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mmu_circCd47_411
Basic information of circular RNA
PanCircBase ID:
mmu_circCd47_411
mm39_Chr. Position ID:
chr16|49688127|49689443|+
Gene name:
Cd47
Transcript:
ENSMUST00000229640.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
5,6
Exon/intron offsets:
0,1253
Genomic length:
1316
Exon/intron sizes in nt:
348,63
Flanking exon/introns:
chr16:49628507-49688127|chr16:49689443-49704527
Splice length:
411
Other database IDs:
circAtlas: mmu-Cd47_0006
Human Ortholog IDs:
Mature spliced Sequence:
GTTCAGCTCAACTACTGTTTAGTAACGTCAACTCCATAGAGTTCACTTCATGCAATGAAACTGTGGTCATCCCTTGCATCGTCCGTAATGTGGAGGCGCAAAGCACCGAAGAAATGTTTGTGAAGTGGAAGTTGAACAAATCGTATATTTTCATCTATGATGGAAATAAAAATAGCACTACTACAGATCAAAACTTTACCAGTGCAAAAATCTCAGTCTCAGACTTAATCAATGGCATTGCCTCTTTGAAAATGGATAAGCGCGATGCCATGGTGGGAAACTACACTTGCGAAGTGACAGAGTTATCCAGAGAAGGCAAAACAGTTATAGAGCTGAAAAACCGCACGGCCTTCAACACTGACCAAGGATCAGCCTGTTCTTACGAGGAGGAGAAAGGAGGTTGCAAATTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACACTGACCAAGGATCAGCC
59.67
TACGGACGATGCAAGGGATG
59.9
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACACTGACCAAGGATCAGCC
59.67
GCCTCCACATTACGGACGAT
59.9
154
PCR template sequence:
GAAGGCAAAACAGTTATAGAGCTGAAAAACCGCACGGCCTTCAACACTGACCAAGGATCAGCCTGTTCTTACGAGGAGGAGAAAGGAGGTTGCAAATTAGGTTCAGCTCAACTACTGTTTAGTAACGTCAACTCCATAGAGTTCACTTCATGCAATGAAACTGTGGTCATCCCTTGCATCGTCCGTAATGTGGAGGCGCA
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-29b-2-5p(1), mmu-miR-300-3p(1), mmu-miR-323-3p(1), mmu-miR-376a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGTTGCAAATTAGGTTCAGCTCAACT
siRNA sets
TGAGCTGAACCTAATTTGC, TTGAGCTGAACCTAATTTG, CTGAACCTAATTTGCAACC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCD47_411_ORF_1
0.8136
0.196133836
0.89675925
708
ORF sequence:
ATGTTTGTGAAGTGGAAGTTGAACAAATCGTATATTTTCATCTATGATGGAAATAAAAATAGCACTACTACAGATCAAAACTTTACCAGTGCAAAAATCTCAGTCTCAGACTTAATCAATGGCATTGCCTCTTTGAAAATGGATAAGCGCGATGCCATGGTGGGAAACTACACTTGCGAAGTGACAGAGTTATCCAGAGAAGGCAAAACAGTTATAGAGCTGAAAAACCGCACGGCCTTCAACACTGACCAAGGATCAGCCTGTTCTTACGAGGAGGAGAAAGGAGGTTGCAAATTAGGTTCAGCTCAACTACTGTTTAGTAACGTCAACTCCATAGAGTTCACTTCATGCAATGAAACTGTGGTCATCCCTTGCATCGTCCGTAATGTGGAGGCGCAAAGCACCGAAGAAATGTTTGTGAAGTGGAAGTTGAACAAATCGTATATTTTCATCTATGATGGAAATAAAAATAGCACTACTACAGATCAAAACTTTACCAGTGCAAAAATCTCAGTCTCAGACTTAATCAATGGCATTGCCTCTTTGAAAATGGATAAGCGCGATGCCATGGTGGGAAACTACACTTGCGAAGTGACAGAGTTATCCAGAGAAGGCAAAACAGTTATAGAGCTGAAAAACCGCACGGCCTTCAACACTGACCAAGGATCAGCCTGTTCTTACGAGGAGGAGAAAGGAGGTTGCAAATTA
Peptide sequence:
MFVKWKLNKSYIFIYDGNKNSTTTDQNFTSAKISVSDLINGIASLKMDKRDAMVGNYTCEVTELSREGKTVIELKNRTAFNTDQGSACSYEEEKGGCKLGSAQLLFSNVNSIEFTSCNETVVIPCIVRNVEAQSTEEMFVKWKLNKSYIFIYDGNKNSTTTDQNFTSAKISVSDLINGIASLKMDKRDAMVGNYTCEVTELSREGKTVIELKNRTAFNTDQGSACSYEEEKGGCKL
IRESfinder result
IRESfinder score
0.538447233
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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