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mmu_circSnrk_1264
Basic information of circular RNA
PanCircBase ID:
mmu_circSnrk_1264
mm39_Chr. Position ID:
chr9|121961693|121989601|+
Gene name:
Snrk
Transcript:
ENSMUST00000134949.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
3,4,5,6,7
Exon/intron offsets:
0,1359,4278,24528,27695
Genomic length:
27908
Exon/intron sizes in nt:
1,23,90,69,61,42,213
Flanking exon/introns:
chr9:121961008-121961693|chr9:121989601-121992982
Splice length:
1264
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AATGCATCTTAACAGAAATACAGAGGAAAAGAATAAAGACGAGAAAATGGCGTAGGCAGTCCCAAGAAATGTTTTGAAGGTGAAAGTTGAATTTGCAAAAATATGCAGCATATACTTAGACAGTTTCCTTGGCTTTAAGATGAGACAGTCTGACCTCAGGAACCTGTGACAGAGTACAGTCCCACTTCCACGAGTGCCTGTGGAAAGATTTCAGTATCCATTATGATGTTGACAATGAAGGCCTTATTTCCAACAGATATACTCATATGAGAAGACCCACTTCAAGCACTTTTAAGTATCTTTCTGTTTGTTGAACCAGCATGGCAGGGTTCAAGCGAGGATATGATGGGAAAATTGCTGGATTATATGATCTGGATAAAACCTTGGGTCGAGGTCATTTTGCAGTGGTCAAACTTGCCAGGCATGTCTTCACAGGTGAGAAGGTGGCAGTGAAAGTCATTGACAAGACGAAGCTGGACACTCTAGCCACTGGTCATCTCTTCCAGGAAGTGAGGTGCATGAAACTAGTGCAGCACCCCAACATTGTGCGTCTCTATGAAGTCATAGACACCCAGACCAAACTTTATCTCATTCTAGAACTTGGAGATGGAGGAGATATGTTTGATTATATAATGAAGCACGAGGAGGGTCTTAATGAAGACTTGGCCAAGAAGTACTTTGCTCAGATAGTTCATGCTATATCTTATTGCCATAAACTCCATGTGGTCCACAGAGACTTGAAACCAGAGAATGTAGTCTTTTTTGAAAAACAAGGTCTTGTGAAGTTGACAGACTTTGGCTTCAGCAACAAATTTCAGCCTGGAAAGAAACTCACCACGAGCTGCGGGTCTCTTGCATACTCTGCTCCAGAAATCCTGCTTGGCGATGAGTACGATGCCCCTGCAGTAGACATATGGAGCCTGGGCGTGATCCTTTTCATGCTGGTGTGTGGGCAGCCACCCTTCCAAGAAGCCAACGACAGCGAGACACTGACCATGATCATGGACTGCAAGTACACGGTGCCACCCCGCGTGTCTGCAGGGTGCAGGGACCTGATCACACGAATGCTACAGAGAGACCCCAAAAGGAGAGCCTCTCTGGAAGAGATTGAAAGCCACCCTTGGCTCCAGGGAGTGGACCCATCACCAGCCACCAAGTATAACATTCCCCTCGTGTCCTACAAGAACCTCTCCGAGGAAGAGCACAACAGCATCATCCAGCGCATGGTGCTCGGGGACATCGCGGACCGAGACGCCATCGTAGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCCCTCGTGTCCTACAAGA
59.59
TGCCTACGCCATTTTCTCGT
60.04
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCGAGGAAGAGCACAACAG
59.68
TTTCTTGGGACTGCCTACGC
60.32
143
PCR template sequence:
TTCCCCTCGTGTCCTACAAGAACCTCTCCGAGGAAGAGCACAACAGCATCATCCAGCGCATGGTGCTCGGGGACATCGCGGACCGAGACGCCATCGTAGAAATGCATCTTAACAGAAATACAGAGGAAAAGAATAAAGACGAGAAAATGGCGTAGGCAGTCCCAAGAAATGTTTTGAAGGTGAAAGTTGAATTTGCAAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-20a-5p(2), mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-17-5p(1), mmu-miR-106b-5p(1), mmu-miR-495-3p(1), mmu-miR-434-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-129-5p(1), mmu-miR-3065-5p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACGCCATCGTAGAAATGCATCTTAAC
siRNA sets
GTTAAGATGCATTTCTACG,TTAAGATGCATTTCTACGA,GATGCATTTCTACGATGGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSNRK_1264_ORF_1
1.2803
0.295318397
0.995910646
999
ORF sequence:
ATGGCAGGGTTCAAGCGAGGATATGATGGGAAAATTGCTGGATTATATGATCTGGATAAAACCTTGGGTCGAGGTCATTTTGCAGTGGTCAAACTTGCCAGGCATGTCTTCACAGGTGAGAAGGTGGCAGTGAAAGTCATTGACAAGACGAAGCTGGACACTCTAGCCACTGGTCATCTCTTCCAGGAAGTGAGGTGCATGAAACTAGTGCAGCACCCCAACATTGTGCGTCTCTATGAAGTCATAGACACCCAGACCAAACTTTATCTCATTCTAGAACTTGGAGATGGAGGAGATATGTTTGATTATATAATGAAGCACGAGGAGGGTCTTAATGAAGACTTGGCCAAGAAGTACTTTGCTCAGATAGTTCATGCTATATCTTATTGCCATAAACTCCATGTGGTCCACAGAGACTTGAAACCAGAGAATGTAGTCTTTTTTGAAAAACAAGGTCTTGTGAAGTTGACAGACTTTGGCTTCAGCAACAAATTTCAGCCTGGAAAGAAACTCACCACGAGCTGCGGGTCTCTTGCATACTCTGCTCCAGAAATCCTGCTTGGCGATGAGTACGATGCCCCTGCAGTAGACATATGGAGCCTGGGCGTGATCCTTTTCATGCTGGTGTGTGGGCAGCCACCCTTCCAAGAAGCCAACGACAGCGAGACACTGACCATGATCATGGACTGCAAGTACACGGTGCCACCCCGCGTGTCTGCAGGGTGCAGGGACCTGATCACACGAATGCTACAGAGAGACCCCAAAAGGAGAGCCTCTCTGGAAGAGATTGAAAGCCACCCTTGGCTCCAGGGAGTGGACCCATCACCAGCCACCAAGTATAACATTCCCCTCGTGTCCTACAAGAACCTCTCCGAGGAAGAGCACAACAGCATCATCCAGCGCATGGTGCTCGGGGACATCGCGGACCGAGACGCCATCGTAGAAATGCATCTTAACAGAAATACAGAGGAAAAGAATAAAGACGAGAAAATGGCGTAG
Peptide sequence:
MAGFKRGYDGKIAGLYDLDKTLGRGHFAVVKLARHVFTGEKVAVKVIDKTKLDTLATGHLFQEVRCMKLVQHPNIVRLYEVIDTQTKLYLILELGDGGDMFDYIMKHEEGLNEDLAKKYFAQIVHAISYCHKLHVVHRDLKPENVVFFEKQGLVKLTDFGFSNKFQPGKKLTTSCGSLAYSAPEILLGDEYDAPAVDIWSLGVILFMLVCGQPPFQEANDSETLTMIMDCKYTVPPRVSAGCRDLITRMLQRDPKRRASLEEIESHPWLQGVDPSPATKYNIPLVSYKNLSEEEHNSIIQRMVLGDIADRDAIVEMHLNRNTEEKNKDEKMA
IRESfinder result
IRESfinder score
0.625937139
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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