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mmu_circSmc5_1346
Basic information of circular RNA
PanCircBase ID:
mmu_circSmc5_1346
mm39_Chr. Position ID:
chr19|23213237|23243082|-
Gene name:
Smc5
Transcript:
ENSMUST00000087556.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
12,11,10,9,8,7,6,5,4,3
Exon/intron offsets:
0,3011,6762,7981,18803,21614,23773,25459,27730,29792
Genomic length:
29845
Exon/intron sizes in nt:
95,114,155,256,72,162,141,135,163,53
Flanking exon/introns:
chr19:23211459-23213237|chr19:23243082-23246090
Splice length:
1346
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTGGGTTTTTCGTGAAGAGAGGATGTTCCAAAGGTTTGGTTGAAATTGAACTGTTCAGGACTTCTGGAAATCTTATAATCACCCGCGAGATTGATGTGATAAAAAATCAGTCCTTTTGGTTCATCAACAAAAAGCCTGTAACCCAGAAGATAGTGGAAGAACAGGTTGCAGCCTTAAACATCCAAGTGGGCAATCTGTGCCAGTTCTTGCCTCAGGACAAAGTTGGGGAATTTGCTAAACTCAGCAAAATTGAACTCCTTGAAGCTACTGAGAAGTCAGTTGGTCCTCCAGAGATGCACAGATACCACTGTGAACTCAAAAACTTCAGGGAGAAGGAGAAGCAGCTAGAGACCTCTTGCAAAGAGAAAACTGAATACCTAGAGAAAATGGTTCAGAGAAATGAAAGGTACAAACAAGATGTGGAAAGATTCTATGAACGAAAACGACATTTAGATTTAATTGAGATGCTTGAGGCCAAAAGACCATGGGTGGAATATGAGAATGTACGTCAGGAATATGAAGGTGTGAAACTAATTCGTGACCGAGTGAAGGAAGAGGTCAGGAAACTTAAAGAAGGGCAGATTCCTATGACACGGCGGATTGAGGAGATTGACCGGCAGCGTCACACTTTGGAAGTTCGAATCAAAGAAAAGTCAACCGATATTAAGGAAGCATCTCAGAAATGCAAGCAAAGGCAAGACTTGATTGAACGGAAGGACAGACAGATTAAGGAACTTCAGCAGGCATTAACAGTCAAGCAGAATGAAGAGCTGGACCGGCAGAAGAGAATAAGTAACACCCGCAAGATGATAGAGGATCTGCAGAGTGAGCTCAAGACTGCGGAAAACTGCGAGAACCTTCAGCCTCAGATCGACACCGTCACAAATGATCTGAGGCGTGTGCAGGAGGAGAAAGCCTTATGTGAAGGCGAGATCATTGATAAACAGCGAGAAAAGGAAATGCTGGAGAAGCAGAGACGGAGTGTGAGTGATCATATTACACGGTTTGACAATCTTATGAATCAGAAGGAAGATAAGCTGAGACAGCGGTACCGGGATACGTATGATGCAGTCTTGTGGCTGAGAAATAACAGAGACAGGTTTAAACAAAGAGTCTGTGAACCCATAATGCTCACGATTAATATGAAAGATAATAAAAATGCAAAATATGTTGAAAATCATATTTCATCAAATGACTTAAGAGCCTTTGTGTTTGAAAGTCAAGAAGATATGGAGATTTTCCTCAGAGAGGTTCGTGACAACAAGAAGTTAAGAGTAAATGCTGTTATTGCCCCCAAGATCTCATATGCAGACAAAGCCCCTTCAAGATCTCTGAATGACTTAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCAGACAAAGCCCCTTCA
59.89
TCACATCAATCTCGCGGGTG
60.46
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTGTTATTGCCCCCAAGA
59.59
CACATCAATCTCGCGGGTGA
60.46
165
PCR template sequence:
