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mmu_circKdm2a_1042
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm2a_1042
mm39_Chr. Position ID:
chr19|4395545|4412942|-
Gene name:
Kdm2a
Transcript:
ENSMUST00000047898.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
11,10,9,8,7,6,5,4,3
Exon/intron offsets:
0,3128,4659,6219,6750,11230,16020,16459,17258
Genomic length:
17397
Exon/intron sizes in nt:
127,116,154,94,107,179,47,79,139
Flanking exon/introns:
chr19:4393269-4395545|chr19:4412942-4444819
Splice length:
1042
Other database IDs:
circAtlas: mmu-Kdm2a_0006
circBase: hsa_circ_0023055, circAtlas: hsa-KDM2A_0007
Human Ortholog IDs:
Mature spliced Sequence:
CGTGGTACCATGCGTCGTCGCTATGAAGATGATGGCATTTCAGATGATGAAATTGAAGGGAAAAGAACTTTTGACTTGGAAGAGAAGCTCCAAACCAACAAATATAATGCCAATTTTGTTACTTTTATGGAGGGAAAAGATTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATAAAGATGCCGGATCCAGACTTCACAGTGAATGATGTCAAAATGTGTGTGGGGAGTCGTCGGATGGTGGATGTCATGGATGTGAACACACAGAAGGGGATTGAAATGACCATGGCACAATGGACACGATACTATGAGACTCCAGAGGAAGAGCGAGAAAAACTCTATAATGTTATCAGCCTAGAGTTTAGCCACACCAGGCTTGAGAATATGGTGCAGCGGCCTTCCACGGTGGATTTCATTGACTGGGTAGATAACATGTGGCCAAGGCACTTGAAAGAAAGTCAGACAGAATCAACAAATGCCATCTTAGAGATGCAGTACCCTAAAGTGCAAAAGTACTGTCTAATGAGTGTTCGAGGCTGCTATACTGACTTCCATGTGGATTTTGGAGGTACTTCTGTTTGGTATCACATCCACCAAGGTGGAAAGGTCTTCTGGCTCATCCCCCCTACAGCCCACAACCTGGAGCTGTACGAGAATTGGCTGCTATCAGGGAAACAGGGAGACATCTTTCTGGGTGACCGGGTGTCAGATTGCCAACGAATTGAGCTCAAGCAGGGCTATACCTTCGTTATTCCCTCAGGTTGGATTCATGCTGTGTATACTCCTACAGACACATTAGTGTTTGGAGGCAATTTTTTGCATAGCTTCAACATCCCCATGCAATTAAAGATATACAGCATTGAAGATCGAACACGGGTTCCAAATAAATTCCGTTACCCATTTTACTATGAAATGTGTTGGTATGTGTTGGAGCGCTATGTATACTGCATAACCAACCGATCCCACCTAACTAAGGATTTTCAGAAAGAATCCCTTAGCATGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGTATGTGTTGGAGCGCT
59.96
TGGAGCTTCTCTTCCAAGTCA
58.67
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCAACCGATCCCACCTAAC
59.38
TGGTTTGGAGCTTCTCTTCCA
59.23
149
PCR template sequence:
TACTATGAAATGTGTTGGTATGTGTTGGAGCGCTATGTATACTGCATAACCAACCGATCCCACCTAACTAAGGATTTTCAGAAAGAATCCCTTAGCATGGCGTGGTACCATGCGTCGTCGCTATGAAGATGATGGCATTTCAGATGATGAAATTGAAGGGAAAAGAACTTTTGACTTGGAAGAGAAGCTCCAAACCAACA
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-382-3p(1), mmu-miR-182-5p(1), mmu-miR-541-5p(1), mmu-miR-466d-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCCTTAGCATGGCGTGGTACCATGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM2A_1042_ORF_1
0.9584
0.202180217
0.993030236
1059
ORF sequence:
ATGCGTCGTCGCTATGAAGATGATGGCATTTCAGATGATGAAATTGAAGGGAAAAGAACTTTTGACTTGGAAGAGAAGCTCCAAACCAACAAATATAATGCCAATTTTGTTACTTTTATGGAGGGAAAAGATTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATAAAGATGCCGGATCCAGACTTCACAGTGAATGATGTCAAAATGTGTGTGGGGAGTCGTCGGATGGTGGATGTCATGGATGTGAACACACAGAAGGGGATTGAAATGACCATGGCACAATGGACACGATACTATGAGACTCCAGAGGAAGAGCGAGAAAAACTCTATAATGTTATCAGCCTAGAGTTTAGCCACACCAGGCTTGAGAATATGGTGCAGCGGCCTTCCACGGTGGATTTCATTGACTGGGTAGATAACATGTGGCCAAGGCACTTGAAAGAAAGTCAGACAGAATCAACAAATGCCATCTTAGAGATGCAGTACCCTAAAGTGCAAAAGTACTGTCTAATGAGTGTTCGAGGCTGCTATACTGACTTCCATGTGGATTTTGGAGGTACTTCTGTTTGGTATCACATCCACCAAGGTGGAAAGGTCTTCTGGCTCATCCCCCCTACAGCCCACAACCTGGAGCTGTACGAGAATTGGCTGCTATCAGGGAAACAGGGAGACATCTTTCTGGGTGACCGGGTGTCAGATTGCCAACGAATTGAGCTCAAGCAGGGCTATACCTTCGTTATTCCCTCAGGTTGGATTCATGCTGTGTATACTCCTACAGACACATTAGTGTTTGGAGGCAATTTTTTGCATAGCTTCAACATCCCCATGCAATTAAAGATATACAGCATTGAAGATCGAACACGGGTTCCAAATAAATTCCGTTACCCATTTTACTATGAAATGTGTTGGTATGTGTTGGAGCGCTATGTATACTGCATAACCAACCGATCCCACCTAACTAAGGATTTTCAGAAAGAATCCCTTAGCATGGCGTGGTACCATGCGTCGTCGCTATGA
Peptide sequence:
MRRRYEDDGISDDEIEGKRTFDLEEKLQTNKYNANFVTFMEGKDFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFTVNDVKMCVGSRRMVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKESQTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDFGGTSVWYHIHQGGKVFWLIPPTAHNLELYENWLLSGKQGDIFLGDRVSDCQRIELKQGYTFVIPSGWIHAVYTPTDTLVFGGNFLHSFNIPMQLKIYSIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKDFQKESLSMAWYHASSL
IRESfinder result
IRESfinder score
0.498375866
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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