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mmu_circKmt2c_575
Basic information of circular RNA
PanCircBase ID:
mmu_circKmt2c_575
mm39_Chr. Position ID:
chr5|25525304|25534271|-
Gene name:
Kmt2c
Transcript:
ENSMUST00000045291.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
34,33,32,31,30
Exon/intron offsets:
0,3345,3782,8716,8934
Genomic length:
8967
Exon/intron sizes in nt:
74,215,133,120,33
Flanking exon/introns:
chr5:25524172-25525304|chr5:25534271-25534444
Splice length:
575
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GAGCAATTCTTGGAAAGTTATATAAAATTCCAGAGCTTGGAGGAAAGGATGTTGAAGACTTGTTTACTGCTGTACTTAGCCCTGCTACCACTCAGCCAGCTCCATTACCACAGCCTCCCCCTCCACCACAGCTATTGCCAATGCACAATCAGGATGTTTTTTCCCGGATGCCACTCATGAATGGCCTTATTGGACCCAGTCCTCACCTTCCACATAATTCTTTGCCTCCTGGAAGTGGATTGGGGACTTTCCCTGCTATAGCACAATCCCCTTATACTGATGTCAGGGATAAAAGTCCAGCATTTAATGCAATTGCAAGTGATCCTAACAGCTCCTGGGCACCAACAACTCCAAGTATGGAAGGAGAAAATGACACCCTGTCAAATGCACAGAGGAGCACATTGAAGTGGGAGAAAGAGGAGGCTCTTGGTGAGATGGCAACAGTAGCACCAGTTCTCTACACAAATATTAATTTCCCCAATTTAAAGGAAGAATTCCCAGATTGGACTACTCGAGTGAAACAAATTGCCAAGTTGTGGAGAAAAGCCAGCTCTCAGGAAAGAGCACCATATGTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGGAGAAAAGCCAGCTCT
59.23
CTGGCTGAGTGGTAGCAGG
59.78
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGGAGAAAAGCCAGCTCT
59.23
GCTGGCTGAGTGGTAGCAG
60.45
141
PCR template sequence:
CCCCAATTTAAAGGAAGAATTCCCAGATTGGACTACTCGAGTGAAACAAATTGCCAAGTTGTGGAGAAAAGCCAGCTCTCAGGAAAGAGCACCATATGTGGAGCAATTCTTGGAAAGTTATATAAAATTCCAGAGCTTGGAGGAAAGGATGTTGAAGACTTGTTTACTGCTGTACTTAGCCCTGCTACCACTCAGCCAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-182-5p(2), mmu-miR-210-3p(1), mmu-miR-30e-5p(1), mmu-miR-33-5p(1), mmu-miR-30a-5p(1), mmu-miR-705(1), mmu-miR-670-5p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
AGCACCATATGTGGAGCAATTCTTGG
siRNA sets
AGAATTGCTCCACATATGG, GAATTGCTCCACATATGGT, AAGAATTGCTCCACATATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKMT2C_575_ORF_1
0.6195
-0.031516784
0.547658726
615
ORF sequence:
ATGCACAATCAGGATGTTTTTTCCCGGATGCCACTCATGAATGGCCTTATTGGACCCAGTCCTCACCTTCCACATAATTCTTTGCCTCCTGGAAGTGGATTGGGGACTTTCCCTGCTATAGCACAATCCCCTTATACTGATGTCAGGGATAAAAGTCCAGCATTTAATGCAATTGCAAGTGATCCTAACAGCTCCTGGGCACCAACAACTCCAAGTATGGAAGGAGAAAATGACACCCTGTCAAATGCACAGAGGAGCACATTGAAGTGGGAGAAAGAGGAGGCTCTTGGTGAGATGGCAACAGTAGCACCAGTTCTCTACACAAATATTAATTTCCCCAATTTAAAGGAAGAATTCCCAGATTGGACTACTCGAGTGAAACAAATTGCCAAGTTGTGGAGAAAAGCCAGCTCTCAGGAAAGAGCACCATATGTGGAGCAATTCTTGGAAAGTTATATAAAATTCCAGAGCTTGGAGGAAAGGATGTTGAAGACTTGTTTACTGCTGTACTTAGCCCTGCTACCACTCAGCCAGCTCCATTACCACAGCCTCCCCCTCCACCACAGCTATTGCCAATGCACAATCAGGATGTTTTTTCCCGGATGCCACTCATGA
Peptide sequence:
MHNQDVFSRMPLMNGLIGPSPHLPHNSLPPGSGLGTFPAIAQSPYTDVRDKSPAFNAIASDPNSSWAPTTPSMEGENDTLSNAQRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVEQFLESYIKFQSLEERMLKTCLLLYLALLPLSQLHYHSLPLHHSYCQCTIRMFFPGCHS
IRESfinder result
IRESfinder score
0.610057343
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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