top of page
mmu_circFxr2_886
Basic information of circular RNA
PanCircBase ID:
mmu_circFxr2_886
mm39_Chr. Position ID:
chr11|69531059|69540663|+
Gene name:
Fxr2
Transcript:
ENSMUST00000018909.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
3,4,5,6,7,8,9,10
Exon/intron offsets:
0,1048,1207,1813,3604,8571,8916,9494
Genomic length:
9604
Exon/intron sizes in nt:
9,47,21,49,94,11,71,71,00,000
Flanking exon/introns:
chr11:69530268-69531059|chr11:69540663-69541288
Splice length:
886
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CTGGCAGAGTGAGAGACAGATTCCCTTTGGGGATGTCCGACTACCGCCTCCAGCTGACTACAATAAGGAAATCACAGAAGGAGATGAAGTAGAGGTCTATTCGAGAGCCAATGAACAGGAACCTTGTGGCTGGTGGCTGGCCCGGGTGCGGATGATGAAGGGAGATTTCTATGTCATTGAGTACGCTGCCTGTGATGCTACCTACAATGAGATTGTCACTCTGGAACGACTTCGGCCAGTCAATCCCAGTCCCCTTGCAACCAAAGGCAGCTTCTTCAAGGTTACCATGGCTGTGCCTGAGGACCTCAGGGAGGCCTGCTCCAATGAAAATGTCCATAAGGAGTTCAAGAAAGCACTGGGAGCCAACTGCATCTTTCTCAACATCACAAACAGTGAGCTCTTTATTCTGTCAACCACAGAAGCCCCTGTGAAGAGGGCATCTTTGTTGGGTGATATGCATTTCCGAAGCCTTCGCACCAAATTGCTGCTCATGTCCCGCAATGAAGAAGCTACTAAGCACCTAGAGACAAGTAAGCAGCTGGCAGCAGCCTTCCAAGAGGAGTTCACAGTGCGAGAGGACCTGATGGGTCTGGCGATCGGAACGCACGGTGCCAACATCCAGCAGGCTCGGAAAGTGCCCGGAGTGACTGCCATTGAGTTGGGTGAAGAGACCTGCACTTTCCGAATCTATGGGGAGACACCAGAGGCATGCAGACAGGCTCGAAGCTACCTTGAATTTTCCGAGGACTCTGTACAAGTGCCCAGGAACCTGGTTGGCAAAGTGATCGGAAAGAACGGGAAAGTGATTCAGGAGATTGTGGATAAGTCTGGTGTGGTGAGGGTTCGTGTGGAAGGAGATAACGACAAGAAGAACCCCAGGGAGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGGAAAGAACGGGAAAGTGA
58.13
GGTAGTCGGACATCCCCAAA
59.09
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGGAAAGAACGGGAAAGTGA
58.13
GTAGTCGGACATCCCCAAAGG
60.13
144
PCR template sequence:
CGGAAAGAACGGGAAAGTGATTCAGGAGATTGTGGATAAGTCTGGTGTGGTGAGGGTTCGTGTGGAAGGAGATAACGACAAGAAGAACCCCAGGGAGGAGCTGGCAGAGTGAGAGACAGATTCCCTTTGGGGATGTCCGACTACCGCCTCCAGCTGACTACAATAAGGAAATCACAGAAGGAGATGAAGTAGAGGTCTAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-34c-5p(1), mmu-miR-205-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-322-5p(1), mmu-miR-324-5p(1), mmu-miR-125b-5p(1), mmu-miR-125a-5p(1), mmu-miR-370-3p(1), mmu-miR-34b-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCCAGGGAGGAGCTGGCAGAGTGAG
siRNA sets
TCACTCTGCCAGCTCCTCC, CACTCTGCCAGCTCCTCCC, CTCACTCTGCCAGCTCCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFXR2_886_ORF_1
1.2096
0.405750164
0.98226702
747
ORF sequence:
ATGATGAAGGGAGATTTCTATGTCATTGAGTACGCTGCCTGTGATGCTACCTACAATGAGATTGTCACTCTGGAACGACTTCGGCCAGTCAATCCCAGTCCCCTTGCAACCAAAGGCAGCTTCTTCAAGGTTACCATGGCTGTGCCTGAGGACCTCAGGGAGGCCTGCTCCAATGAAAATGTCCATAAGGAGTTCAAGAAAGCACTGGGAGCCAACTGCATCTTTCTCAACATCACAAACAGTGAGCTCTTTATTCTGTCAACCACAGAAGCCCCTGTGAAGAGGGCATCTTTGTTGGGTGATATGCATTTCCGAAGCCTTCGCACCAAATTGCTGCTCATGTCCCGCAATGAAGAAGCTACTAAGCACCTAGAGACAAGTAAGCAGCTGGCAGCAGCCTTCCAAGAGGAGTTCACAGTGCGAGAGGACCTGATGGGTCTGGCGATCGGAACGCACGGTGCCAACATCCAGCAGGCTCGGAAAGTGCCCGGAGTGACTGCCATTGAGTTGGGTGAAGAGACCTGCACTTTCCGAATCTATGGGGAGACACCAGAGGCATGCAGACAGGCTCGAAGCTACCTTGAATTTTCCGAGGACTCTGTACAAGTGCCCAGGAACCTGGTTGGCAAAGTGATCGGAAAGAACGGGAAAGTGATTCAGGAGATTGTGGATAAGTCTGGTGTGGTGAGGGTTCGTGTGGAAGGAGATAACGACAAGAAGAACCCCAGGGAGGAGCTGGCAGAGTGA
Peptide sequence:
MMKGDFYVIEYAACDATYNEIVTLERLRPVNPSPLATKGSFFKVTMAVPEDLREACSNENVHKEFKKALGANCIFLNITNSELFILSTTEAPVKRASLLGDMHFRSLRTKLLLMSRNEEATKHLETSKQLAAAFQEEFTVREDLMGLAIGTHGANIQQARKVPGVTAIELGEETCTFRIYGETPEACRQARSYLEFSEDSVQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRVEGDNDKKNPREELAE
IRESfinder result
IRESfinder score
0.381956435
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page