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mmu_circGpatch11_680
Basic information of circular RNA
PanCircBase ID:
mmu_circGpatch11_680
mm39_Chr. Position ID:
chr17|79146415|79151329|+
Gene name:
Gpatch11
Transcript:
ENSMUST00000170759.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
4,5,6,7,8,9
Exon/intron offsets:
0,1091,1976,2232,3126,4832
Genomic length:
4914
Exon/intron sizes in nt:
227,42,121,91,117,82
Flanking exon/introns:
chr17:79145331-79146415|chr17:79151329-79152572
Splice length:
680
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGAAGATGTCAGACCCGGTGTGCCGATGCTGAGGCAGATCCGAGAAGCCCGTCGGAAAGAAGAAAAGCAACAGCAAGCTAATCTGAGAAACAGGCAGAAGAGCGTAAAAGAAGAAGAGCGGGAAAGACGTGACATCGGGTTGAAGAATGCACTCGGCTGTGAAAACAAAGGGTTCGCTCTGCTCCAAAAGATGGGATACAAGAGTGGGCAGGCTCTAGGCAAGAGCGGAGATGGTATTGTTGAACCAATTCCTCTCAATGTCAAAACAGGAAAAAGTGGCATAGGTCATGAGTCATCATTAAAACGGAAAGCGGAGGAGAGGCTGGAAAACTACAGGAGAAAAATTCACATGAAAAACCAAAATGAAGCAAAGGCCGCCGAGGAGTTTCGGATGCGACTGAAGAGTAAGCAGGATGAAATGAGGCTCGAAGGAGACCTGAGAAGAAGCCAGCGAGCTTGCCAGCAGCTGGATGCCCAGAAGAATATTCAGGTTCCCAGGGAGGCGTGGTACTGGCTGAGGCCTGAAGAGGAGACCGAGGAAGAGGAAGAGGAAAAGGAAGAACAGGATGAAGATGAGTGCCCGAGTGAAGATTTGAGTGTGCTAGAAAAGCTGCAGATCCTCACTGGCTACTTGCGAGAAGAGCACCTGTATTGCATTTGGTGTGGGACAGCCTATGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCTGCAGATCCTCACTGG
59.75
CTTTTCTTCTTTCCGACGGGC
59.8
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCTGCAGATCCTCACTGG
59.75
GCTTTTCTTCTTTCCGACGGG
59.8
141
PCR template sequence:
CCGAGTGAAGATTTGAGTGTGCTAGAAAAGCTGCAGATCCTCACTGGCTACTTGCGAGAAGAGCACCTGTATTGCATTTGGTGTGGGACAGCCTATGAAGAGAAGATGTCAGACCCGGTGTGCCGATGCTGAGGCAGATCCGAGAAGCCCGTCGGAAAGAAGAAAAGCAACAGCAAGCTAATCTGAGAAACAGGCAGAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-192-5p(1), mmu-miR-215-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACAGCCTATGAAGAGAAGATGTCAGA
siRNA sets
GACATCTTCTCTTCATAGG, ATCTTCTCTTCATAGGCTG, ACATCTTCTCTTCATAGGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGPATCH11_680_ORF_1
0.904
0.352415528
0.942928724
687
ORF sequence:
ATGCTGAGGCAGATCCGAGAAGCCCGTCGGAAAGAAGAAAAGCAACAGCAAGCTAATCTGAGAAACAGGCAGAAGAGCGTAAAAGAAGAAGAGCGGGAAAGACGTGACATCGGGTTGAAGAATGCACTCGGCTGTGAAAACAAAGGGTTCGCTCTGCTCCAAAAGATGGGATACAAGAGTGGGCAGGCTCTAGGCAAGAGCGGAGATGGTATTGTTGAACCAATTCCTCTCAATGTCAAAACAGGAAAAAGTGGCATAGGTCATGAGTCATCATTAAAACGGAAAGCGGAGGAGAGGCTGGAAAACTACAGGAGAAAAATTCACATGAAAAACCAAAATGAAGCAAAGGCCGCCGAGGAGTTTCGGATGCGACTGAAGAGTAAGCAGGATGAAATGAGGCTCGAAGGAGACCTGAGAAGAAGCCAGCGAGCTTGCCAGCAGCTGGATGCCCAGAAGAATATTCAGGTTCCCAGGGAGGCGTGGTACTGGCTGAGGCCTGAAGAGGAGACCGAGGAAGAGGAAGAGGAAAAGGAAGAACAGGATGAAGATGAGTGCCCGAGTGAAGATTTGAGTGTGCTAGAAAAGCTGCAGATCCTCACTGGCTACTTGCGAGAAGAGCACCTGTATTGCATTTGGTGTGGGACAGCCTATGAAGAGAAGATGTCAGACCCGGTGTGCCGATGCTGA
Peptide sequence:
MLRQIREARRKEEKQQQANLRNRQKSVKEEERERRDIGLKNALGCENKGFALLQKMGYKSGQALGKSGDGIVEPIPLNVKTGKSGIGHESSLKRKAEERLENYRRKIHMKNQNEAKAAEEFRMRLKSKQDEMRLEGDLRRSQRACQQLDAQKNIQVPREAWYWLRPEEETEEEEEEKEEQDEDECPSEDLSVLEKLQILTGYLREEHLYCIWCGTAYEEKMSDPVCRC
IRESfinder result
IRESfinder score
0.2001626
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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