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mmu_circSfi1_683
Basic information of circular RNA
PanCircBase ID:
mmu_circSfi1_683
mm39_Chr. Position ID:
chr11|3120586|3139056|-
Gene name:
Sfi1
Transcript:
ENSMUST00000081318.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
7,6,5,4,3,2
Exon/intron offsets:
0,6840,8810,15478,16653,18354
Genomic length:
18470
Exon/intron sizes in nt:
1,18,95,11,17,21,71,110
Flanking exon/introns:
chr11:3115678-3120586|chr11:3139056-3143359
Splice length:
683
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
TTATAAGAGGAAGTTAAAAGGCTTTGGTTCATCAATAACCTAGTCACAAAAATACATATCAACCACTGGTTGAATTTCCATCAAGAGGAAAGAATGGAGAAGAAGATTGGTTCCAGGTCTTTTAGGGATGGTGTGGTTAAGAAACCTTGTTCTCCAAAGACCCTGCCCCTCAAAAAGTCTTCTGCCTTCTCTGGGATCCAGAGGGAGCCATCTAGAAGCTGCCACTCTATATACTATCATGCCTCACAAAACTGGACTCGGTACCGATTACAAGAACTTCGAATCAGGTGTGTGGCCAGAAAGTTCCTGTATTTGTGGATTCGAGTGACTTTTGGAAGAGTGACTCCCTCTAGAGCCAGGATTTTCCATGAGCAGAAAATATTACAGAAGGTCTTCGGAGAATGGAGGGAAGAATGGTGGGTCTCCCAGAGGGAGTGGAAGCTCTGTGTCCGAGCTGACTGTCACTACAGATACTACTTGTACAACCTGATTTTCCAGAACTGGAAGACCTTTGTGCACCAGCAACGGGAGATGAGGAAGAGGTTCCGAATAGCTGAGCATCATGATACGAAGCAGAAGATGTGCCAAGCCTGGAAGTCCTGGTTGATATACATGGTTTCTCGTAGGACCAAACTTCACATGAAGACTACTGCTCTAGAGTTTAGGAGGCAGAGTGTCTTATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACATGGTTTCTCGTAGGACCA
58.75
TGATGGAAATTCAACCAGTGGT
58.16
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACATGGTTTCTCGTAGGACCA
58.75
TTGATGGAAATTCAACCAGTGGT
58.78
157
PCR template sequence:
GCCAAGCCTGGAAGTCCTGGTTGATATACATGGTTTCTCGTAGGACCAAACTTCACATGAAGACTACTGCTCTAGAGTTTAGGAGGCAGAGTGTCTTATGTTATAAGAGGAAGTTAAAAGGCTTTGGTTCATCAATAACCTAGTCACAAAAATACATATCAACCACTGGTTGAATTTCCATCAAGAGGAAAGAATGGAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-136-5p(2), mmu-miR-205-5p(1), mmu-miR-433-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-224-5p(1), mmu-miR-190b-5p(1), mmu-miR-207(1), mmu-miR-3470b(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AGAGTGTCTTATGTTATAAGAGGAAG
siRNA sets
TTATAACATAAGACACTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSFI1_683_ORF_1
0.8666
0.035664919
0.740827844
633
ORF sequence:
ATGGAGAAGAAGATTGGTTCCAGGTCTTTTAGGGATGGTGTGGTTAAGAAACCTTGTTCTCCAAAGACCCTGCCCCTCAAAAAGTCTTCTGCCTTCTCTGGGATCCAGAGGGAGCCATCTAGAAGCTGCCACTCTATATACTATCATGCCTCACAAAACTGGACTCGGTACCGATTACAAGAACTTCGAATCAGGTGTGTGGCCAGAAAGTTCCTGTATTTGTGGATTCGAGTGACTTTTGGAAGAGTGACTCCCTCTAGAGCCAGGATTTTCCATGAGCAGAAAATATTACAGAAGGTCTTCGGAGAATGGAGGGAAGAATGGTGGGTCTCCCAGAGGGAGTGGAAGCTCTGTGTCCGAGCTGACTGTCACTACAGATACTACTTGTACAACCTGATTTTCCAGAACTGGAAGACCTTTGTGCACCAGCAACGGGAGATGAGGAAGAGGTTCCGAATAGCTGAGCATCATGATACGAAGCAGAAGATGTGCCAAGCCTGGAAGTCCTGGTTGATATACATGGTTTCTCGTAGGACCAAACTTCACATGAAGACTACTGCTCTAGAGTTTAGGAGGCAGAGTGTCTTATGTTATAAGAGGAAGTTAAAAGGCTTTGGTTCATCAATAACCTAG
Peptide sequence:
MEKKIGSRSFRDGVVKKPCSPKTLPLKKSSAFSGIQREPSRSCHSIYYHASQNWTRYRLQELRIRCVARKFLYLWIRVTFGRVTPSRARIFHEQKILQKVFGEWREEWWVSQREWKLCVRADCHYRYYLYNLIFQNWKTFVHQQREMRKRFRIAEHHDTKQKMCQAWKSWLIYMVSRRTKLHMKTTALEFRRQSVLCYKRKLKGFGSSIT
IRESfinder result
IRESfinder score
0.666278924
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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