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mmu_circSfmbt1_1245
Basic information of circular RNA
PanCircBase ID:
mmu_circSfmbt1_1245
mm39_Chr. Position ID:
chr14|30460495|30509564|+
Gene name:
Sfmbt1
Transcript:
ENSMUST00000227201.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
2,3,4,5,6,7,8,9,10
Exon/intron offsets:
0,27424,31260,35346,39365,45404,46162,47275,48918
Genomic length:
49069
Exon/intron sizes in nt:
92,13,99,52,41,89,24,70,00,00,000
Flanking exon/introns:
chr14:30437198-30460495|chr14:30509564-30512690
Splice length:
1245
Other database IDs:
CIRCpedia: MMU_CIRCpedia_216093, circAtlas: mmu-Sfmbt1_0021
Human Ortholog IDs:
Mature spliced Sequence:
ACAAGATTAGACCTCAGACTTGCCATGTAACAAAGGATGACTTTAGAACTTTTGCTCTTCCTGTCTCCATCTCCCAAGTGCTTGGATTCTAGATCCGTGGATGCCACTGGACAGAAACTTGACGCTTCAGATCATCTTGGTAACATAGCAGAGCCCTCGGCCTACTCATTACTTGGGGGAGAGGTAGCCCCTGTGCTGTGGAGATGAGCGGGGAGCAGCAGCTTGATGCAGATCTTGGGTCTGGTGTAGAAGTAGAAGAATTCAGCTGGGAAGATTATCTAGAAGAGACAGGCTCCACCACAGTTCCCTACGCATCGTTTAAACATGTGGATATACGTTTGCAAAATGGATTTGCTCCTGGGATGAAGCTGGAGGTAGCTCTGAAAAATGACCCTGAGACTTATTGGGTTGCCACCATCATCACCGCCTGTGAGCAGTTGCTCCTGCTTCGTTATGAAGGCTATGGGGAAGACCGAAAAGCAGACTTCTGGTGTGACATCAGGAAAGCTGGCCTCTACCCCATTGGGTGGTGTCAGCAGAACAAGAAGACCCTCGAAGCTCCAGAAGGCATCAGAGATAAAGTGTCTGATTGGAATGCATTCCTACAGCAGACCCTGATAGGAGCCTGTGGTCCTCCCGTGTCTCTGCTAGAGGGCCTCCGTAATGGAAGGAATCCTTTAGATCTCATTGCTCCAGGGTCCAAACTAGAATGCCAGGATTTTCGGGACTCTTTAAGCACTTGGCTTGTTACTGTTGTGGAGAACATTGGGGGACGGTTGAAGCTGCGGTATGAAGGCCTTGAGAGCCGTGACGGTTTTGAACACTGGTTGTATTACTTAGATCCATTTCTTCATCACATTGGTTGGGCTGCTCAGCAAGGATGTGACCTTCAGCCCCCATTAGCCATCAAACATCTGAAGAGTGAAGCTGACTGGCAAGAGATTTTGGCCAAAGTGAAAGAGGAAGAGCCATTACCCTCTTACTTATTTAAGGATAAGCAAGTTATTGGAACCCATGAATTTTCTATAAACATGAAGTTGGAAGCTGTGGACCCGTGGTCTCCTTTTGGGATTTCTCCTGCAACGATTGCTAAGGTGTTTGATGATAAGTACTTTCTAGTGGAAATGGATGACCTTCGGCCAGAAGACCATACAAGGCGATCATTTGTGTGCCATGCTAACAGTCCTGGTATCTTTCCTGTGCAGTGGAGTCTAAAGAATGGTTTACATATCAATCCTCCTCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCATGCTAACAGTCCTGGT
60.04
AGCACTTGGGAGATGGAGAC
59.09
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCATGCTAACAGTCCTGG
60.04
AGCACTTGGGAGATGGAGAC
59.09
158
PCR template sequence:
