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mmu_circTm9sf4_1127
Basic information of circular RNA
PanCircBase ID:
mmu_circTm9sf4_1127
mm39_Chr. Position ID:
chr2|153032750|153046544|+
Gene name:
Tm9sf4
Transcript:
ENSMUST00000089027.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
7,8,9,10,11,12,13,14,15,16,17
Exon/intron offsets:
0,220,1099,3446,4480,4659,7519,9812,11507,12951,13704
Genomic length:
13794
Exon/intron sizes in nt:
119,112,71,133,82,76,84,176,64,120,90
Flanking exon/introns:
chr2:153030997-153032750|chr2:153046544-153050526
Splice length:
1127
Other database IDs:
circAtlas: mmu-Tm9sf4_0025
circBase: hsa_circ_0059759
Human Ortholog IDs:
Mature spliced Sequence:
ACCTCAAAACAGGCGAGAAGAGTTCATGTACCCTACCCGAGGGTGCCAACTCCTTACCCCAAGAAATTGACCCCACTAAGGAGAATCAGCTGTACTTCACCTACTCTGTGCACTGGGAGGAAAGTGACATCAAATGGGCCTCTCGATGGGACACTTACCTAACCATGAGTGATGTGCAGATCCACTGGTTTTCCATCATTAACTCTGTCGTGGTAGTCTTCTTCCTGTCAGGCATCCTCAGCATGATTATCATCCGGACCCTGCGGAAGGACATCGCCAACTACAACAAGGAGGATGACATTGAAGACACCATGGAGGAGTCTGGGTGGAAGCTTGTGCATGGTGATGTCTTCAGGCCACCCCAATATCCCATGATCCTCAGCTCTCTGCTGGGCTCAGGCATTCAGCTCTTCTGCATGATCCTGATTGTCATCTTCGTGGCCATGCTTGGGATGCTGTCGCCGTCCAGCCGGGGAGCTCTCATGACCACTGCCTGCTTCCTCTTCATGTTCATGGGGGTATTTGGTGGATTTTCTGCTGGCCGTCTCTACCGAACTCTAAAAGGCCATAGGTGGAAGAAAGGAGCCTTCTGTACAGCGACACTGTATCCTGGTGTGGTTTTCGGCATCTGCTTTGTGTTGAATTGCTTCATCTGGGGAAAGCACTCATCAGGAGCAGTACCGTTTCCCACCATGGTGGCGTTGCTGTGTATGTGGTTCGGGATCTCCCTGCCCCTTGTCTACTTGGGCTACTATTTCGGCTTCCGCAAGCAGCCATATGACAACCCTGTGCGCACAAACCAGATTCCCCGGCAGATCCCTGAACAACGGTGGTACATGAACCGATTTGTGGGCATCCTCATGGCTGGGATCCTGCCCTTTGGTGCCATGTTCATTGAGCTGTTCTTCATCTTCAGTGCAATCTGGGAGAACCAGTTCTATTACCTCTTCGGTTTCCTGTTCCTCGTTTTCATCATCCTGGTGGTGTCCTGCTCACAAATCAGCATAGTCATGGTGTACTTCCAGCTGTGTGCAGAGGATTACCGCTGGTGGTGGAGGAATTTCCTTGTCTCAGGGGGATCTGCATTCTACGTCCTGGTCTATGCCATCTTTTATTTTGTTAACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGTGCAGAGGATTACCGCT
60.11
GGTAAGGAGTTGGCACCCTC
60.04
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTGTGCAGAGGATTACCGCT
60.11
TTGGGGTAAGGAGTTGGCAC
59.89
162
PCR template sequence:
