATCTGCAAGATGGCTGCATTTCCAGAGAAGTTGGATCTAAATCTAGCAGTGGCAGTTCACAAGGAGATGTTCATTATGGTACAGGAGGAGCGACGCCTACGAAAGACCTTGTTGGAGAAGGGCATCACGGAAGCTGAGCGAGAGGCTTTTGAGCTACTCCCAGATGATGAGCGTCAGTGCATCAAGTGTAAGACCACGTGTTTCCTATCAGCCTTGGCCTGTTATGACTGTCCAGATAGTCTTGTCTGCCTTTCCCATATCAATGATCTGTGCAAGTGCTCAAGGAATCGACAGTACTTACGGTACAGGTACACATTGGATGAACTGCCTGCTATGCTACAAAAGCTGAAGATTCGAGCTGAGTCATTTGACAACTGGGCCAACAAAGTACAAGCAGCCCTAGAGGTGGAGGATGGTCGGAAACGGAGTTTTGAAGAGCTAAGAGCATTGGAATCTGAGGCTCGTGATAGACGATTTCCTAATAGTGAGCTGCTTCAGCGATTGAAGAAATGCCTAACTGAAGCAGAGGCTTGTATTTCCCAAGTTCTTGGACTGATCAGTAACTCAGAGGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCTAACTGAAGCAGAGGC
60.04
TCACTGCAGCCATCACAGAG
60.04
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCTAACTGAAGCAGAGGC
60.04
ATCACTGCAGCCATCACAGA
59.38
143
PCR template sequence:
TTCCTAATAGTGAGCTGCTTCAGCGATTGAAGAAATGCCTAACTGAAGCAGAGGCTTGTATTTCCCAAGTTCTTGGACTGATCAGTAACTCAGAGGACAGATGAATTCATATGTTTGCCGAATATGCTCTCGTGGGGATGAAGTCGATAAGTTTCTGCTCTGTGATGGCTGCAGTGATAATTACCACATCTTTTGCCTAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-34c-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-33-5p(1), mmu-miR-298-5p(1), mmu-miR-301b-3p(1), mmu-miR-324-3p(1), mmu-miR-34b-5p(1), mmu-miR-301a-3p(1), mmu-miR-1187(1), mmu-miR-344d-3p(1), mmu-miR-3087-3p(1), mmu-miR-3065-5p(1), mmu-miR-1904(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTCAGAGGACAGATGAATTCATATG
siRNA sets
TATGAATTCATCTGTCCTC, CATATGAATTCATCTGTCC, ATATGAATTCATCTGTCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM5D_1553_ORF_1
0.8451
0.173024519
0.999725181
1557
ORF sequence:
ATGAATTCATATGTTTGCCGAATATGCTCTCGTGGGGATGAAGTCGATAAGTTTCTGCTCTGTGATGGCTGCAGTGATAATTACCACATCTTTTGCCTATTGCCACCGCTTTCTGAAGTCCCCAAGGGAGTATGGAGATGCCCGAAGTGTATCTTAGCAGAGTGTAAGAGTCCCCCTGAAGCTTTTGGCTTTGAGCAGGCTACACAGGAGTATACTTTGCAGAGTTTTGGTGAGATGGCTGACTCCTTCAAGGCTGACTACTTCAACATGCCTGTGCATATGGTACCTACAGAAGTTGTGGAAAAGGAATTCTGGAGGCTGGTGAGCAGCATTGAGGAGGATGTGACAGTTGAATATGGAGCAGACATTCACTCCAAAGAATTTGGCAGTGGGTTTCCTGTCAACAATAGCAAATGGGACTTATCTCCTGAAGAAAAGGAATATGCTGCTTGTGGTTGGAATCTCAATGTGATGCCAGTGCTGGATCAGTCTGTTCTCTGCCACATCAATGCAGACATCTCAGGCATGAAAGTGCCCTGGTTATATGTGGGCATGGTGTTTTCAGCATTTTGTTGGCATATTGAGGATCACTGGAGTTATTCCATTAACTACCTGCACTGGGGTGAACCAAAGACCTGGTATGGAGTACCTTCGCTAGCAGCAGAACACTTAGAGGATGTAATGAAGAGACTTACACCAGAGTTGTTTGACAGCCAACCTGACCTCCTGCACCAACTTGTCACTCTGATGAATCCTAACACTCTCATGTCACATGGAGTGCCAGTTGTTCGTACAAACCAGTGTGCAGGGGAATTTGTCATTACTTTTCCCCGTGCTTACCACAGTGGCTTTAACCAAGGCTATAACTTTGCTGAGGCAGTGAACTTTTGCACTGCCGATTGGCTACCTGTTGGACGCCAGTGTATTGAACACTACCGCCGACTCCGGCGCTATTGTGTCTTCTCCCATGAAGAACTTATCTGCAAGATGGCTGCATTTCCAGAGAAGTTGGATCTAAATCTAGCAGTGGCAGTTCACAAGGAGATGTTCATTATGGTACAGGAGGAGCGACGCCTACGAAAGACCTTGTTGGAGAAGGGCATCACGGAAGCTGAGCGAGAGGCTTTTGAGCTACTCCCAGATGATGAGCGTCAGTGCATCAAGTGTAAGACCACGTGTTTCCTATCAGCCTTGGCCTGTTATGACTGTCCAGATAGTCTTGTCTGCCTTTCCCATATCAATGATCTGTGCAAGTGCTCAAGGAATCGACAGTACTTACGGTACAGGTACACATTGGATGAACTGCCTGCTATGCTACAAAAGCTGAAGATTCGAGCTGAGTCATTTGACAACTGGGCCAACAAAGTACAAGCAGCCCTAGAGGTGGAGGATGGTCGGAAACGGAGTTTTGAAGAGCTAAGAGCATTGGAATCTGAGGCTCGTGATAGACGATTTCCTAATAGTGAGCTGCTTCAGCGATTGAAGAAATGCCTAACTGAAGCAGAGGCTTGTATTTCCCAAGTTCTTGGACTGATCAGTAACTCAGAGGACAGATGA
Peptide sequence:
MNSYVCRICSRGDEVDKFLLCDGCSDNYHIFCLLPPLSEVPKGVWRCPKCILAECKSPPEAFGFEQATQEYTLQSFGEMADSFKADYFNMPVHMVPTEVVEKEFWRLVSSIEEDVTVEYGADIHSKEFGSGFPVNNSKWDLSPEEKEYAACGWNLNVMPVLDQSVLCHINADISGMKVPWLYVGMVFSAFCWHIEDHWSYSINYLHWGEPKTWYGVPSLAAEHLEDVMKRLTPELFDSQPDLLHQLVTLMNPNTLMSHGVPVVRTNQCAGEFVITFPRAYHSGFNQGYNFAEAVNFCTADWLPVGRQCIEHYRRLRRYCVFSHEELICKMAAFPEKLDLNLAVAVHKEMFIMVQEERRLRKTLLEKGITEAEREAFELLPDDERQCIKCKTTCFLSALACYDCPDSLVCLSHINDLCKCSRNRQYLRYRYTLDELPAMLQKLKIRAESFDNWANKVQAALEVEDGRKRSFEELRALESEARDRRFPNSELLQRLKKCLTEAEACISQVLGLISNSEDR
IRESfinder result
IRESfinder score
0.535527942
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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