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mmu_circCd48_570
Basic information of circular RNA
PanCircBase ID:
mmu_circCd48_570
mm39_Chr. Position ID:
chr1|171523231|171527218|+
Gene name:
Cd48
Transcript:
ENSMUST00000068584.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
2,3
Exon/intron offsets:
0,3720
Genomic length:
3987
Exon/intron sizes in nt:
3,03,267
Flanking exon/introns:
chr1:171509734-171523231|chr1:171527218-171532365
Splice length:
570
Other database IDs:
circAtlas: mmu-Cd48_0001
CIRCpedia: HSA_CIRCpedia_371197
Human Ortholog IDs:
Mature spliced Sequence:
GTCATTCAATACCAGATATAAATGCCACCACCGGCAGCAATGTAACCCTGAAAATCCATAAGGACCCACTTGGACCATATAAACGTATCACCTGGCTTCATACTAAAAATCAGAAGATTTTAGAGTACAACTATAATAGTACAAAGACAATCTTCGAGTCTGAATTTAAAGGCAGGGTTTATCTTGAAGAAAACAATGGTGCACTTCATATCTCTAATGTCCGGAAAGAGGACAAAGGTACCTACTACATGAGAGTGCTGCGTGAAACTGAGAACGAGTTGAAGATAACCCTGGAAGTATTTGATCCTGTGCCCAAGCCTTCCATAGAAATCAATAAGACTGAAGCGTCGACTGATTCCTGTCACCTGAGGCTATCGTGTGAGGTAAAGGACCAGCATGTTGACTATACTTGGTATGAGAGCTCGGGACCTTTCCCCAAAAAGAGTCCAGGATATGTGCTCGATCTCATCGTCACACCACAGAACAAGTCTACATTTTACACCTGCCAAGTCAGCAATCCTGTAAGCAGCAAGAACGACACAGTGTACTTCACTCTACCTTGTGATCTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCAAGTCAGCAATCCTGT
59.89
GGTCCAAGTGGGTCCTTATGG
60.06
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACACCTGCCAAGTCAGCAAT
60.18
GGTCCAAGTGGGTCCTTATGG
60.06
148
PCR template sequence:
GTCACACCACAGAACAAGTCTACATTTTACACCTGCCAAGTCAGCAATCCTGTAAGCAGCAAGAACGACACAGTGTACTTCACTCTACCTTGTGATCTAGGTCATTCAATACCAGATATAAATGCCACCACCGGCAGCAATGTAACCCTGAAAATCCATAAGGACCCACTTGGACCATATAAACGTATCACCTGGCTTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-342-3p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTTGTGATCTAGGTCATTCAATACC
siRNA sets
ATTGAATGACCTAGATCAC, TATTGAATGACCTAGATCA, TTGAATGACCTAGATCACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCD48_570_ORF_1
1.0261
0.200066479
0.979888644
891
ORF sequence:
ATGAGAGTGCTGCGTGAAACTGAGAACGAGTTGAAGATAACCCTGGAAGTATTTGATCCTGTGCCCAAGCCTTCCATAGAAATCAATAAGACTGAAGCGTCGACTGATTCCTGTCACCTGAGGCTATCGTGTGAGGTAAAGGACCAGCATGTTGACTATACTTGGTATGAGAGCTCGGGACCTTTCCCCAAAAAGAGTCCAGGATATGTGCTCGATCTCATCGTCACACCACAGAACAAGTCTACATTTTACACCTGCCAAGTCAGCAATCCTGTAAGCAGCAAGAACGACACAGTGTACTTCACTCTACCTTGTGATCTAGGTCATTCAATACCAGATATAAATGCCACCACCGGCAGCAATGTAACCCTGAAAATCCATAAGGACCCACTTGGACCATATAAACGTATCACCTGGCTTCATACTAAAAATCAGAAGATTTTAGAGTACAACTATAATAGTACAAAGACAATCTTCGAGTCTGAATTTAAAGGCAGGGTTTATCTTGAAGAAAACAATGGTGCACTTCATATCTCTAATGTCCGGAAAGAGGACAAAGGTACCTACTACATGAGAGTGCTGCGTGAAACTGAGAACGAGTTGAAGATAACCCTGGAAGTATTTGATCCTGTGCCCAAGCCTTCCATAGAAATCAATAAGACTGAAGCGTCGACTGATTCCTGTCACCTGAGGCTATCGTGTGAGGTAAAGGACCAGCATGTTGACTATACTTGGTATGAGAGCTCGGGACCTTTCCCCAAAAAGAGTCCAGGATATGTGCTCGATCTCATCGTCACACCACAGAACAAGTCTACATTTTACACCTGCCAAGTCAGCAATCCTGTAAGCAGCAAGAACGACACAGTGTACTTCACTCTACCTTGTGATCTA
Peptide sequence:
MRVLRETENELKITLEVFDPVPKPSIEINKTEASTDSCHLRLSCEVKDQHVDYTWYESSGPFPKKSPGYVLDLIVTPQNKSTFYTCQVSNPVSSKNDTVYFTLPCDLGHSIPDINATTGSNVTLKIHKDPLGPYKRITWLHTKNQKILEYNYNSTKTIFESEFKGRVYLEENNGALHISNVRKEDKGTYYMRVLRETENELKITLEVFDPVPKPSIEINKTEASTDSCHLRLSCEVKDQHVDYTWYESSGPFPKKSPGYVLDLIVTPQNKSTFYTCQVSNPVSSKNDTVYFTLPCDL
IRESfinder result
IRESfinder score
0.653379038
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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