GTGTGCAGAGGATTACCGCTGGTGGTGGAGGAATTTCCTTGTCTCAGGGGGATCTGCATTCTACGTCCTGGTCTATGCCATCTTTTATTTTGTTAACAAGACCTCAAAACAGGCGAGAAGAGTTCATGTACCCTACCCGAGGGTGCCAACTCCTTACCCCAAGAAATTGACCCCACTAAGGAGAATCAGCTGTACTTCAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-7a-5p(1), mmu-miR-125b-5p(1), mmu-miR-143-3p(1), mmu-miR-125a-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-183-5p(1), mmu-miR-34b-5p(1), mmu-miR-544-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTGTTAACAAGACCTCAAAACAGG
siRNA sets
TTTTGAGGTCTTGTTAACA, TTTGAGGTCTTGTTAACAA, GTTTTGAGGTCTTGTTAAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTM9SF4_1127_ORF_1
1.1471
0.25618271
0.997535274
1125
ORF sequence:
ATGAGTGATGTGCAGATCCACTGGTTTTCCATCATTAACTCTGTCGTGGTAGTCTTCTTCCTGTCAGGCATCCTCAGCATGATTATCATCCGGACCCTGCGGAAGGACATCGCCAACTACAACAAGGAGGATGACATTGAAGACACCATGGAGGAGTCTGGGTGGAAGCTTGTGCATGGTGATGTCTTCAGGCCACCCCAATATCCCATGATCCTCAGCTCTCTGCTGGGCTCAGGCATTCAGCTCTTCTGCATGATCCTGATTGTCATCTTCGTGGCCATGCTTGGGATGCTGTCGCCGTCCAGCCGGGGAGCTCTCATGACCACTGCCTGCTTCCTCTTCATGTTCATGGGGGTATTTGGTGGATTTTCTGCTGGCCGTCTCTACCGAACTCTAAAAGGCCATAGGTGGAAGAAAGGAGCCTTCTGTACAGCGACACTGTATCCTGGTGTGGTTTTCGGCATCTGCTTTGTGTTGAATTGCTTCATCTGGGGAAAGCACTCATCAGGAGCAGTACCGTTTCCCACCATGGTGGCGTTGCTGTGTATGTGGTTCGGGATCTCCCTGCCCCTTGTCTACTTGGGCTACTATTTCGGCTTCCGCAAGCAGCCATATGACAACCCTGTGCGCACAAACCAGATTCCCCGGCAGATCCCTGAACAACGGTGGTACATGAACCGATTTGTGGGCATCCTCATGGCTGGGATCCTGCCCTTTGGTGCCATGTTCATTGAGCTGTTCTTCATCTTCAGTGCAATCTGGGAGAACCAGTTCTATTACCTCTTCGGTTTCCTGTTCCTCGTTTTCATCATCCTGGTGGTGTCCTGCTCACAAATCAGCATAGTCATGGTGTACTTCCAGCTGTGTGCAGAGGATTACCGCTGGTGGTGGAGGAATTTCCTTGTCTCAGGGGGATCTGCATTCTACGTCCTGGTCTATGCCATCTTTTATTTTGTTAACAAGACCTCAAAACAGGCGAGAAGAGTTCATGTACCCTACCCGAGGGTGCCAACTCCTTACCCCAAGAAATTGACCCCACTAAGGAGAATCAGCTGTACTTCACCTACTCTGTGCACTGGGAGGAAAGTGACATCAAATGGGCCTCTCGATGGGACACTTACCTAA
Peptide sequence:
MSDVQIHWFSIINSVVVVFFLSGILSMIIIRTLRKDIANYNKEDDIEDTMEESGWKLVHGDVFRPPQYPMILSSLLGSGIQLFCMILIVIFVAMLGMLSPSSRGALMTTACFLFMFMGVFGGFSAGRLYRTLKGHRWKKGAFCTATLYPGVVFGICFVLNCFIWGKHSSGAVPFPTMVALLCMWFGISLPLVYLGYYFGFRKQPYDNPVRTNQIPRQIPEQRWYMNRFVGILMAGILPFGAMFIELFFIFSAIWENQFYYLFGFLFLVFIILVVSCSQISIVMVYFQLCAEDYRWWWRNFLVSGGSAFYVLVYAIFYFVNKTSKQARRVHVPYPRVPTPYPKKLTPLRRISCTSPTLCTGRKVTSNGPLDGTLT
IRESfinder result
IRESfinder score
0.590202894
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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