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mmu_circKif2a_805_1
Basic information of circular RNA
PanCircBase ID:
mmu_circKif2a_805_1
mm39_Chr. Position ID:
chr13|107113493|107123877|-
Gene name:
Kif2a
Transcript:
ENSMUST00000022204.16
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
13,12,11,10,9,8,7,6
Exon/intron offsets:
0,1038,1986,2491,5538,6206,8078,10283
Genomic length:
10384
Exon/intron sizes in nt:
14,39,26,49,11,63,55,90,000
Flanking exon/introns:
chr13:107113368-107113493|chr13:107123877-107124460
Splice length:
805
Other database IDs:
circAtlas: hsa-KIF2A_0018, CIRCpedia: HSA_CIRCpedia_118254
Human Ortholog IDs:
Mature spliced Sequence:
CACGTAGAAAATCCAATTGTGTGAAAGAAGTAGAAAAATTGCAAGAAAAACGAGAAAAAAGGAGATTGCAACAGCAAGAACTTAGAGAAAAAAGAGCCCAGGATGTTGATGCTACAAATCCAAATTACGAAATTATGTGTATGATCAGAGACTTCAGAGGGAGCTTGGATTACAGACCCCTAACAACAGCAGATCCTATTGATGAACATAGGATATGTGTTTGTGTAAGAAAACGACCACTCAATAAAAAAGAAACTCAAATGAAAGATCTTGATGTGATCACAATCCCTAGTAAAGATGTTGTGATGGTCCACGAACCCAAACAGAAAGTAGACTTAACAAGGTACTTAGAAAATCAGACATTTCGGTTTGATTACGCCTTCGATGACTCAGCTCCTAATGAAATGGTTTACAGGTTTACTGCTAGGCCACTAGTGGAAACAATATTTGAAAGGGGCATGGCTACGTGCTTTGCTTATGGGCAGACTGGAAGTGGGAAAACTCATACTATGGGTGGTGACTTTTCAGGAAAGAACCAGGATTGTTCTAAGGGAATTTATGCATTAGCAGCTCGCGATGTCTTTTTAATGCTGAAGAAGCCAAACTATAAGAAACTAGAACTTCAAGTATATGCAACATTTTTTGAAATTTATAGTGGAAAGGTGTTTGACTTACTAAATAGGAAAACAAAATTAAGAGTACTAGAAGATGGGAAGCAGCAGGTCCAAGTGGTGGGGCTGCAGGAGCGGGAGGTGAAGTGTGTGGAGGACGTGCTGAAGCTCATCGACATAGGCAACAGCTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGGTGAAGTGTGTGGAGG
59.96
TCTCTAAGTTCTTGCTGTTGC
56.2
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGAGGTGAAGTGTGTGGAG
59.96
TCTCTAAGTTCTTGCTGTTGC
56.2
146
PCR template sequence:
AAGATGGGAAGCAGCAGGTCCAAGTGGTGGGGCTGCAGGAGCGGGAGGTGAAGTGTGTGGAGGACGTGCTGAAGCTCATCGACATAGGCAACAGCTGCAGCACGTAGAAAATCCAATTGTGTGAAAGAAGTAGAAAAATTGCAAGAAAAACGAGAAAAAAGGAGATTGCAACAGCAAGAACTTAGAGAAAAAAGAGCCCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-29b-1-5p(1), mmu-miR-541-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-377-3p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
GCAACAGCTGCAGCACGTAGAAAATC
siRNA sets
ATTTTCTACGTGCTGCAGC, TTTTCTACGTGCTGCAGCT, GATTTTCTACGTGCTGCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKIF2A_805_1_ORF_1
0.8737
0.084237177
0.829360515
678
ORF sequence:
ATGTGTATGATCAGAGACTTCAGAGGGAGCTTGGATTACAGACCCCTAACAACAGCAGATCCTATTGATGAACATAGGATATGTGTTTGTGTAAGAAAACGACCACTCAATAAAAAAGAAACTCAAATGAAAGATCTTGATGTGATCACAATCCCTAGTAAAGATGTTGTGATGGTCCACGAACCCAAACAGAAAGTAGACTTAACAAGGTACTTAGAAAATCAGACATTTCGGTTTGATTACGCCTTCGATGACTCAGCTCCTAATGAAATGGTTTACAGGTTTACTGCTAGGCCACTAGTGGAAACAATATTTGAAAGGGGCATGGCTACGTGCTTTGCTTATGGGCAGACTGGAAGTGGGAAAACTCATACTATGGGTGGTGACTTTTCAGGAAAGAACCAGGATTGTTCTAAGGGAATTTATGCATTAGCAGCTCGCGATGTCTTTTTAATGCTGAAGAAGCCAAACTATAAGAAACTAGAACTTCAAGTATATGCAACATTTTTTGAAATTTATAGTGGAAAGGTGTTTGACTTACTAAATAGGAAAACAAAATTAAGAGTACTAGAAGATGGGAAGCAGCAGGTCCAAGTGGTGGGGCTGCAGGAGCGGGAGGTGAAGTGTGTGGAGGACGTGCTGAAGCTCATCGACATAGGCAACAGCTGCAGCACGTAG
Peptide sequence:
MCMIRDFRGSLDYRPLTTADPIDEHRICVCVRKRPLNKKETQMKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDSAPNEMVYRFTARPLVETIFERGMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLELQVYATFFEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLIDIGNSCST
IRESfinder result
IRESfinder score
0.512140307
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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