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mmu_circMadd_1228
Basic information of circular RNA
PanCircBase ID:
mmu_circMadd_1228
mm39_Chr. Position ID:
chr2|91003457|91008841|-
Gene name:
Madd
Transcript:
ENSMUST00000111373.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,2530,3043,3693,4787
Genomic length:
5384
Exon/intron sizes in nt:
8,11,14,13,23,04,597
Flanking exon/introns:
chr2:91001092-91003457|chr2:91008841-91009523
Splice length:
1228
Other database IDs:
circAtlas: mmu-Madd_0008
Human Ortholog IDs:
Mature spliced Sequence:
GCACCCAAGCAGTGACAGTGTGGCTCAGACTCCTGAGCTGCTGCGGAGGTACCCACTAGAGGATCACCCAGAGTTCCCCCTGCCCCCAGATGTGGTGTTCTTCTGCCAGCCAGAAGGATGTCTGAGTGTGCGGCAGCGGCGGATGAGCCTTCGGGACGATACCTCTTTTGTCTTCACCCTAACCGATAAGGACACCGGAGTCACCCGCTATGGCATCTGTGTCAACTTCTACCGTTCCTTCCAAAAGCGAATGCCAAAGGAAAAGGTGGAAGGCGGAGCAGGACCCCGTGGGAAGGAAGGCGCTCACACCTCTGGTGCCTCAGAAGAGGCTGCCGCTGGGAGCTCAGAGAGTGGCTCAACCTTGCAGCCGCCTAGTGCTGACTCCACTCCTGACGTAAACCAGTCTCCTCGGGGCAAACGTAGGGCAAAAGCGGGCAGCCGCTCCCGCAACAGTACCCTGACATCCCTGTGTGTGCTTAGCCACTACCCTTTCTTCTCTACCTTCAGAGAGTGTCTGTATACTCTCAAACGTTTGGTAGACTGCTGTAGTGAACGGCTGCTAGGCAAGAAACTGGGCATCCCTCGAGGTGTACAAAGGGACACCATGTGGCGAATCTTTACTGGATCACTGCTAGTGGAGGAGAAGTCCAGTGCCCTTCTGCAAGACCTTCGAGAGATTGAGGCCTGGATCTATCGGTTGCTACGTTCCCCAGTGCCTGTCTCTGGGCAGAAGCGAGTGGACATTGAGGTCCTGCCCCAGGAACTCCAGCAGGCCCTGACATTTGCTCTTCCAGATCCATCTCGATTCACCCTAGTAGATTTCCCTCTTCACCTTCCCTTGGAACTTCTGGGTGTAGATGCTTGTCTTCAGGTGCTAACCTGCATCCTGTTGGAGCACAAGGTGGTGCTGCAGTCTCGAGACTACAATGCACTCTCCATGTCTGTGATGGCGTTCGTGGCAATGATCTACCCCCTGGAGTACATGTTCCCGGTCATCCCGCTGCTTCCCACCTGCATGGCCTCGGCAGAGCAGCTACTCTTGGCTCCAACCCCATACATCATTGGAGTTCCTGCCAGCTTCTTCCTCTACAAGCTAGATTTCAAAATGCCCGATGACGTGTGGCTAGTGGATCTGGACAGCAATAGGGTGATTGCCCCCACCAATGCAGAAGTGCTACCCATCCTGCCAGAACCAGAATCATTAGAGCTGAAAAAACACTTAAAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGTGCTACCCATCCTGCC
60.46
AGGGGGAACTCTGGGTGATC
60.62
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGAAGTGCTACCCATCCTGC
59.46
GGGGAACTCTGGGTGATCCT
60.62
140
PCR template sequence:
GGATCTGGACAGCAATAGGGTGATTGCCCCCACCAATGCAGAAGTGCTACCCATCCTGCCAGAACCAGAATCATTAGAGCTGAAAAAACACTTAAAGCAGGCACCCAAGCAGTGACAGTGTGGCTCAGACTCCTGAGCTGCTGCGGAGGTACCCACTAGAGGATCACCCAGAGTTCCCCCTGCCCCCAGATGTGGTGTTC
