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mmu_circRaf1_627
Basic information of circular RNA
PanCircBase ID:
mmu_circRaf1_627
mm39_Chr. Position ID:
chr6|115608175|115614672|-
Gene name:
Raf1
Transcript:
ENSMUST00000112949.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
7,6,5,4,3
Exon/intron offsets:
0,1682,3338,3763,6384
Genomic length:
6497
Exon/intron sizes in nt:
1,54,99,15,81,03,113
Flanking exon/introns:
chr6:115603927-115608175|chr6:115614672-115621370
Splice length:
627
Other database IDs:
circAtlas: mmu-Raf1_0009
circAtlas: hsa-RAF1_0012, CIRCpedia: HSA_CIRCpedia_43413
Human Ortholog IDs:
Mature spliced Sequence:
GTCAATGTGCGGAATGGAATGAGCTTACATGACTGCCTTATGAAAGCTCTGAAGGTGAGAGGCCTGCAGCCAGAGTGCTGTGCAGTGTTCAGACTTCTCCAGGAACACAAAGGTAAGAAAGCACGCTTAGATTGGAACACCGATGCCGCCTCTCTGATTGGAGAAGAACTGCAAGTGGATTTTTTGGATCATGTTCCACTCACAACTCACAACTTTGCTCGGAAAACGTTCCTGAAGCTTGCATTCTGTGACATCTGTCAGAAGTTCCTGCTAAATGGATTTCGATGTCAGACTTGTGGCTACAAGTTTCATGAGCACTGTAGCACCAAAGTACCTACTATGTGTGTGGACTGGAGTAATATCAGACAGCTCTTGCTGTTTCCAAATTCCACTGTTGGTGACAGTGGAGTCCCAGCACCACCTTCTTTCCCAATGCGTCGGATGCGAGAATCTGTTTCCCGGATGCCTGCTAGTTCCCAGCACAGATACTCTACACCCCATGCCTTCACTTTCAACACCTCCAGCCCTTCCTCAGAAGGTTCCCTGTCCCAGAGGCAGAGGTCAACGTCCACTCCCAATGTCCACATGGTCAGCACCACCCTGCATGTGGACAGCAGGATGATTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACGTCCACTCCCAATGTCC
59.96
TGAACACTGCACAGCACTCT
59.82
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACGTCCACTCCCAATGTCC
59.96
TCTGAACACTGCACAGCACT
59.82
157
PCR template sequence:
TTCCTCAGAAGGTTCCCTGTCCCAGAGGCAGAGGTCAACGTCCACTCCCAATGTCCACATGGTCAGCACCACCCTGCATGTGGACAGCAGGATGATTGAGGTCAATGTGCGGAATGGAATGAGCTTACATGACTGCCTTATGAAAGCTCTGAAGGTGAGAGGCCTGCAGCCAGAGTGCTGTGCAGTGTTCAGACTTCTCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-139-5p(1), mmu-miR-382-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGGATGATTGAGGTCAATGTGCGGA
siRNA sets
ATTGACCTCAATCATCCTG, ACATTGACCTCAATCATCC, CATTGACCTCAATCATCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAF1_627_ORF_1
0.7101
0.161453722
0.996415626
1236
ORF sequence:
ATGAGCTTACATGACTGCCTTATGAAAGCTCTGAAGGTGAGAGGCCTGCAGCCAGAGTGCTGTGCAGTGTTCAGACTTCTCCAGGAACACAAAGGTAAGAAAGCACGCTTAGATTGGAACACCGATGCCGCCTCTCTGATTGGAGAAGAACTGCAAGTGGATTTTTTGGATCATGTTCCACTCACAACTCACAACTTTGCTCGGAAAACGTTCCTGAAGCTTGCATTCTGTGACATCTGTCAGAAGTTCCTGCTAAATGGATTTCGATGTCAGACTTGTGGCTACAAGTTTCATGAGCACTGTAGCACCAAAGTACCTACTATGTGTGTGGACTGGAGTAATATCAGACAGCTCTTGCTGTTTCCAAATTCCACTGTTGGTGACAGTGGAGTCCCAGCACCACCTTCTTTCCCAATGCGTCGGATGCGAGAATCTGTTTCCCGGATGCCTGCTAGTTCCCAGCACAGATACTCTACACCCCATGCCTTCACTTTCAACACCTCCAGCCCTTCCTCAGAAGGTTCCCTGTCCCAGAGGCAGAGGTCAACGTCCACTCCCAATGTCCACATGGTCAGCACCACCCTGCATGTGGACAGCAGGATGATTGAGGTCAATGTGCGGAATGGAATGAGCTTACATGACTGCCTTATGAAAGCTCTGAAGGTGAGAGGCCTGCAGCCAGAGTGCTGTGCAGTGTTCAGACTTCTCCAGGAACACAAAGGTAAGAAAGCACGCTTAGATTGGAACACCGATGCCGCCTCTCTGATTGGAGAAGAACTGCAAGTGGATTTTTTGGATCATGTTCCACTCACAACTCACAACTTTGCTCGGAAAACGTTCCTGAAGCTTGCATTCTGTGACATCTGTCAGAAGTTCCTGCTAAATGGATTTCGATGTCAGACTTGTGGCTACAAGTTTCATGAGCACTGTAGCACCAAAGTACCTACTATGTGTGTGGACTGGAGTAATATCAGACAGCTCTTGCTGTTTCCAAATTCCACTGTTGGTGACAGTGGAGTCCCAGCACCACCTTCTTTCCCAATGCGTCGGATGCGAGAATCTGTTTCCCGGATGCCTGCTAGTTCCCAGCACAGATACTCTACACCCCATGCCTTCACTTTCAACACCTCCAGCCCTTCCTCAGAAGGTTCCCTGTCCCAGAGGCAGAGGTCAACGTCCACTCCCAATGTCCACATGGTCAGCACCACCCTGCATGTGGACAGCAGGATGATTGAG
Peptide sequence:
MSLHDCLMKALKVRGLQPECCAVFRLLQEHKGKKARLDWNTDAASLIGEELQVDFLDHVPLTTHNFARKTFLKLAFCDICQKFLLNGFRCQTCGYKFHEHCSTKVPTMCVDWSNIRQLLLFPNSTVGDSGVPAPPSFPMRRMRESVSRMPASSQHRYSTPHAFTFNTSSPSSEGSLSQRQRSTSTPNVHMVSTTLHVDSRMIEVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLQEHKGKKARLDWNTDAASLIGEELQVDFLDHVPLTTHNFARKTFLKLAFCDICQKFLLNGFRCQTCGYKFHEHCSTKVPTMCVDWSNIRQLLLFPNSTVGDSGVPAPPSFPMRRMRESVSRMPASSQHRYSTPHAFTFNTSSPSSEGSLSQRQRSTSTPNVHMVSTTLHVDSRMIE
IRESfinder result
IRESfinder score
0.545751539
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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