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mmu_circSlc12a6_560
Basic information of circular RNA
PanCircBase ID:
mmu_circSlc12a6_560
mm39_Chr. Position ID:
chr2|112163727|112168334|+
Gene name:
Slc12a6
Transcript:
ENSMUST00000110991.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
3,4,5,6,7
Exon/intron offsets:
0,986,2393,3975,4476
Genomic length:
4607
Exon/intron sizes in nt:
95,13,21,47,55,131
Flanking exon/introns:
chr2:112146630-112163727|chr2:112168334-112169590
Splice length:
560
Other database IDs:
CIRCpedia: MMU_CIRCpedia_3353, circAtlas: mmu-Slc12a6_0010
Human Ortholog IDs:
Mature spliced Sequence:
ATGACGGCCATAAAAAAGCCCGAAATGCTTATCTCAATAATTCCAACTATGAAGAAGGAGACGAATATTTTGATAAAAATTTGGCACTCTTTGAGGAAGAAATGGACACCAGACCAAAGGTGTCTTCTCTCCTCAACCGCATGGCCAACTATACAAATCTGACACAAGGAGCAAAGGAACATGAAGAGGCAGAGAACATCACTGAAGGGAAAAAGAAGCCTACCAAGAGCCCCCAAATGGGTACTTTCATGGGTGTCTACCTCCCATGTCTACAGAACATCTTTGGAGTGATCCTCTTCCTGCGTCTTACCTGGGTAGTGGGAACAGCTGGAATCCTTCAGGCCTTTGCAATTGTCCTCATCTGCTGCTGCTGTACAATGTTAACTGCCATCTCCATGAGCGCCATCGCCACTAACGGAGTGGTGCCAGCTGGGGGCTCATACTTCATGATTTCCAGAGCCCTGGGCCCAGAGTTTGGCGGGGCTGTAGGCCTCTGCTTTTATCTTGGCACCACATTTGCAGCAGCCATGTATATTCTTGGTGCCATTGAAATCTTTCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACATTTGCAGCAGCCATGT
60.04
TCTTCCTCAAAGAGTGCCAA
56.68
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACATTTGCAGCAGCCATGT
60.04
TCTTCCTCAAAGAGTGCCAAA
57.42
149
PCR template sequence:
CCTGGGCCCAGAGTTTGGCGGGGCTGTAGGCCTCTGCTTTTATCTTGGCACCACATTTGCAGCAGCCATGTATATTCTTGGTGCCATTGAAATCTTTCTGATGACGGCCATAAAAAAGCCCGAAATGCTTATCTCAATAATTCCAACTATGAAGAAGGAGACGAATATTTTGATAAAAATTTGGCACTCTTTGAGGAAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-15b-5p(1), mmu-miR-326-3p(1), mmu-miR-185-5p(1), mmu-miR-183-5p(1), mmu-miR-669d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAAATCTTTCTGATGACGGCCATAA
siRNA sets
TATGGCCGTCATCAGAAAG,ATGGCCGTCATCAGAAAGA,TTATGGCCGTCATCAGAAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSLC12A6_560_ORF_1
1.1309
0.104726957
0.851107746
621
ORF sequence:
ATGGACACCAGACCAAAGGTGTCTTCTCTCCTCAACCGCATGGCCAACTATACAAATCTGACACAAGGAGCAAAGGAACATGAAGAGGCAGAGAACATCACTGAAGGGAAAAAGAAGCCTACCAAGAGCCCCCAAATGGGTACTTTCATGGGTGTCTACCTCCCATGTCTACAGAACATCTTTGGAGTGATCCTCTTCCTGCGTCTTACCTGGGTAGTGGGAACAGCTGGAATCCTTCAGGCCTTTGCAATTGTCCTCATCTGCTGCTGCTGTACAATGTTAACTGCCATCTCCATGAGCGCCATCGCCACTAACGGAGTGGTGCCAGCTGGGGGCTCATACTTCATGATTTCCAGAGCCCTGGGCCCAGAGTTTGGCGGGGCTGTAGGCCTCTGCTTTTATCTTGGCACCACATTTGCAGCAGCCATGTATATTCTTGGTGCCATTGAAATCTTTCTGATGACGGCCATAAAAAAGCCCGAAATGCTTATCTCAATAATTCCAACTATGAAGAAGGAGACGAATATTTTGATAAAAATTTGGCACTCTTTGAGGAAGAAATGGACACCAGACCAAAGGTGTCTTCTCTCCTCAACCGCATGGCCAACTATACAAATCTGA
Peptide sequence:
MDTRPKVSSLLNRMANYTNLTQGAKEHEEAENITEGKKKPTKSPQMGTFMGVYLPCLQNIFGVILFLRLTWVVGTAGILQAFAIVLICCCCTMLTAISMSAIATNGVVPAGGSYFMISRALGPEFGGAVGLCFYLGTTFAAAMYILGAIEIFLMTAIKKPEMLISIIPTMKKETNILIKIWHSLRKKWTPDQRCLLSSTAWPTIQI
IRESfinder result
IRESfinder score
0.577589372
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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