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mmu_circKdm2a_792
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm2a_792
mm39_Chr. Position ID:
chr19|4392874|4400358|-
Gene name:
Kdm2a
Transcript:
ENSMUST00000047898.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
12,11,10,9
Exon/intron offsets:
0,2671,5799,7330
Genomic length:
7484
Exon/intron sizes in nt:
3,95,12,71,16,154
Flanking exon/introns:
chr19:4381297-4392874|chr19:4400358-4401764
Splice length:
792
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_5210
Human Ortholog IDs:
Mature spliced Sequence:
GTCTTCTGGCTCATCCCCCCTACAGCCCACAACCTGGAGCTGTACGAGAATTGGCTGCTATCAGGGAAACAGGGAGACATCTTTCTGGGTGACCGGGTGTCAGATTGCCAACGAATTGAGCTCAAGCAGGGCTATACCTTCGTTATTCCCTCAGGTTGGATTCATGCTGTGTATACTCCTACAGACACATTAGTGTTTGGAGGCAATTTTTTGCATAGCTTCAACATCCCCATGCAATTAAAGATATACAGCATTGAAGATCGAACACGGGTTCCAAATAAATTCCGTTACCCATTTTACTATGAAATGTGTTGGTATGTGTTGGAGCGCTATGTATACTGCATAACCAACCGATCCCACCTAACTAAGGATTTTCAGAAAGAATCCCTTAGCATGGATATGGAGTTAAATGAGTTGGAGTCTGGAAATGGTGATGAGGAAGGGGTGGACAGAGAAGCCCGACGCATGAACAATAAGCGATCTGTGCTTACCAGCCCTGTTGCTAATGGAGTGAACCTGGATTACGATGGACTTGGCAAAGCCTGCCGAAGTCTTCCAAGTCTGAAGAAAACTTTGTCTGGAGACTCATCCTCAGACTCTACCCGGGGATCCCACAATGGCCAAGTTTGGGATCCCCAATGTAGCCCTAAAAAGGATAGGCAAGTGCATCTCACCCATTTTGAACTTGAAGGTCTTCGATGTCTTGTAGATAAGTTAGAGTCACTGCCACTGCACAAGAAGTGTGTCCCCACAGGAATAGAAGACGAAGATGCTCTGATTGCTGATGTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGCCACTGCACAAGAAGT
60.11
CCGGTCACCCAGAAAGATGT
59.68
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCACTGCCACTGCACAAGAA
60.11
CCGGTCACCCAGAAAGATGT
59.68
168
PCR template sequence:
TCTTCGATGTCTTGTAGATAAGTTAGAGTCACTGCCACTGCACAAGAAGTGTGTCCCCACAGGAATAGAAGACGAAGATGCTCTGATTGCTGATGTAAAGGTCTTCTGGCTCATCCCCCCTACAGCCCACAACCTGGAGCTGTACGAGAATTGGCTGCTATCAGGGAAACAGGGAGACATCTTTCTGGGTGACCGGGTGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-7b-5p(1), mmu-miR-221-3p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-7a-5p(1), mmu-miR-182-5p(1), mmu-miR-541-5p(1), mmu-miR-34b-5p(1), mmu-miR-466d-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCTGATGTAAAGGTCTTCTGGCTCA
siRNA sets
GAAGACCTTTACATCAGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM2A_792_ORF_1
0.8646
0.195187575
0.998982543
1353
ORF sequence:
ATGCAATTAAAGATATACAGCATTGAAGATCGAACACGGGTTCCAAATAAATTCCGTTACCCATTTTACTATGAAATGTGTTGGTATGTGTTGGAGCGCTATGTATACTGCATAACCAACCGATCCCACCTAACTAAGGATTTTCAGAAAGAATCCCTTAGCATGGATATGGAGTTAAATGAGTTGGAGTCTGGAAATGGTGATGAGGAAGGGGTGGACAGAGAAGCCCGACGCATGAACAATAAGCGATCTGTGCTTACCAGCCCTGTTGCTAATGGAGTGAACCTGGATTACGATGGACTTGGCAAAGCCTGCCGAAGTCTTCCAAGTCTGAAGAAAACTTTGTCTGGAGACTCATCCTCAGACTCTACCCGGGGATCCCACAATGGCCAAGTTTGGGATCCCCAATGTAGCCCTAAAAAGGATAGGCAAGTGCATCTCACCCATTTTGAACTTGAAGGTCTTCGATGTCTTGTAGATAAGTTAGAGTCACTGCCACTGCACAAGAAGTGTGTCCCCACAGGAATAGAAGACGAAGATGCTCTGATTGCTGATGTAAAGGTCTTCTGGCTCATCCCCCCTACAGCCCACAACCTGGAGCTGTACGAGAATTGGCTGCTATCAGGGAAACAGGGAGACATCTTTCTGGGTGACCGGGTGTCAGATTGCCAACGAATTGAGCTCAAGCAGGGCTATACCTTCGTTATTCCCTCAGGTTGGATTCATGCTGTGTATACTCCTACAGACACATTAGTGTTTGGAGGCAATTTTTTGCATAGCTTCAACATCCCCATGCAATTAAAGATATACAGCATTGAAGATCGAACACGGGTTCCAAATAAATTCCGTTACCCATTTTACTATGAAATGTGTTGGTATGTGTTGGAGCGCTATGTATACTGCATAACCAACCGATCCCACCTAACTAAGGATTTTCAGAAAGAATCCCTTAGCATGGATATGGAGTTAAATGAGTTGGAGTCTGGAAATGGTGATGAGGAAGGGGTGGACAGAGAAGCCCGACGCATGAACAATAAGCGATCTGTGCTTACCAGCCCTGTTGCTAATGGAGTGAACCTGGATTACGATGGACTTGGCAAAGCCTGCCGAAGTCTTCCAAGTCTGAAGAAAACTTTGTCTGGAGACTCATCCTCAGACTCTACCCGGGGATCCCACAATGGCCAAGTTTGGGATCCCCAATGTAGCCCTAAAAAGGATAGGCAAGTGCATCTCACCCATTTTGAACTTGAAGGTCTTCGATGTCTTGTAGATAAGTTAGAGTCACTGCCACTGCACAAGAAGTGTGTCCCCACAGGAATAGAAGACGAAGATGCTCTGATTGCTGATGTAAAG
Peptide sequence:
MQLKIYSIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKDFQKESLSMDMELNELESGNGDEEGVDREARRMNNKRSVLTSPVANGVNLDYDGLGKACRSLPSLKKTLSGDSSSDSTRGSHNGQVWDPQCSPKKDRQVHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDEDALIADVKVFWLIPPTAHNLELYENWLLSGKQGDIFLGDRVSDCQRIELKQGYTFVIPSGWIHAVYTPTDTLVFGGNFLHSFNIPMQLKIYSIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKDFQKESLSMDMELNELESGNGDEEGVDREARRMNNKRSVLTSPVANGVNLDYDGLGKACRSLPSLKKTLSGDSSSDSTRGSHNGQVWDPQCSPKKDRQVHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDEDALIADVK
IRESfinder result
IRESfinder score
0.567323353
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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