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mmu_circRab11fip3_486
Basic information of circular RNA
PanCircBase ID:
mmu_circRab11fip3_486
mm39_Chr. Position ID:
chr17|26223524|26235129|-
Gene name:
Rab11fip3
Transcript:
ENSMUST00000118828.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,4304,9223,11393
Genomic length:
11605
Exon/intron sizes in nt:
9,43,61,44,212
Flanking exon/introns:
chr17:26217006-26223524|chr17:26235129-26240661
Splice length:
486
Other database IDs:
circAtlas: mmu-Rab11fip3_0011
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GCCAACGAGGTGACAGACAGTGCATATATGGGGTCTGAGAGCACCTACAGTGAGTGTGAGACCTTCACAGATGAGGACACCAGCACCCTGGTGCACCCCGAGCTGCAGCCTGAAGGGGACGTGGACAGTGCTGGTGGCTCAGGGGTGCCCTCTGAGTGCCTGGACACCATGGAGGAGCCTGACCATGGTGCATTGCTGCTGCTCCCAGGCAGATCCCGCCCCCACAGCCAAGCTGTCGTCATGGTGATTGGCAGTGAGGAACATTTTGAAGATTATGGTGAGGGCAATGAGGCAGAACTATCCCCGGAGACCCTCTGCGATGGGGACGGCGAGGACCCTGCTTTTCTCACCCCCAGCCCAGCCAAGCGGCTCTCCAGCAGGAAGGTGGCAAGGTATCTGCACCAGTCGGGGACCCTGACTATGGAGGCCCTGGAGGACCCTCCCCCAGAGCCTGTGGAGTGCCCAGAGGAGGACATTGCAGACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCAAGGTATCTGCACCAGT
60.04
AGGTGCTCTCAGACCCCATA
59.66
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCAAGGTATCTGCACCAGT
60.04
TAGGTGCTCTCAGACCCCAT
59.66
147
PCR template sequence:
GGCAAGGTATCTGCACCAGTCGGGGACCCTGACTATGGAGGCCCTGGAGGACCCTCCCCCAGAGCCTGTGGAGTGCCCAGAGGAGGACATTGCAGACAAGGCCAACGAGGTGACAGACAGTGCATATATGGGGTCTGAGAGCACCTACAGTGAGTGTGAGACCTTCACAGATGAGGACACCAGCACCCTGGTGCACCCCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-326-3p(2), mmu-miR-15a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-125b-5p(1), mmu-miR-138-5p(1), mmu-miR-125a-5p(1), mmu-miR-501-3p(1), mmu-miR-370-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CATTGCAGACAAGGCCAACGAGGTGA
siRNA sets
GTTGGCCTTGTCTGCAATG, CTCGTTGGCCTTGTCTGCA, TCACCTCGTTGGCCTTGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAB11FIP3_486_ORF_1
1.1623
0.478558478
0.99656971
945
ORF sequence:
ATGGGGTCTGAGAGCACCTACAGTGAGTGTGAGACCTTCACAGATGAGGACACCAGCACCCTGGTGCACCCCGAGCTGCAGCCTGAAGGGGACGTGGACAGTGCTGGTGGCTCAGGGGTGCCCTCTGAGTGCCTGGACACCATGGAGGAGCCTGACCATGGTGCATTGCTGCTGCTCCCAGGCAGATCCCGCCCCCACAGCCAAGCTGTCGTCATGGTGATTGGCAGTGAGGAACATTTTGAAGATTATGGTGAGGGCAATGAGGCAGAACTATCCCCGGAGACCCTCTGCGATGGGGACGGCGAGGACCCTGCTTTTCTCACCCCCAGCCCAGCCAAGCGGCTCTCCAGCAGGAAGGTGGCAAGGTATCTGCACCAGTCGGGGACCCTGACTATGGAGGCCCTGGAGGACCCTCCCCCAGAGCCTGTGGAGTGCCCAGAGGAGGACATTGCAGACAAGGCCAACGAGGTGACAGACAGTGCATATATGGGGTCTGAGAGCACCTACAGTGAGTGTGAGACCTTCACAGATGAGGACACCAGCACCCTGGTGCACCCCGAGCTGCAGCCTGAAGGGGACGTGGACAGTGCTGGTGGCTCAGGGGTGCCCTCTGAGTGCCTGGACACCATGGAGGAGCCTGACCATGGTGCATTGCTGCTGCTCCCAGGCAGATCCCGCCCCCACAGCCAAGCTGTCGTCATGGTGATTGGCAGTGAGGAACATTTTGAAGATTATGGTGAGGGCAATGAGGCAGAACTATCCCCGGAGACCCTCTGCGATGGGGACGGCGAGGACCCTGCTTTTCTCACCCCCAGCCCAGCCAAGCGGCTCTCCAGCAGGAAGGTGGCAAGGTATCTGCACCAGTCGGGGACCCTGACTATGGAGGCCCTGGAGGACCCTCCCCCAGAGCCTGTGGAGTGCCCAGAGGAGGACATTGCAGACAAG
Peptide sequence:
MGSESTYSECETFTDEDTSTLVHPELQPEGDVDSAGGSGVPSECLDTMEEPDHGALLLLPGRSRPHSQAVVMVIGSEEHFEDYGEGNEAELSPETLCDGDGEDPAFLTPSPAKRLSSRKVARYLHQSGTLTMEALEDPPPEPVECPEEDIADKANEVTDSAYMGSESTYSECETFTDEDTSTLVHPELQPEGDVDSAGGSGVPSECLDTMEEPDHGALLLLPGRSRPHSQAVVMVIGSEEHFEDYGEGNEAELSPETLCDGDGEDPAFLTPSPAKRLSSRKVARYLHQSGTLTMEALEDPPPEPVECPEEDIADK
IRESfinder result
IRESfinder score
0.426156826
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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