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mmu_circGpatch11_598
Basic information of circular RNA
PanCircBase ID:
mmu_circGpatch11_598
mm39_Chr. Position ID:
chr17|79146415|79149658|+
Gene name:
Gpatch11
Transcript:
ENSMUST00000170759.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
4,5,6,7,8
Exon/intron offsets:
0,1091,1976,2232,3126
Genomic length:
3243
Exon/intron sizes in nt:
22,74,21,21,91,117
Flanking exon/introns:
chr17:79145331-79146415|chr17:79149658-79151247
Splice length:
598
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGAAGATGTCAGACCCGGTGTGCCGATGCTGAGGCAGATCCGAGAAGCCCGTCGGAAAGAAGAAAAGCAACAGCAAGCTAATCTGAGAAACAGGCAGAAGAGCGTAAAAGAAGAAGAGCGGGAAAGACGTGACATCGGGTTGAAGAATGCACTCGGCTGTGAAAACAAAGGGTTCGCTCTGCTCCAAAAGATGGGATACAAGAGTGGGCAGGCTCTAGGCAAGAGCGGAGATGGTATTGTTGAACCAATTCCTCTCAATGTCAAAACAGGAAAAAGTGGCATAGGTCATGAGTCATCATTAAAACGGAAAGCGGAGGAGAGGCTGGAAAACTACAGGAGAAAAATTCACATGAAAAACCAAAATGAAGCAAAGGCCGCCGAGGAGTTTCGGATGCGACTGAAGAGTAAGCAGGATGAAATGAGGCTCGAAGGAGACCTGAGAAGAAGCCAGCGAGCTTGCCAGCAGCTGGATGCCCAGAAGAATATTCAGGTTCCCAGGGAGGCGTGGTACTGGCTGAGGCCTGAAGAGGAGACCGAGGAAGAGGAAGAGGAAAAGGAAGAACAGGATGAAGATGAGTGCCCGAGTGAAGATTTGAGT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGAAGAGGAGACCGAGGA
60.03
CTTCTTTCCGACGGGCTTCT
60.04
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGAAGAGGAGACCGAGGA
60.03
TCTTCTTTCCGACGGGCTTC
60.04
141
PCR template sequence:
GGAGGCGTGGTACTGGCTGAGGCCTGAAGAGGAGACCGAGGAAGAGGAAGAGGAAAAGGAAGAACAGGATGAAGATGAGTGCCCGAGTGAAGATTTGAGTAGAAGATGTCAGACCCGGTGTGCCGATGCTGAGGCAGATCCGAGAAGCCCGTCGGAAAGAAGAAAAGCAACAGCAAGCTAATCTGAGAAACAGGCAGAAG
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
TGAAGATTTGAGTAGAAGATGTCAGA
siRNA sets
TCTTCTACTCAAATCTTCA, ACATCTTCTACTCAAATCT, ATCTTCTACTCAAATCTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGPATCH11_598_ORF_1
0.9354
0.300724289
0.91814742
654
ORF sequence:
ATGCTGAGGCAGATCCGAGAAGCCCGTCGGAAAGAAGAAAAGCAACAGCAAGCTAATCTGAGAAACAGGCAGAAGAGCGTAAAAGAAGAAGAGCGGGAAAGACGTGACATCGGGTTGAAGAATGCACTCGGCTGTGAAAACAAAGGGTTCGCTCTGCTCCAAAAGATGGGATACAAGAGTGGGCAGGCTCTAGGCAAGAGCGGAGATGGTATTGTTGAACCAATTCCTCTCAATGTCAAAACAGGAAAAAGTGGCATAGGTCATGAGTCATCATTAAAACGGAAAGCGGAGGAGAGGCTGGAAAACTACAGGAGAAAAATTCACATGAAAAACCAAAATGAAGCAAAGGCCGCCGAGGAGTTTCGGATGCGACTGAAGAGTAAGCAGGATGAAATGAGGCTCGAAGGAGACCTGAGAAGAAGCCAGCGAGCTTGCCAGCAGCTGGATGCCCAGAAGAATATTCAGGTTCCCAGGGAGGCGTGGTACTGGCTGAGGCCTGAAGAGGAGACCGAGGAAGAGGAAGAGGAAAAGGAAGAACAGGATGAAGATGAGTGCCCGAGTGAAGATTTGAGTAGAAGATGTCAGACCCGGTGTGCCGATGCTGAGGCAGATCCGAGAAGCCCGTCGGAAAGAAGAAAAGCAACAGCAAGCTAA
Peptide sequence:
MLRQIREARRKEEKQQQANLRNRQKSVKEEERERRDIGLKNALGCENKGFALLQKMGYKSGQALGKSGDGIVEPIPLNVKTGKSGIGHESSLKRKAEERLENYRRKIHMKNQNEAKAAEEFRMRLKSKQDEMRLEGDLRRSQRACQQLDAQKNIQVPREAWYWLRPEEETEEEEEEKEEQDEDECPSEDLSRRCQTRCADAEADPRSPSERRKATAS
IRESfinder result
IRESfinder score
0.173299974
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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