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mmu_circAtr_242
Basic information of circular RNA
PanCircBase ID:
mmu_circAtr_242
mm39_Chr. Position ID:
chr9|95743421|95744985|+
Gene name:
Atr
Transcript:
ENSMUST00000187356.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
2,3
Exon/intron offsets:
0,1414
Genomic length:
1564
Exon/intron sizes in nt:
92,150
Flanking exon/introns:
chr9:95739836-95743421|chr9:95744985-95747020
Splice length:
242
Other database IDs:
circBase: mmu_circ_0015998, CIRCpedia: MMU_CIRCpedia_35186, circAtlas: mmu-Atr_0042
circBase: hsa_circ_0067655, circAtlas: hsa-ATR_0048, CIRCpedia: HSA_CIRCpedia_43924
Human Ortholog IDs:
Mature spliced Sequence:
TGCTACTCCAGAAGAATATAACACTGTTGTACAGAAACCAAGACAGATTCTCTGCCAGTTCATTGACAGAATACTTACAGATGTAAATGTTGTTGCTCTAGAACTTGTAAAGAAAACTGACGCTCAGCCGACCTCTGTGATGTTACTTGATTTTATCCAGCACATCATGAAGTCTTCTCCGCTTATGTTTGTAAATGTGAATGGAAGCCAGGGCCAAAATGAGGCCAAAGACAGTTGTATTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACATCATGAAGTCTTCTCCGCT
59.5
TGTCAATGAACTGGCAGAGA
56.77
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACATCATGAAGTCTTCTCCGC
59.39
TGTCAATGAACTGGCAGAGA
56.77
150
PCR template sequence:
TTACTTGATTTTATCCAGCACATCATGAAGTCTTCTCCGCTTATGTTTGTAAATGTGAATGGAAGCCAGGGCCAAAATGAGGCCAAAGACAGTTGTATTGTGCTACTCCAGAAGAATATAACACTGTTGTACAGAAACCAAGACAGATTCTCTGCCAGTTCATTGACAGAATACTTACAGATGTAAATGTTGTTGCTCTA
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-23b-3p(1), mmu-miR-7b-5p(1), mmu-miR-26a-5p(1), mmu-miR-328-3p(1), mmu-miR-23a-3p(1), mmu-miR-433-3p(1), mmu-miR-26b-5p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GACAGTTGTATTGTGCTACTCCAGAA
siRNA sets
TTCTGGAGTAGCACAATAC,AGTAGCACAATACAACTGT,TCTGGAGTAGCACAATACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATR_242_ORF_1
0.8456
-0.037784353
0.077807231
189
ORF sequence:
ATGTTACTTGATTTTATCCAGCACATCATGAAGTCTTCTCCGCTTATGTTTGTAAATGTGAATGGAAGCCAGGGCCAAAATGAGGCCAAAGACAGTTGTATTGTGCTACTCCAGAAGAATATAACACTGTTGTACAGAAACCAAGACAGATTCTCTGCCAGTTCATTGACAGAATACTTACAGATGTAA
Peptide sequence:
MLLDFIQHIMKSSPLMFVNVNGSQGQNEAKDSCIVLLQKNITLLYRNQDRFSASSLTEYLQM
IRESfinder result
IRESfinder score
0.680068185
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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