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mmu_circKdm2a_1538
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm2a_1538
mm39_Chr. Position ID:
chr19|4392874|4444920|-
Gene name:
Kdm2a
Transcript:
ENSMUST00000047898.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
12,11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,2671,5799,7330,8890,9421,13901,18691,19130,19929,51945
Genomic length:
52046
Exon/intron sizes in nt:
395,127,116,154,94,107,179,47,79,139,101
Flanking exon/introns:
chr19:4381297-4392874|chr19:4444920-4447961
Splice length:
1538
Other database IDs:
circBase: mmu_circ_0007804, CIRCpedia: MMU_CIRCpedia_20084, circAtlas: mmu-Kdm2a_0020
Human Ortholog IDs:
Mature spliced Sequence:
GAAGAGGAAGGCATCCCTGGAGTGGTTTCTTTACTGTACTTCCATCAGAAGAGTGAGAGATGGAACCTGAAGAAGAAAGGATTCGGTACAGCCAGAGATTGCGTGGTACCATGCGTCGTCGCTATGAAGATGATGGCATTTCAGATGATGAAATTGAAGGGAAAAGAACTTTTGACTTGGAAGAGAAGCTCCAAACCAACAAATATAATGCCAATTTTGTTACTTTTATGGAGGGAAAAGATTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATAAAGATGCCGGATCCAGACTTCACAGTGAATGATGTCAAAATGTGTGTGGGGAGTCGTCGGATGGTGGATGTCATGGATGTGAACACACAGAAGGGGATTGAAATGACCATGGCACAATGGACACGATACTATGAGACTCCAGAGGAAGAGCGAGAAAAACTCTATAATGTTATCAGCCTAGAGTTTAGCCACACCAGGCTTGAGAATATGGTGCAGCGGCCTTCCACGGTGGATTTCATTGACTGGGTAGATAACATGTGGCCAAGGCACTTGAAAGAAAGTCAGACAGAATCAACAAATGCCATCTTAGAGATGCAGTACCCTAAAGTGCAAAAGTACTGTCTAATGAGTGTTCGAGGCTGCTATACTGACTTCCATGTGGATTTTGGAGGTACTTCTGTTTGGTATCACATCCACCAAGGTGGAAAGGTCTTCTGGCTCATCCCCCCTACAGCCCACAACCTGGAGCTGTACGAGAATTGGCTGCTATCAGGGAAACAGGGAGACATCTTTCTGGGTGACCGGGTGTCAGATTGCCAACGAATTGAGCTCAAGCAGGGCTATACCTTCGTTATTCCCTCAGGTTGGATTCATGCTGTGTATACTCCTACAGACACATTAGTGTTTGGAGGCAATTTTTTGCATAGCTTCAACATCCCCATGCAATTAAAGATATACAGCATTGAAGATCGAACACGGGTTCCAAATAAATTCCGTTACCCATTTTACTATGAAATGTGTTGGTATGTGTTGGAGCGCTATGTATACTGCATAACCAACCGATCCCACCTAACTAAGGATTTTCAGAAAGAATCCCTTAGCATGGATATGGAGTTAAATGAGTTGGAGTCTGGAAATGGTGATGAGGAAGGGGTGGACAGAGAAGCCCGACGCATGAACAATAAGCGATCTGTGCTTACCAGCCCTGTTGCTAATGGAGTGAACCTGGATTACGATGGACTTGGCAAAGCCTGCCGAAGTCTTCCAAGTCTGAAGAAAACTTTGTCTGGAGACTCATCCTCAGACTCTACCCGGGGATCCCACAATGGCCAAGTTTGGGATCCCCAATGTAGCCCTAAAAAGGATAGGCAAGTGCATCTCACCCATTTTGAACTTGAAGGTCTTCGATGTCTTGTAGATAAGTTAGAGTCACTGCCACTGCACAAGAAGTGTGTCCCCACAGGAATAGAAGACGAAGATGCTCTGATTGCTGATGTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGCCACTGCACAAGAAGT
60.11
TCTCTGGCTGTACCGAATCC
58.89
168
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCACTGCCACTGCACAAGAA
60.11
TCTCTGGCTGTACCGAATCC
58.89
170
PCR template sequence:
TCTTCGATGTCTTGTAGATAAGTTAGAGTCACTGCCACTGCACAAGAAGTGTGTCCCCACAGGAATAGAAGACGAAGATGCTCTGATTGCTGATGTAAAGGAAGAGGAAGGCATCCCTGGAGTGGTTTCTTTACTGTACTTCCATCAGAAGAGTGAGAGATGGAACCTGAAGAAGAAAGGATTCGGTACAGCCAGAGATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
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-382-3p(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
