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mmu_circCstf3_360
Basic information of circular RNA
PanCircBase ID:
mmu_circCstf3_360
mm39_Chr. Position ID:
chr2|104474633|104477195|+
Gene name:
Cstf3
Transcript:
ENSMUST00000028599.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
4,5,6,7,8
Exon/intron offsets:
0,690,2111,2320,2435
Genomic length:
2562
Exon/intron sizes in nt:
33,98,67,35,127
Flanking exon/introns:
chr2:104439531-104474633|chr2:104477195-104478514
Splice length:
360
Other database IDs:
CIRCpedia: MMU_CIRCpedia_222934, circAtlas: mmu-Cstf3_0005
circBase: hsa_circ_0095711, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_4132
Human Ortholog IDs:
Mature spliced Sequence:
ATTAAAGCTAAAAATTATGACAAGGTTGAAAAGCTATTTCAAAGATGCCTTATGAAGGTTTTGCACATTGATTTATGGAAGTGTTATCTTTCATACGTCAGAGAAACCAAGGGTAAACTGCCCAGCTACAAAGAAAAAATGGCTCAAGCTTATGACTTTGCACTAGATAAAATTGGAATGGAAATTATGTCCTATCAGATTTGGGTGGATTACATCAATTTCTTAAAAGGAGTGGAAGCTGTAGGATCTTATGCAGAAAATCAGAGAATAACTGCTGTCCGAAGAGTTTATCAACGAGGTTGTGTTAATCCAATGATCAACATTGAACAACTCTGGAGAGACTACAACAAGTATGAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACTGCTGTCCGAAGAGTTT
57.38
ACACTTCCATAAATCAATGTGCA
57.02
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACTGCTGTCCGAAGAGTTT
57.38
GGCATCTTTGAAATAGCTTTTCAACC
59.91
140
PCR template sequence:
TCAGAGAATAACTGCTGTCCGAAGAGTTTATCAACGAGGTTGTGTTAATCCAATGATCAACATTGAACAACTCTGGAGAGACTACAACAAGTATGAAGAGATTAAAGCTAAAAATTATGACAAGGTTGAAAAGCTATTTCAAAGATGCCTTATGAAGGTTTTGCACATTGATTTATGGAAGTGTTATCTTTCATACGTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-19b-3p(2), mmu-miR-130a-3p(1), mmu-miR-19a-3p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-721(1), mmu-miR-680(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAAGTATGAAGAGATTAAAGCTAAAA
siRNA sets
TTTTAGCTTTAATCTCTTC, TTTAGCTTTAATCTCTTCA, TTAGCTTTAATCTCTTCAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCSTF3_360_ORF_1
0.8165
0.084880499
0.807399886
669
ORF sequence:
ATGAAGGTTTTGCACATTGATTTATGGAAGTGTTATCTTTCATACGTCAGAGAAACCAAGGGTAAACTGCCCAGCTACAAAGAAAAAATGGCTCAAGCTTATGACTTTGCACTAGATAAAATTGGAATGGAAATTATGTCCTATCAGATTTGGGTGGATTACATCAATTTCTTAAAAGGAGTGGAAGCTGTAGGATCTTATGCAGAAAATCAGAGAATAACTGCTGTCCGAAGAGTTTATCAACGAGGTTGTGTTAATCCAATGATCAACATTGAACAACTCTGGAGAGACTACAACAAGTATGAAGAGATTAAAGCTAAAAATTATGACAAGGTTGAAAAGCTATTTCAAAGATGCCTTATGAAGGTTTTGCACATTGATTTATGGAAGTGTTATCTTTCATACGTCAGAGAAACCAAGGGTAAACTGCCCAGCTACAAAGAAAAAATGGCTCAAGCTTATGACTTTGCACTAGATAAAATTGGAATGGAAATTATGTCCTATCAGATTTGGGTGGATTACATCAATTTCTTAAAAGGAGTGGAAGCTGTAGGATCTTATGCAGAAAATCAGAGAATAACTGCTGTCCGAAGAGTTTATCAACGAGGTTGTGTTAATCCAATGATCAACATTGAACAACTCTGGAGAGACTACAACAAGTATGAAGAG
Peptide sequence:
MKVLHIDLWKCYLSYVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQLWRDYNKYEEIKAKNYDKVEKLFQRCLMKVLHIDLWKCYLSYVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQLWRDYNKYEE
IRESfinder result
IRESfinder score
0.49298748
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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