GACCATACAAGGCGATCATTTGTGTGCCATGCTAACAGTCCTGGTATCTTTCCTGTGCAGTGGAGTCTAAAGAATGGTTTACATATCAATCCTCCTCCAGACAAGATTAGACCTCAGACTTGCCATGTAACAAAGGATGACTTTAGAACTTTTGCTCTTCCTGTCTCCATCTCCCAAGTGCTTGGATTCTAGATCCGTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-20a-5p(1), mmu-miR-199a-5p(1), mmu-miR-205-5p(1), mmu-miR-483-5p(1), mmu-miR-802-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AATCCTCCTCCAGACAAGATTAGACC
siRNA sets
TAATCTTGTCTGGAGGAGG,AATCTTGTCTGGAGGAGGA,CTAATCTTGTCTGGAGGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSFMBT1_1245_ORF_1
0.9738
0.14591046
0.99498103
1134
ORF sequence:
ATGAGCGGGGAGCAGCAGCTTGATGCAGATCTTGGGTCTGGTGTAGAAGTAGAAGAATTCAGCTGGGAAGATTATCTAGAAGAGACAGGCTCCACCACAGTTCCCTACGCATCGTTTAAACATGTGGATATACGTTTGCAAAATGGATTTGCTCCTGGGATGAAGCTGGAGGTAGCTCTGAAAAATGACCCTGAGACTTATTGGGTTGCCACCATCATCACCGCCTGTGAGCAGTTGCTCCTGCTTCGTTATGAAGGCTATGGGGAAGACCGAAAAGCAGACTTCTGGTGTGACATCAGGAAAGCTGGCCTCTACCCCATTGGGTGGTGTCAGCAGAACAAGAAGACCCTCGAAGCTCCAGAAGGCATCAGAGATAAAGTGTCTGATTGGAATGCATTCCTACAGCAGACCCTGATAGGAGCCTGTGGTCCTCCCGTGTCTCTGCTAGAGGGCCTCCGTAATGGAAGGAATCCTTTAGATCTCATTGCTCCAGGGTCCAAACTAGAATGCCAGGATTTTCGGGACTCTTTAAGCACTTGGCTTGTTACTGTTGTGGAGAACATTGGGGGACGGTTGAAGCTGCGGTATGAAGGCCTTGAGAGCCGTGACGGTTTTGAACACTGGTTGTATTACTTAGATCCATTTCTTCATCACATTGGTTGGGCTGCTCAGCAAGGATGTGACCTTCAGCCCCCATTAGCCATCAAACATCTGAAGAGTGAAGCTGACTGGCAAGAGATTTTGGCCAAAGTGAAAGAGGAAGAGCCATTACCCTCTTACTTATTTAAGGATAAGCAAGTTATTGGAACCCATGAATTTTCTATAAACATGAAGTTGGAAGCTGTGGACCCGTGGTCTCCTTTTGGGATTTCTCCTGCAACGATTGCTAAGGTGTTTGATGATAAGTACTTTCTAGTGGAAATGGATGACCTTCGGCCAGAAGACCATACAAGGCGATCATTTGTGTGCCATGCTAACAGTCCTGGTATCTTTCCTGTGCAGTGGAGTCTAAAGAATGGTTTACATATCAATCCTCCTCCAGACAAGATTAGACCTCAGACTTGCCATGTAACAAAGGATGACTTTAGAACTTTTGCTCTTCCTGTCTCCATCTCCCAAGTGCTTGGATTCTAG
Peptide sequence:
MSGEQQLDADLGSGVEVEEFSWEDYLEETGSTTVPYASFKHVDIRLQNGFAPGMKLEVALKNDPETYWVATIITACEQLLLLRYEGYGEDRKADFWCDIRKAGLYPIGWCQQNKKTLEAPEGIRDKVSDWNAFLQQTLIGACGPPVSLLEGLRNGRNPLDLIAPGSKLECQDFRDSLSTWLVTVVENIGGRLKLRYEGLESRDGFEHWLYYLDPFLHHIGWAAQQGCDLQPPLAIKHLKSEADWQEILAKVKEEEPLPSYLFKDKQVIGTHEFSINMKLEAVDPWSPFGISPATIAKVFDDKYFLVEMDDLRPEDHTRRSFVCHANSPGIFPVQWSLKNGLHINPPPDKIRPQTCHVTKDDFRTFALPVSISQVLGF
IRESfinder result
IRESfinder score
0.586380168
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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