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mmu_circRps6ka5_515
Basic information of circular RNA
PanCircBase ID:
mmu_circRps6ka5_515
mm39_Chr. Position ID:
chr12|100582255|100644848|-
Gene name:
Rps6ka5
Transcript:
ENSMUST00000222731.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,3529,38274,62521
Genomic length:
62593
Exon/intron sizes in nt:
108,116,219,72
Flanking exon/introns:
chr12:100564232-100582255|chr12:100644848-100691039
Splice length:
515
Other database IDs:
CIRCpedia: MMU_CIRCpedia_218, circAtlas: mmu-Rps6ka5_0004
circBase: hsa_circ_0032940, circAtlas: hsa-RPS6KA5_0003, CIRCpedia: HSA_CIRCpedia_13393
Human Ortholog IDs:
Mature spliced Sequence:
CCAACTTAACAGGACACGCAGAGAAGGTGGGGATTGAAAACTTTGAGCTGCTGAAGGTCCTAGGAACTGGAGCTTATGGGAAAGTATTTCTAGTTCGTAAAATAAGCGGCCATGATGCTGGAAAGCTGTATGCTATGAAGGTTTTAAAAAAGGCAACAATAGTTCAGAAGGCTAAAACTACAGAGCATACAAGGACAGAACGACAGGTTCTGGAGCACATTAGACAGTCGCCATTTTTGGTGACATTGCACTATGCTTTCCAGACAGAGACCAAGCTTCATCTCATCTTAGATTATATAAATGGTGGAGAACTTTTTACTCATCTTTCTCAAAGAGAGCGTTTCACAGAGCACGAAGTGCAGATCTATGTTGGAGAGATTGTGCTTGCCCTGGAACACCTGCACAAGTTGGGGATTATATACCGTGACATTAAGCTTGAAAATATTCTCCTGGATTCTAACGGCCATGTGGTGCTGACAGATTTCGGTCTGAGTAAGGAGTTTGTGGCCGATGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCCTGGATTCTAACGGCCA
59.17
AGCTCCAGTTCCTAGGACCT
59.29
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTCCTGGATTCTAACGGCC
58.88
AGCTCCAGTTCCTAGGACCT
59.29
144
PCR template sequence:
TATATACCGTGACATTAAGCTTGAAAATATTCTCCTGGATTCTAACGGCCATGTGGTGCTGACAGATTTCGGTCTGAGTAAGGAGTTTGTGGCCGATGAACCAACTTAACAGGACACGCAGAGAAGGTGGGGATTGAAAACTTTGAGCTGCTGAAGGTCCTAGGAACTGGAGCTTATGGGAAAGTATTTCTAGTTCGTAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-130a-3p(1), mmu-miR-143-3p(1), mmu-miR-127-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-301a-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGTGGCCGATGAACCAACTTAACAGG
siRNA sets
TGTTAAGTTGGTTCATCGG, CTGTTAAGTTGGTTCATCG, TTAAGTTGGTTCATCGGCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRPS6KA5_515_ORF_1
1.1624
0.12487402
0.554630859
390
ORF sequence:
ATGAAGGTTTTAAAAAAGGCAACAATAGTTCAGAAGGCTAAAACTACAGAGCATACAAGGACAGAACGACAGGTTCTGGAGCACATTAGACAGTCGCCATTTTTGGTGACATTGCACTATGCTTTCCAGACAGAGACCAAGCTTCATCTCATCTTAGATTATATAAATGGTGGAGAACTTTTTACTCATCTTTCTCAAAGAGAGCGTTTCACAGAGCACGAAGTGCAGATCTATGTTGGAGAGATTGTGCTTGCCCTGGAACACCTGCACAAGTTGGGGATTATATACCGTGACATTAAGCTTGAAAATATTCTCCTGGATTCTAACGGCCATGTGGTGCTGACAGATTTCGGTCTGAGTAAGGAGTTTGTGGCCGATGAACCAACTTAA
Peptide sequence:
MKVLKKATIVQKAKTTEHTRTERQVLEHIRQSPFLVTLHYAFQTETKLHLILDYINGGELFTHLSQRERFTEHEVQIYVGEIVLALEHLHKLGIIYRDIKLENILLDSNGHVVLTDFGLSKEFVADEPT
IRESfinder result
IRESfinder score
0.619905734
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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