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mmu_circMatr3_1197
Basic information of circular RNA
PanCircBase ID:
mmu_circMatr3_1197
mm39_Chr. Position ID:
chr18|35704895|35711510|+
Gene name:
Matr3
Transcript:
ENSMUST00000166793.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,5715,6573
Genomic length:
6615
Exon/intron sizes in nt:
1093,62,42
Flanking exon/introns:
chr18:35695345-35704895|chr18:35711510-35711957
Splice length:
1197
Other database IDs:
circAtlas: mmu-RP23-461O23_0002
Human Ortholog IDs:
Mature spliced Sequence:
AGTTGTCTGCTGGTTCTCAGCTTGAAGAAGATTCTACAGTCCTTATTGATCCTTTTTCTTGGCGTTACCATTTTTGAAGCAAAGTTAACCTAGCTTTCTAGCTTGAGCTTTCTTTTTGGCCATCTTTTAAAACTTTTTTTTTTTTTTTTGATCTATAAAATAGACAAGAGATAGTTCTACAATGTCCAAGTCATTCCAGCAGTCATCTCTCGGTAGGGATTCACAGGGTCATGGGCGTGACCTGTCTGCAGCAGGAATAGGCCTTCTTGCTGCTGCTACCCAGTCTTTAAGTATGCCAGCATCTCTTGGAAGGATGAACCAGGGTACTGCACGCCTTGCTAGTTTAATGAATCTTGGAATGAGTTCTTCATTGAATCAACAAGGAGCTCATAGTGCACTGTCTTCTGCTAGTACTTCTTCCCATAATTTGCAGTCTATATTTAACATTGGAAGTAGAGGTCCACTCCCTTTGTCTTCTCAACACCGTGGAGATACAGACCAGGCCAGTAATATTTTGGCCAGCTTTGGTCTGTCTGCTAGAGACTTAGATGAACTGAGTCGCTATCCAGAGGACAAGATTACTCCTGAGAACTTGCCCCAAATTCTTCTACAGCTTAAAAGGAGGAGAACTGAAGAAGGCCCTACATTGAGTTATGGTAGAGATGGCAGATCTGCTACACGGGAGCCACCATACAGAGTACCTAGGGATGATTGGGAAGAAAAAAGGCACTTTAGAAGAGATAGTTTTGATGATCGTGGTCCTAGTCTCAACCCAGTGCTTGATTATGACCATGGAAGTCGTTCTCAAGAATCTGGTTATTATGACAGAATGGATTATGAAGATGACAGATTAAGAGATGGAGAAAGGTGTAGGGATGATTCTTTTTTTGGTGAGACCTCGCATAACTATCATAAATTTGACAGTGAGTATGAGAGAATGGGACGTGGTCCTGGCCCCTTACAAGAGAGATCTCTCTTTGAGAAAAAGAGGGGCGCTCCTCCAAGTAGCAATATTGAAGACTTCCATGGACTCTTACCGAAGGGTTATCCCCATCTGTGCTCTATATGTGATTTGCCAGTTCATTCTAATAAGGAGTGGAGTCAACATATCAATGGAGCAAGTCACAGTCGTCGATGCCAGCTTCTTCTTGAAATCTACCCAGAATGGAATCCTGACAATGATACTGGACACACAAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGCAAGTCACAGTCGTC
59.97
TGGTAACGCCAAGAAAAAGGA
58.07
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGCAAGTCACAGTCGTCGA
60.04
TGGTAACGCCAAGAAAAAGGA
58.07
152
PCR template sequence:
GGAGTCAACATATCAATGGAGCAAGTCACAGTCGTCGATGCCAGCTTCTTCTTGAAATCTACCCAGAATGGAATCCTGACAATGATACTGGACACACAATAGTTGTCTGCTGGTTCTCAGCTTGAAGAAGATTCTACAGTCCTTATTGATCCTTTTTCTTGGCGTTACCATTTTTGAAGCAAAGTTAACCTAGCTTTCTA
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-320-3p(2), mmu-miR-15a-5p(1), mmu-miR-15b-5p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-10b-5p(1), mmu-miR-10a-5p(1), mmu-miR-136-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGGACACACAATAGTTGTCTGCTGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMATR3_1197_ORF_1
1.0045
-0.03118957
0.981176417
1041
ORF sequence:
ATGTCCAAGTCATTCCAGCAGTCATCTCTCGGTAGGGATTCACAGGGTCATGGGCGTGACCTGTCTGCAGCAGGAATAGGCCTTCTTGCTGCTGCTACCCAGTCTTTAAGTATGCCAGCATCTCTTGGAAGGATGAACCAGGGTACTGCACGCCTTGCTAGTTTAATGAATCTTGGAATGAGTTCTTCATTGAATCAACAAGGAGCTCATAGTGCACTGTCTTCTGCTAGTACTTCTTCCCATAATTTGCAGTCTATATTTAACATTGGAAGTAGAGGTCCACTCCCTTTGTCTTCTCAACACCGTGGAGATACAGACCAGGCCAGTAATATTTTGGCCAGCTTTGGTCTGTCTGCTAGAGACTTAGATGAACTGAGTCGCTATCCAGAGGACAAGATTACTCCTGAGAACTTGCCCCAAATTCTTCTACAGCTTAAAAGGAGGAGAACTGAAGAAGGCCCTACATTGAGTTATGGTAGAGATGGCAGATCTGCTACACGGGAGCCACCATACAGAGTACCTAGGGATGATTGGGAAGAAAAAAGGCACTTTAGAAGAGATAGTTTTGATGATCGTGGTCCTAGTCTCAACCCAGTGCTTGATTATGACCATGGAAGTCGTTCTCAAGAATCTGGTTATTATGACAGAATGGATTATGAAGATGACAGATTAAGAGATGGAGAAAGGTGTAGGGATGATTCTTTTTTTGGTGAGACCTCGCATAACTATCATAAATTTGACAGTGAGTATGAGAGAATGGGACGTGGTCCTGGCCCCTTACAAGAGAGATCTCTCTTTGAGAAAAAGAGGGGCGCTCCTCCAAGTAGCAATATTGAAGACTTCCATGGACTCTTACCGAAGGGTTATCCCCATCTGTGCTCTATATGTGATTTGCCAGTTCATTCTAATAAGGAGTGGAGTCAACATATCAATGGAGCAAGTCACAGTCGTCGATGCCAGCTTCTTCTTGAAATCTACCCAGAATGGAATCCTGACAATGATACTGGACACACAATAGTTGTCTGCTGGTTCTCAGCTTGA
Peptide sequence:
MSKSFQQSSLGRDSQGHGRDLSAAGIGLLAAATQSLSMPASLGRMNQGTARLASLMNLGMSSSLNQQGAHSALSSASTSSHNLQSIFNIGSRGPLPLSSQHRGDTDQASNILASFGLSARDLDELSRYPEDKITPENLPQILLQLKRRRTEEGPTLSYGRDGRSATREPPYRVPRDDWEEKRHFRRDSFDDRGPSLNPVLDYDHGSRSQESGYYDRMDYEDDRLRDGERCRDDSFFGETSHNYHKFDSEYERMGRGPGPLQERSLFEKKRGAPPSSNIEDFHGLLPKGYPHLCSICDLPVHSNKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTIVVCWFSA
IRESfinder result
IRESfinder score
0.804134458
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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