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mmu_circKpna4_649
Basic information of circular RNA
PanCircBase ID:
mmu_circKpna4_649
mm39_Chr. Position ID:
chr3|68993019|69002071|-
Gene name:
Kpna4
Transcript:
ENSMUST00000029353.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
12,11,10,9,8,7
Exon/intron offsets:
0,1770,4089,4221,7123,8966
Genomic length:
9052
Exon/intron sizes in nt:
129,132,45,170,87,86
Flanking exon/introns:
chr3:68991487-68993019|chr3:69002071-69002852
Splice length:
649
Other database IDs:
CIRCpedia: MMU_CIRCpedia_27113, circAtlas: mmu-Kpna4_0020
Human Ortholog IDs:
Mature spliced Sequence:
TCCTTCTTTACAGTTTGAAGCTGCGTGGGCTTTGACAAACATTGCATCTGGAACGTCTGAACAAACGCAAGCAGTGGTTCAGTCCAATGCTGTGCCACTTTTCTTGAGGCTTCTGCATTCACCCCATCAGAATGTCTGTGAACAGGCAGTATGGGCGTTGGGAAACATCATAGGTGATGGACCTCAGTGTAGAGATTATGTGATAAGTCTTGGAGTTGTAAAACCTCTGCTTTCATTCATAAGTCCATCTATTCCTATAACATTCTTAAGAAATGTTACCTGGGTTATGGTCAATTTATGTCGCCACAAAGACCCACCACCACCAATGGAGACAATTCAGGAGATTCTTCCAGCTCTTTGTGTATTAATTCATCACACAGATGTAAATATCCTGGTAGATACTGTCTGGGCCCTGTCTTACCTTACGGATGCTGGCAATGAACAGATACAGATGGTAATAGACTCTGGCATAGTTCCTCACTTGGTTCCGCTACTCAGCCACCAGGAAGTTAAAGTTCAGACTGCTGCACTGCGAGCTGTGGGCAACATTGTCACTGGAACTGATGAGCAAACACAAGTAGTTTTAAACTGTGATGCTCTCTCACACTTCCCAGCACTCCTCACTCATCCCAAAGAGAAAATTAATAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAGCACTCCTCACTCATC
59.82
AAGTGGCACAGCATTGGACT
60.18
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTTCCCAGCACTCCTCACTC
59.75
AAGTGGCACAGCATTGGACT
60.18
143
PCR template sequence:
TGTCACTGGAACTGATGAGCAAACACAAGTAGTTTTAAACTGTGATGCTCTCTCACACTTCCCAGCACTCCTCACTCATCCCAAAGAGAAAATTAATAAATCCTTCTTTACAGTTTGAAGCTGCGTGGGCTTTGACAAACATTGCATCTGGAACGTCTGAACAAACGCAAGCAGTGGTTCAGTCCAATGCTGTGCCACTT
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-103-3p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-136-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-107-3p(1), mmu-miR-669d-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAAATTAATAAATCCTTCTTTACAG
siRNA sets
GAAGGATTTATTAATTTTC, AAAGAAGGATTTATTAATT, TAAAGAAGGATTTATTAAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKPNA4_649_ORF_1
0.9915
-0.04838462
0.811545474
705
ORF sequence:
ATGCTCTCTCACACTTCCCAGCACTCCTCACTCATCCCAAAGAGAAAATTAATAAATCCTTCTTTACAGTTTGAAGCTGCGTGGGCTTTGACAAACATTGCATCTGGAACGTCTGAACAAACGCAAGCAGTGGTTCAGTCCAATGCTGTGCCACTTTTCTTGAGGCTTCTGCATTCACCCCATCAGAATGTCTGTGAACAGGCAGTATGGGCGTTGGGAAACATCATAGGTGATGGACCTCAGTGTAGAGATTATGTGATAAGTCTTGGAGTTGTAAAACCTCTGCTTTCATTCATAAGTCCATCTATTCCTATAACATTCTTAAGAAATGTTACCTGGGTTATGGTCAATTTATGTCGCCACAAAGACCCACCACCACCAATGGAGACAATTCAGGAGATTCTTCCAGCTCTTTGTGTATTAATTCATCACACAGATGTAAATATCCTGGTAGATACTGTCTGGGCCCTGTCTTACCTTACGGATGCTGGCAATGAACAGATACAGATGGTAATAGACTCTGGCATAGTTCCTCACTTGGTTCCGCTACTCAGCCACCAGGAAGTTAAAGTTCAGACTGCTGCACTGCGAGCTGTGGGCAACATTGTCACTGGAACTGATGAGCAAACACAAGTAGTTTTAAACTGTGATGCTCTCTCACACTTCCCAGCACTCCTCACTCATCCCAAAGAGAAAATTAATAAA
Peptide sequence:
MLSHTSQHSSLIPKRKLINPSLQFEAAWALTNIASGTSEQTQAVVQSNAVPLFLRLLHSPHQNVCEQAVWALGNIIGDGPQCRDYVISLGVVKPLLSFISPSIPITFLRNVTWVMVNLCRHKDPPPPMETIQEILPALCVLIHHTDVNILVDTVWALSYLTDAGNEQIQMVIDSGIVPHLVPLLSHQEVKVQTAALRAVGNIVTGTDEQTQVVLNCDALSHFPALLTHPKEKINK
IRESfinder result
IRESfinder score
0.74849707
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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