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mmu_circKdm4c_722
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm4c_722
mm39_Chr. Position ID:
chr4|74225201|74252105|+
Gene name:
Kdm4c
Transcript:
ENSMUST00000077851.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,7,8,9,10
Exon/intron offsets:
0,4682,8547,23690,26668
Genomic length:
26904
Exon/intron sizes in nt:
5,01,04,13,81,94,236
Flanking exon/introns:
chr4:74216871-74225201|chr4:74252105-74252785
Splice length:
722
Other database IDs:
circAtlas: hsa-KDM4C_0115
Human Ortholog IDs:
Mature spliced Sequence:
GTATGCTATACCTCCGGAGCATGGAAAGCGACTTGAAAGACTAGCCCAAGGCTTCTTCCCCAGTAGCTCCCAAGGCTGTGATGCATTTCTCCGGCACAAGATGACCCTCATTTCCCCCTCAGTGCTGAAGAAGTATGGCATTCCCTTCGACAAGATCACCCAGGAGGCTGGAGAGTTTATGATCACTTTTCCTTATGGATATCATGCTGGTTTTAATCATGGTTTCAATTGTGCTGAGTCTACAAATTTTGCTACAGTCAGATGGATTGACTACGGCAAGGTTGCTAAGTTGTGCACTTGTCGGAATGACATGGTGAAGATATCAATGGATATATTTGTGAAGAAATTTCAGCCAGATAGATACCAGATTTGGAAACAAGGAAAGGATATATATACTATTGACCATACAAAGCCCACTCCAGAATCTACTCCAGAAGTAAAAACATGGCTACAGAGGAAGAAAAAATTAAGAAAGCCTCCCAAGAGCTTACAGGGCAATAAGCCACTTTGTAAAAGGCCTAAACCTGAAGAAGATGAGGAATTTGCTGAATTTAGTGGGGAAGAGGGTGCAAACCCTGCCATGGGCCCTAGGCACCTCAAAGTCACTGAAAAGCCAGAAAAAGCATTAAAGCTGGGGAAATTAGAAGAATCTTCAGCAAAAGAAGCTTTGGATACCAGGATACAAGTGGATCAAAGCTTACTGAACGACACCAAGCTCTCGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGGATACAAGTGGATCAAAGC
59.37
GTGCCGGAGAAATGCATCAC
59.9
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGGATACAAGTGGATCAAAGC
59.37
TGCCGGAGAAATGCATCACA
60.32
144
PCR template sequence:
GCATTAAAGCTGGGGAAATTAGAAGAATCTTCAGCAAAAGAAGCTTTGGATACCAGGATACAAGTGGATCAAAGCTTACTGAACGACACCAAGCTCTCGGGTATGCTATACCTCCGGAGCATGGAAAGCGACTTGAAAGACTAGCCCAAGGCTTCTTCCCCAGTAGCTCCCAAGGCTGTGATGCATTTCTCCGGCACAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-155-5p(1), mmu-miR-673-5p(1), mmu-miR-3061-5p(1), mmu-miR-202-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCAAGCTCTCGGGTATGCTATACCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM4C_722_ORF_1
0.927
0.126409858
0.854449172
666
ORF sequence:
ATGACCCTCATTTCCCCCTCAGTGCTGAAGAAGTATGGCATTCCCTTCGACAAGATCACCCAGGAGGCTGGAGAGTTTATGATCACTTTTCCTTATGGATATCATGCTGGTTTTAATCATGGTTTCAATTGTGCTGAGTCTACAAATTTTGCTACAGTCAGATGGATTGACTACGGCAAGGTTGCTAAGTTGTGCACTTGTCGGAATGACATGGTGAAGATATCAATGGATATATTTGTGAAGAAATTTCAGCCAGATAGATACCAGATTTGGAAACAAGGAAAGGATATATATACTATTGACCATACAAAGCCCACTCCAGAATCTACTCCAGAAGTAAAAACATGGCTACAGAGGAAGAAAAAATTAAGAAAGCCTCCCAAGAGCTTACAGGGCAATAAGCCACTTTGTAAAAGGCCTAAACCTGAAGAAGATGAGGAATTTGCTGAATTTAGTGGGGAAGAGGGTGCAAACCCTGCCATGGGCCCTAGGCACCTCAAAGTCACTGAAAAGCCAGAAAAAGCATTAAAGCTGGGGAAATTAGAAGAATCTTCAGCAAAAGAAGCTTTGGATACCAGGATACAAGTGGATCAAAGCTTACTGAACGACACCAAGCTCTCGGGTATGCTATACCTCCGGAGCATGGAAAGCGACTTGAAAGACTAG
Peptide sequence:
MTLISPSVLKKYGIPFDKITQEAGEFMITFPYGYHAGFNHGFNCAESTNFATVRWIDYGKVAKLCTCRNDMVKISMDIFVKKFQPDRYQIWKQGKDIYTIDHTKPTPESTPEVKTWLQRKKKLRKPPKSLQGNKPLCKRPKPEEDEEFAEFSGEEGANPAMGPRHLKVTEKPEKALKLGKLEESSAKEALDTRIQVDQSLLNDTKLSGMLYLRSMESDLKD
IRESfinder result
IRESfinder score
0.422969715
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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