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mmu_circChfr_1120
Basic information of circular RNA
PanCircBase ID:
mmu_circChfr_1120
mm39_Chr. Position ID:
chr5|110288219|110302848|+
Gene name:
Chfr
Transcript:
ENSMUST00000199672.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
4,5,6,7,8,9,10,11
Exon/intron offsets:
0,3197,4237,4418,6116,11173,12764,14483
Genomic length:
14629
Exon/intron sizes in nt:
10,01,10,60,21,61,65,10,00,00,000
Flanking exon/introns:
chr5:110288055-110288219|chr5:110302848-110306667
Splice length:
1120
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCTGTGACCTCTCTTTCCCCAGCAATAAACTGGTCTCTGGAGATCACTGTAAACTTACAGTGGATGAAATATCTGGTGAGGTGACACTGGAAGACACCAGCACCAATGGAACAGTGATCAATAAGCTGCAAGTTGTTAAGAAGCAGACTTACCCTTTACAGAGCGGGGATATCATCTATTTGGTGTACAGGAAGAATGAGCCAGAACACAATGTGGCATACCTCTATGAATCTTTAAGTGGCAAACAGAGCTTAACTCAAGACTCCCTTGAAGCCAATAAGGAAAATATGTTCCATGTGACCAAAGATTGCTCAGGTCCAGGGCAGGGTGATGATCCCCAGGTTCCACTATTGTCACCCATGGCTCAGACATGCTTAGAGGAACCACAGCCATCAACATCGACATCAGACCTCCTCCCCACGGCCTCTACCTCTTCTACGGAGCCAGAGCTGACCTCTGCAGGGCAAAAGCATTCTTCTAGCTCTGGACCTGGGAACACAAGCATCTCCCCAAAAGGACGCAGTTCACTTGTTGCAAATGGCGAACTCTCTAGCCTTTCTCCAGTTTTCCAAGACAAAGAAGCATCCTTTTCTTTGCTGGAAAGTAAAGACCATGAGGAATTGGAGCCTGCCAAAAAAAAGATGAAAGGAGATGGGGAACTTGACACGAACCTCCAGTTATTAGTTTCAGGCCAGCGTGGAAATGCCCAAACCTCAAGTGAAGATGTCAAAGATGCCTCTGTGAAGCCAGACAAGATGGAGGAGACACTAACCTGTATCATCTGCCAGGACCTTCTGCACGATTGTGTGAGATAAAAGTCGCAGTGAAGAAGATGTGAGAAGTATGGATGCAAGGAATAAAATCACTCAAGATATGCTGCAACCCAAAGTCAGGAGGTCTTTCTCTGATGAAGAGGGGAGTTCAGAGGACCTGCTAGAGCTGTCTGATGTCGACAGTGAATCCTCAGATATCAGTCAGCCATACATTGTCTGCAGACAGTGTCCTGAATACAGAAGGCAAGCGGTGCAGTCTCTTCCTTGCCCAGTCCCAGAGAGTGAGCTGGGAGCTACACTGGCCCTTGGTGGGGAGGCACCTTCAACATCTGCCAGCTTGCCAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTCCTTGCCCAGTCCCAG
60
TCCAGTGTCACCTCACCAGA
60.11
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTACACTGGCCCTTGGTGG
60
TCCAGTGTCACCTCACCAGA
60.11
145
PCR template sequence:
GCGGTGCAGTCTCTTCCTTGCCCAGTCCCAGAGAGTGAGCTGGGAGCTACACTGGCCCTTGGTGGGGAGGCACCTTCAACATCTGCCAGCTTGCCAACAGGCTGTGACCTCTCTTTCCCCAGCAATAAACTGGTCTCTGGAGATCACTGTAAACTTACAGTGGATGAAATATCTGGTGAGGTGACACTGGAAGACACCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
22