GAGAGGTTCGTGACAACAAGAAGTTAAGAGTAAATGCTGTTATTGCCCCCAAGATCTCATATGCAGACAAAGCCCCTTCAAGATCTCTGAATGACTTAAAGTTGGGTTTTTCGTGAAGAGAGGATGTTCCAAAGGTTTGGTTGAAATTGAACTGTTCAGGACTTCTGGAAATCTTATAATCACCCGCGAGATTGATGTGA
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-207(3), mmu-miR-5101(2), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-31-5p(1), mmu-miR-217-5p(1), mmu-miR-370-3p(1), mmu-miR-335-3p(1), mmu-miR-3470b(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAATGACTTAAAGTTGGGTTTTTCG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMC5_1346_ORF_1
1.2309
0.269053365
0.996951674
1068
ORF sequence:
ATGCACAGATACCACTGTGAACTCAAAAACTTCAGGGAGAAGGAGAAGCAGCTAGAGACCTCTTGCAAAGAGAAAACTGAATACCTAGAGAAAATGGTTCAGAGAAATGAAAGGTACAAACAAGATGTGGAAAGATTCTATGAACGAAAACGACATTTAGATTTAATTGAGATGCTTGAGGCCAAAAGACCATGGGTGGAATATGAGAATGTACGTCAGGAATATGAAGGTGTGAAACTAATTCGTGACCGAGTGAAGGAAGAGGTCAGGAAACTTAAAGAAGGGCAGATTCCTATGACACGGCGGATTGAGGAGATTGACCGGCAGCGTCACACTTTGGAAGTTCGAATCAAAGAAAAGTCAACCGATATTAAGGAAGCATCTCAGAAATGCAAGCAAAGGCAAGACTTGATTGAACGGAAGGACAGACAGATTAAGGAACTTCAGCAGGCATTAACAGTCAAGCAGAATGAAGAGCTGGACCGGCAGAAGAGAATAAGTAACACCCGCAAGATGATAGAGGATCTGCAGAGTGAGCTCAAGACTGCGGAAAACTGCGAGAACCTTCAGCCTCAGATCGACACCGTCACAAATGATCTGAGGCGTGTGCAGGAGGAGAAAGCCTTATGTGAAGGCGAGATCATTGATAAACAGCGAGAAAAGGAAATGCTGGAGAAGCAGAGACGGAGTGTGAGTGATCATATTACACGGTTTGACAATCTTATGAATCAGAAGGAAGATAAGCTGAGACAGCGGTACCGGGATACGTATGATGCAGTCTTGTGGCTGAGAAATAACAGAGACAGGTTTAAACAAAGAGTCTGTGAACCCATAATGCTCACGATTAATATGAAAGATAATAAAAATGCAAAATATGTTGAAAATCATATTTCATCAAATGACTTAAGAGCCTTTGTGTTTGAAAGTCAAGAAGATATGGAGATTTTCCTCAGAGAGGTTCGTGACAACAAGAAGTTAAGAGTAAATGCTGTTATTGCCCCCAAGATCTCATATGCAGACAAAGCCCCTTCAAGATCTCTGAATGACTTAAAGTTGGGTTTTTCGTGA
Peptide sequence:
MHRYHCELKNFREKEKQLETSCKEKTEYLEKMVQRNERYKQDVERFYERKRHLDLIEMLEAKRPWVEYENVRQEYEGVKLIRDRVKEEVRKLKEGQIPMTRRIEEIDRQRHTLEVRIKEKSTDIKEASQKCKQRQDLIERKDRQIKELQQALTVKQNEELDRQKRISNTRKMIEDLQSELKTAENCENLQPQIDTVTNDLRRVQEEKALCEGEIIDKQREKEMLEKQRRSVSDHITRFDNLMNQKEDKLRQRYRDTYDAVLWLRNNRDRFKQRVCEPIMLTINMKDNKNAKYVENHISSNDLRAFVFESQEDMEIFLREVRDNKKLRVNAVIAPKISYADKAPSRSLNDLKLGFS
IRESfinder result
IRESfinder score
0.546379958
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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