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mmu_circMindy3_427
Basic information of circular RNA
PanCircBase ID:
mmu_circMindy3_427
mm39_Chr. Position ID:
chr2|12404833|12414891|-
Gene name:
Mindy3
Transcript:
ENSMUST00000155530.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,3975,5837,9978
Genomic length:
10058
Exon/intron sizes in nt:
115,171,61,80
Flanking exon/introns:
chr2:12402377-12404833|chr2:12414891-12423969
Splice length:
427
Other database IDs:
CIRCpedia: MMU_CIRCpedia_6236, circAtlas: mmu-Fam188a_0010
circBase: hsa_circ_0017852, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_1123
Human Ortholog IDs:
Mature spliced Sequence:
GGTTTGTGTTTAGTGAATCAGAGGGATCTGCATTAGAGCAGTTTGAAGGTGGCCCCTGTGCTGTTATTGCACCTGTCCAGGCGTTTCTTTTGAAGAAGCTTCTGTTCTCCTCCGAGAAGTCGTCCTGGCGGGATTGCTCAGAGGAAGAGCAGAAGGAGCTCCTTTGTCACACCTTGTGTGATATTGTAGAGAGTGCTTATGACAGCTCTGGATCATACTGCTTGGTTTCATGGTTGAGAGGAAGGACCCCCGAGGAAGCGGCTAGGATTTCTGGGAGTCCTGCACAGTCTAGTTGCCAAGTGGAACATTCTTAAAAAGATCATTCAGAACTGTATCAGAATTAAAAGATGCTGTCTTGGACCAGTATTCAATGTGGGGAAACAAATTTGGAGTCTTGCTTTTTCTCTATTCTGTATTACTGACAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGATGCTGTCTTGGACCAGT
58.64
CAATAACAGCACAGGGGCCA
60.61
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGATGCTGTCTTGGACCAGT
58.64
AATAACAGCACAGGGGCCAC
60.61
150
PCR template sequence:
AACTGTATCAGAATTAAAAGATGCTGTCTTGGACCAGTATTCAATGTGGGGAAACAAATTTGGAGTCTTGCTTTTTCTCTATTCTGTATTACTGACAAAGGGTTTGTGTTTAGTGAATCAGAGGGATCTGCATTAGAGCAGTTTGAAGGTGGCCCCTGTGCTGTTATTGCACCTGTCCAGGCGTTTCTTTTGAAGAAGCT
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-20b-5p(1), mmu-miR-429-3p(1), mmu-miR-326-3p(1), mmu-miR-182-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
ATTACTGACAAAGGGTTTGTGTTTAG
siRNA sets
AAACACAAACCCTTTGTCA, CTAAACACAAACCCTTTGT, AACACAAACCCTTTGTCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMINDY3_427_ORF_1
0.6622
-0.417766224
0.006252093
93
ORF sequence:
ATGTGGGGAAACAAATTTGGAGTCTTGCTTTTTCTCTATTCTGTATTACTGACAAAGGGTTTGTGTTTAGTGAATCAGAGGGATCTGCATTAG
Peptide sequence:
MWGNKFGVLLFLYSVLLTKGLCLVNQRDLH
IRESfinder result
IRESfinder score
0.815646318
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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