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-211-5p(1), mmu-miR-204-5p(1), mmu-miR-29a-3p(1), mmu-miR-33-5p(1), mmu-miR-298-5p(1), mmu-miR-503-5p(1), mmu-miR-431-5p(1), mmu-miR-370-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACACTTAAAGCAGGCACCCAAGCAGT
siRNA sets
TTGGGTGCCTGCTTTAAGT, CTTGGGTGCCTGCTTTAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMADD_1228_ORF_1
0.9356
0.322352129
0.996673478
1101
ORF sequence:
ATGAGCCTTCGGGACGATACCTCTTTTGTCTTCACCCTAACCGATAAGGACACCGGAGTCACCCGCTATGGCATCTGTGTCAACTTCTACCGTTCCTTCCAAAAGCGAATGCCAAAGGAAAAGGTGGAAGGCGGAGCAGGACCCCGTGGGAAGGAAGGCGCTCACACCTCTGGTGCCTCAGAAGAGGCTGCCGCTGGGAGCTCAGAGAGTGGCTCAACCTTGCAGCCGCCTAGTGCTGACTCCACTCCTGACGTAAACCAGTCTCCTCGGGGCAAACGTAGGGCAAAAGCGGGCAGCCGCTCCCGCAACAGTACCCTGACATCCCTGTGTGTGCTTAGCCACTACCCTTTCTTCTCTACCTTCAGAGAGTGTCTGTATACTCTCAAACGTTTGGTAGACTGCTGTAGTGAACGGCTGCTAGGCAAGAAACTGGGCATCCCTCGAGGTGTACAAAGGGACACCATGTGGCGAATCTTTACTGGATCACTGCTAGTGGAGGAGAAGTCCAGTGCCCTTCTGCAAGACCTTCGAGAGATTGAGGCCTGGATCTATCGGTTGCTACGTTCCCCAGTGCCTGTCTCTGGGCAGAAGCGAGTGGACATTGAGGTCCTGCCCCAGGAACTCCAGCAGGCCCTGACATTTGCTCTTCCAGATCCATCTCGATTCACCCTAGTAGATTTCCCTCTTCACCTTCCCTTGGAACTTCTGGGTGTAGATGCTTGTCTTCAGGTGCTAACCTGCATCCTGTTGGAGCACAAGGTGGTGCTGCAGTCTCGAGACTACAATGCACTCTCCATGTCTGTGATGGCGTTCGTGGCAATGATCTACCCCCTGGAGTACATGTTCCCGGTCATCCCGCTGCTTCCCACCTGCATGGCCTCGGCAGAGCAGCTACTCTTGGCTCCAACCCCATACATCATTGGAGTTCCTGCCAGCTTCTTCCTCTACAAGCTAGATTTCAAAATGCCCGATGACGTGTGGCTAGTGGATCTGGACAGCAATAGGGTGATTGCCCCCACCAATGCAGAAGTGCTACCCATCCTGCCAGAACCAGAATCATTAGAGCTGAAAAAACACTTAAAGCAGGCACCCAAGCAGTGA
Peptide sequence:
MSLRDDTSFVFTLTDKDTGVTRYGICVNFYRSFQKRMPKEKVEGGAGPRGKEGAHTSGASEEAAAGSSESGSTLQPPSADSTPDVNQSPRGKRRAKAGSRSRNSTLTSLCVLSHYPFFSTFRECLYTLKRLVDCCSERLLGKKLGIPRGVQRDTMWRIFTGSLLVEEKSSALLQDLREIEAWIYRLLRSPVPVSGQKRVDIEVLPQELQQALTFALPDPSRFTLVDFPLHLPLELLGVDACLQVLTCILLEHKVVLQSRDYNALSMSVMAFVAMIYPLEYMFPVIPLLPTCMASAEQLLLAPTPYIIGVPASFFLYKLDFKMPDDVWLVDLDSNRVIAPTNAEVLPILPEPESLELKKHLKQAPKQ
IRESfinder result
IRESfinder score
0.493942943
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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