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-let-7a-5p(1), mmu-miR-200a-3p(1), mmu-miR-199a-5p(1), mmu-miR-7b-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-221-3p(1), mmu-let-7c-5p(1), mmu-miR-298-5p(1), mmu-miR-7a-5p(1), mmu-let-7d-5p(1), mmu-miR-149-5p(1), mmu-miR-182-5p(1), mmu-miR-98-5p(1), mmu-miR-325-3p(1), mmu-miR-680(1), mmu-miR-29b-2-5p(1), mmu-miR-669d-5p(1), mmu-miR-484(1), mmu-miR-490-3p(1), mmu-miR-202-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCTTGCCAACAGGCTGTGACCTCTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCHFR_1120_ORF_1
0.9121
0.161781649
0.992913121
1092
ORF sequence:
ATGGATGCAAGGAATAAAATCACTCAAGATATGCTGCAACCCAAAGTCAGGAGGTCTTTCTCTGATGAAGAGGGGAGTTCAGAGGACCTGCTAGAGCTGTCTGATGTCGACAGTGAATCCTCAGATATCAGTCAGCCATACATTGTCTGCAGACAGTGTCCTGAATACAGAAGGCAAGCGGTGCAGTCTCTTCCTTGCCCAGTCCCAGAGAGTGAGCTGGGAGCTACACTGGCCCTTGGTGGGGAGGCACCTTCAACATCTGCCAGCTTGCCAACAGGCTGTGACCTCTCTTTCCCCAGCAATAAACTGGTCTCTGGAGATCACTGTAAACTTACAGTGGATGAAATATCTGGTGAGGTGACACTGGAAGACACCAGCACCAATGGAACAGTGATCAATAAGCTGCAAGTTGTTAAGAAGCAGACTTACCCTTTACAGAGCGGGGATATCATCTATTTGGTGTACAGGAAGAATGAGCCAGAACACAATGTGGCATACCTCTATGAATCTTTAAGTGGCAAACAGAGCTTAACTCAAGACTCCCTTGAAGCCAATAAGGAAAATATGTTCCATGTGACCAAAGATTGCTCAGGTCCAGGGCAGGGTGATGATCCCCAGGTTCCACTATTGTCACCCATGGCTCAGACATGCTTAGAGGAACCACAGCCATCAACATCGACATCAGACCTCCTCCCCACGGCCTCTACCTCTTCTACGGAGCCAGAGCTGACCTCTGCAGGGCAAAAGCATTCTTCTAGCTCTGGACCTGGGAACACAAGCATCTCCCCAAAAGGACGCAGTTCACTTGTTGCAAATGGCGAACTCTCTAGCCTTTCTCCAGTTTTCCAAGACAAAGAAGCATCCTTTTCTTTGCTGGAAAGTAAAGACCATGAGGAATTGGAGCCTGCCAAAAAAAAGATGAAAGGAGATGGGGAACTTGACACGAACCTCCAGTTATTAGTTTCAGGCCAGCGTGGAAATGCCCAAACCTCAAGTGAAGATGTCAAAGATGCCTCTGTGAAGCCAGACAAGATGGAGGAGACACTAACCTGTATCATCTGCCAGGACCTTCTGCACGATTGTGTGAGATAA
Peptide sequence:
MDARNKITQDMLQPKVRRSFSDEEGSSEDLLELSDVDSESSDISQPYIVCRQCPEYRRQAVQSLPCPVPESELGATLALGGEAPSTSASLPTGCDLSFPSNKLVSGDHCKLTVDEISGEVTLEDTSTNGTVINKLQVVKKQTYPLQSGDIIYLVYRKNEPEHNVAYLYESLSGKQSLTQDSLEANKENMFHVTKDCSGPGQGDDPQVPLLSPMAQTCLEEPQPSTSTSDLLPTASTSSTEPELTSAGQKHSSSSGPGNTSISPKGRSSLVANGELSSLSPVFQDKEASFSLLESKDHEELEPAKKKMKGDGELDTNLQLLVSGQRGNAQTSSEDVKDASVKPDKMEETLTCIICQDLLHDCVR
IRESfinder result
IRESfinder score
0.550651404
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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