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mmu_circNcoa3_555
Basic information of circular RNA
PanCircBase ID:
mmu_circNcoa3_555
mm39_Chr. Position ID:
chr2|165890374|165893626|+
Gene name:
Ncoa3
Transcript:
ENSMUST00000109252.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,6,7,8
Exon/intron offsets:
0,1611,2857,3159
Genomic length:
3252
Exon/intron sizes in nt:
101,175,186,93
Flanking exon/introns:
chr2:165889875-165890374|chr2:165893626-165894274
Splice length:
555
Other database IDs:
circBase: mmu_circ_0009572, CIRCpedia: MMU_CIRCpedia_39954, circAtlas: mmu-Ncoa3_0004
Human Ortholog IDs:
Mature spliced Sequence:
GAAAAACTATTTCCAGTGATGATGATGTTCAAAAAGCTGATGTGTCTTCTACAGGGCAGGGAGTCATTGATAAAGACTCTTTAGGACCGCTTTTACTACAGGCACTGGATGGTTTCCTGTTTGTGGTGAATCGAGATGGAAACATTGTATTCGTGTCAGAAAATGTCACACAGTATCTGCAGTACAAGCAGGAGGACCTGGTTAACACAAGTGTCTACAGCATCTTACATGAGCAAGACCGGAAGGATTTTCTTAAACACTTACCAAAATCCACAGTTAATGGAGTTTCTTGGACTAATGAGAACCAGAGACAAAAAAGCCATACATTTAATTGTCGTATGTTGATGAAAACACACGACATTTTGGAAGACGTGAATGCCAGTCCCGAAACACGCCAGAGATATGAAACAATGCAGTGCTTTGCCCTGTCTCAGCCTCGCGCTATGCTGGAAGAAGGAGAAGACTTGCAGTGCTGTATGATCTGCGTGGCTCGCCGCGTGACTGCGCCATTCCCATCCAGTCCTGAGAGCTTTATTACCAGACATGACCTTTCCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTATGATCTGCGTGGCTCG
60.25
TCCCTGCCCTGTAGAAGACA
59.88
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTATGATCTGCGTGGCTCG
60.25
TGACTCCCTGCCCTGTAGAA
59.88
148
PCR template sequence:
GGAGAAGACTTGCAGTGCTGTATGATCTGCGTGGCTCGCCGCGTGACTGCGCCATTCCCATCCAGTCCTGAGAGCTTTATTACCAGACATGACCTTTCCGGAAAAACTATTTCCAGTGATGATGATGTTCAAAAAGCTGATGTGTCTTCTACAGGGCAGGGAGTCATTGATAAAGACTCTTTAGGACCGCTTTTACTACA
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-7b-5p(1), mmu-miR-135a-5p(1), mmu-miR-339-5p(1), mmu-miR-136-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATGACCTTTCCGGAAAAACTATTTC
siRNA sets
ATAGTTTTTCCGGAAAGGT, AATAGTTTTTCCGGAAAGG, AAATAGTTTTTCCGGAAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNCOA3_555_ORF_1
0.8132
0.158065893
0.920797957
771
ORF sequence:
ATGTTGATGAAAACACACGACATTTTGGAAGACGTGAATGCCAGTCCCGAAACACGCCAGAGATATGAAACAATGCAGTGCTTTGCCCTGTCTCAGCCTCGCGCTATGCTGGAAGAAGGAGAAGACTTGCAGTGCTGTATGATCTGCGTGGCTCGCCGCGTGACTGCGCCATTCCCATCCAGTCCTGAGAGCTTTATTACCAGACATGACCTTTCCGGAAAAACTATTTCCAGTGATGATGATGTTCAAAAAGCTGATGTGTCTTCTACAGGGCAGGGAGTCATTGATAAAGACTCTTTAGGACCGCTTTTACTACAGGCACTGGATGGTTTCCTGTTTGTGGTGAATCGAGATGGAAACATTGTATTCGTGTCAGAAAATGTCACACAGTATCTGCAGTACAAGCAGGAGGACCTGGTTAACACAAGTGTCTACAGCATCTTACATGAGCAAGACCGGAAGGATTTTCTTAAACACTTACCAAAATCCACAGTTAATGGAGTTTCTTGGACTAATGAGAACCAGAGACAAAAAAGCCATACATTTAATTGTCGTATGTTGATGAAAACACACGACATTTTGGAAGACGTGAATGCCAGTCCCGAAACACGCCAGAGATATGAAACAATGCAGTGCTTTGCCCTGTCTCAGCCTCGCGCTATGCTGGAAGAAGGAGAAGACTTGCAGTGCTGTATGATCTGCGTGGCTCGCCGCGTGACTGCGCCATTCCCATCCAGTCCTGAGAGCTTTATTACCAGACATGACCTTTCC
Peptide sequence:
MLMKTHDILEDVNASPETRQRYETMQCFALSQPRAMLEEGEDLQCCMICVARRVTAPFPSSPESFITRHDLSGKTISSDDDVQKADVSSTGQGVIDKDSLGPLLLQALDGFLFVVNRDGNIVFVSENVTQYLQYKQEDLVNTSVYSILHEQDRKDFLKHLPKSTVNGVSWTNENQRQKSHTFNCRMLMKTHDILEDVNASPETRQRYETMQCFALSQPRAMLEEGEDLQCCMICVARRVTAPFPSSPESFITRHDLS
IRESfinder result
IRESfinder score
0.592748679
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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