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mmu_circRab3ip_540
Basic information of circular RNA
PanCircBase ID:
mmu_circRab3ip_540
mm39_Chr. Position ID:
chr10|116773301|116775386|-
Gene name:
Rab3ip
Transcript:
ENSMUST00000020375.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,1804
Genomic length:
2085
Exon/intron sizes in nt:
259,281
Flanking exon/introns:
chr10:116755556-116773301|chr10:116775386-116786164
Splice length:
540
Other database IDs:
circBase: mmu_circ_0001982, CIRCpedia: MMU_CIRCpedia_4177, circAtlas: mmu-Rab3ip_0006
Human Ortholog IDs:
Mature spliced Sequence:
CTTAGGTTGTCCTATGATGAAGCCTTTGCTATGGCTAACGACCCCTTGGAAGGCTTCCATGAAGTGAACCTTGCTTCGCCTACTTCTCCAGACCTTCTTGGTGTGTGTGACCCGGGAACCCAAGAGCAGACTACCTCCCCGAGCGTCATCTACCGGCCACACCCCTCCACGTTATGCGCTGCCCCTCTCCAGGCCAATGCCTTAGATCTTTCTGATCTTCCTACACAACCTGTGTATTCGTCCCCCAGGCATTTCAACTGTGCAGAAGTATCTAATATCAGCGCTCATGCTCCGGATCCAGCATCATCGGTACCCTCTGCGGTAGCATCAGGGCTCACGAAGTTAACCTCCAGGAAGGACAGCTGTAATGCAGAGAGGGAGTTTCTGCAGGGCGCCACCATCACCGAGGCTTCTGCTGGCAATGATGACATCTTTGGGTTGAGCACGGATAGCCTGTCGCGTTTACGAAGCCCATCTGTTCTGGAAGTTAGAGAGAAGGGCTACGAAAGGTTAAAGGAAGAACTTGCAAAAGCTCAGAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGAAGCCCATCTGTTCTGG
60.04
AGGTCTGGAGAAGTAGGCGA
59.67
171
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGGATAGCCTGTCGCGTTTA
60.25
GGGGTCGTTAGCCATAGCAA
59.82
140
PCR template sequence:
GAGCACGGATAGCCTGTCGCGTTTACGAAGCCCATCTGTTCTGGAAGTTAGAGAGAAGGGCTACGAAAGGTTAAAGGAAGAACTTGCAAAAGCTCAGAGGCTTAGGTTGTCCTATGATGAAGCCTTTGCTATGGCTAACGACCCCTTGGAAGGCTTCCATGAAGTGAACCTTGCTTCGCCTACTTCTCCAGACCTTCTTG
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-let-7a-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-196a-5p(1), mmu-miR-203-3p(1), mmu-let-7d-5p(1), mmu-miR-383-5p(1), mmu-miR-98-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAAGCTCAGAGGCTTAGGTTGTCCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAB3IP_540_ORF_1
1.098
0.201762233
0.994378955
1050
ORF sequence:
ATGGCTAACGACCCCTTGGAAGGCTTCCATGAAGTGAACCTTGCTTCGCCTACTTCTCCAGACCTTCTTGGTGTGTGTGACCCGGGAACCCAAGAGCAGACTACCTCCCCGAGCGTCATCTACCGGCCACACCCCTCCACGTTATGCGCTGCCCCTCTCCAGGCCAATGCCTTAGATCTTTCTGATCTTCCTACACAACCTGTGTATTCGTCCCCCAGGCATTTCAACTGTGCAGAAGTATCTAATATCAGCGCTCATGCTCCGGATCCAGCATCATCGGTACCCTCTGCGGTAGCATCAGGGCTCACGAAGTTAACCTCCAGGAAGGACAGCTGTAATGCAGAGAGGGAGTTTCTGCAGGGCGCCACCATCACCGAGGCTTCTGCTGGCAATGATGACATCTTTGGGTTGAGCACGGATAGCCTGTCGCGTTTACGAAGCCCATCTGTTCTGGAAGTTAGAGAGAAGGGCTACGAAAGGTTAAAGGAAGAACTTGCAAAAGCTCAGAGGCTTAGGTTGTCCTATGATGAAGCCTTTGCTATGGCTAACGACCCCTTGGAAGGCTTCCATGAAGTGAACCTTGCTTCGCCTACTTCTCCAGACCTTCTTGGTGTGTGTGACCCGGGAACCCAAGAGCAGACTACCTCCCCGAGCGTCATCTACCGGCCACACCCCTCCACGTTATGCGCTGCCCCTCTCCAGGCCAATGCCTTAGATCTTTCTGATCTTCCTACACAACCTGTGTATTCGTCCCCCAGGCATTTCAACTGTGCAGAAGTATCTAATATCAGCGCTCATGCTCCGGATCCAGCATCATCGGTACCCTCTGCGGTAGCATCAGGGCTCACGAAGTTAACCTCCAGGAAGGACAGCTGTAATGCAGAGAGGGAGTTTCTGCAGGGCGCCACCATCACCGAGGCTTCTGCTGGCAATGATGACATCTTTGGGTTGAGCACGGATAGCCTGTCGCGTTTACGAAGCCCATCTGTTCTGGAAGTTAGAGAGAAGGGCTACGAAAGGTTAAAGGAAGAACTTGCAAAAGCTCAGAGG
Peptide sequence:
MANDPLEGFHEVNLASPTSPDLLGVCDPGTQEQTTSPSVIYRPHPSTLCAAPLQANALDLSDLPTQPVYSSPRHFNCAEVSNISAHAPDPASSVPSAVASGLTKLTSRKDSCNAEREFLQGATITEASAGNDDIFGLSTDSLSRLRSPSVLEVREKGYERLKEELAKAQRLRLSYDEAFAMANDPLEGFHEVNLASPTSPDLLGVCDPGTQEQTTSPSVIYRPHPSTLCAAPLQANALDLSDLPTQPVYSSPRHFNCAEVSNISAHAPDPASSVPSAVASGLTKLTSRKDSCNAEREFLQGATITEASAGNDDIFGLSTDSLSRLRSPSVLEVREKGYERLKEELAKAQR
IRESfinder result
IRESfinder score
0.396466921
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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