TGCTGATGTAAAGGAAGAGGAAGGCA
siRNA sets
TTCCTCTTCCTTTACATCA, CTCTTCCTTTACATCAGCA, CTTCCTCTTCCTTTACATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM2A_1538_ORF_1
0.8523
0.1873836
0.999927188
1731
ORF sequence:
ATGGAACCTGAAGAAGAAAGGATTCGGTACAGCCAGAGATTGCGTGGTACCATGCGTCGTCGCTATGAAGATGATGGCATTTCAGATGATGAAATTGAAGGGAAAAGAACTTTTGACTTGGAAGAGAAGCTCCAAACCAACAAATATAATGCCAATTTTGTTACTTTTATGGAGGGAAAAGATTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATAAAGATGCCGGATCCAGACTTCACAGTGAATGATGTCAAAATGTGTGTGGGGAGTCGTCGGATGGTGGATGTCATGGATGTGAACACACAGAAGGGGATTGAAATGACCATGGCACAATGGACACGATACTATGAGACTCCAGAGGAAGAGCGAGAAAAACTCTATAATGTTATCAGCCTAGAGTTTAGCCACACCAGGCTTGAGAATATGGTGCAGCGGCCTTCCACGGTGGATTTCATTGACTGGGTAGATAACATGTGGCCAAGGCACTTGAAAGAAAGTCAGACAGAATCAACAAATGCCATCTTAGAGATGCAGTACCCTAAAGTGCAAAAGTACTGTCTAATGAGTGTTCGAGGCTGCTATACTGACTTCCATGTGGATTTTGGAGGTACTTCTGTTTGGTATCACATCCACCAAGGTGGAAAGGTCTTCTGGCTCATCCCCCCTACAGCCCACAACCTGGAGCTGTACGAGAATTGGCTGCTATCAGGGAAACAGGGAGACATCTTTCTGGGTGACCGGGTGTCAGATTGCCAACGAATTGAGCTCAAGCAGGGCTATACCTTCGTTATTCCCTCAGGTTGGATTCATGCTGTGTATACTCCTACAGACACATTAGTGTTTGGAGGCAATTTTTTGCATAGCTTCAACATCCCCATGCAATTAAAGATATACAGCATTGAAGATCGAACACGGGTTCCAAATAAATTCCGTTACCCATTTTACTATGAAATGTGTTGGTATGTGTTGGAGCGCTATGTATACTGCATAACCAACCGATCCCACCTAACTAAGGATTTTCAGAAAGAATCCCTTAGCATGGATATGGAGTTAAATGAGTTGGAGTCTGGAAATGGTGATGAGGAAGGGGTGGACAGAGAAGCCCGACGCATGAACAATAAGCGATCTGTGCTTACCAGCCCTGTTGCTAATGGAGTGAACCTGGATTACGATGGACTTGGCAAAGCCTGCCGAAGTCTTCCAAGTCTGAAGAAAACTTTGTCTGGAGACTCATCCTCAGACTCTACCCGGGGATCCCACAATGGCCAAGTTTGGGATCCCCAATGTAGCCCTAAAAAGGATAGGCAAGTGCATCTCACCCATTTTGAACTTGAAGGTCTTCGATGTCTTGTAGATAAGTTAGAGTCACTGCCACTGCACAAGAAGTGTGTCCCCACAGGAATAGAAGACGAAGATGCTCTGATTGCTGATGTAAAGGAAGAGGAAGGCATCCCTGGAGTGGTTTCTTTACTGTACTTCCATCAGAAGAGTGAGAGATGGAACCTGAAGAAGAAAGGATTCGGTACAGCCAGAGATTGCGTGGTACCATGCGTCGTCGCTATGAAGATGATGGCATTTCAGATGATGAAATTGAAGGGAAAAGAACTTTTGACTTGGAAGAGAAGCTCCAAACCAACAAATATAATGCCAATTTTGTTACTTTTATGGAGGGAAAAGATTTTAATGTAG
Peptide sequence:
MEPEEERIRYSQRLRGTMRRRYEDDGISDDEIEGKRTFDLEEKLQTNKYNANFVTFMEGKDFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFTVNDVKMCVGSRRMVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKESQTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDFGGTSVWYHIHQGGKVFWLIPPTAHNLELYENWLLSGKQGDIFLGDRVSDCQRIELKQGYTFVIPSGWIHAVYTPTDTLVFGGNFLHSFNIPMQLKIYSIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKDFQKESLSMDMELNELESGNGDEEGVDREARRMNNKRSVLTSPVANGVNLDYDGLGKACRSLPSLKKTLSGDSSSDSTRGSHNGQVWDPQCSPKKDRQVHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDEDALIADVKEEEGIPGVVSLLYFHQKSERWNLKKKGFGTARDCVVPCVVAMKMMAFQMMKLKGKELLTWKRSSKPTNIMPILLLLWREKILM
IRESfinder result
IRESfinder score
0.484629341
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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