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mmu_circSmc5_929
Basic information of circular RNA
PanCircBase ID:
mmu_circSmc5_929
mm39_Chr. Position ID:
chr19|23221218|23241130|-
Gene name:
Smc5
Transcript:
ENSMUST00000087556.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
9,8,7,6,5,4
Exon/intron offsets:
0,10822,13633,15792,17478,19749
Genomic length:
19912
Exon/intron sizes in nt:
25,67,21,62,14,11,35,100
Flanking exon/introns:
chr19:23220154-23221218|chr19:23241130-23243029
Splice length:
929
Other database IDs:
circAtlas: mmu-Smc5_0017
Human Ortholog IDs:
Mature spliced Sequence:
GTTCAGGACTTCTGGAAATCTTATAATCACCCGCGAGATTGATGTGATAAAAAATCAGTCCTTTTGGTTCATCAACAAAAAGCCTGTAACCCAGAAGATAGTGGAAGAACAGGTTGCAGCCTTAAACATCCAAGTGGGCAATCTGTGCCAGTTCTTGCCTCAGGACAAAGTTGGGGAATTTGCTAAACTCAGCAAAATTGAACTCCTTGAAGCTACTGAGAAGTCAGTTGGTCCTCCAGAGATGCACAGATACCACTGTGAACTCAAAAACTTCAGGGAGAAGGAGAAGCAGCTAGAGACCTCTTGCAAAGAGAAAACTGAATACCTAGAGAAAATGGTTCAGAGAAATGAAAGGTACAAACAAGATGTGGAAAGATTCTATGAACGAAAACGACATTTAGATTTAATTGAGATGCTTGAGGCCAAAAGACCATGGGTGGAATATGAGAATGTACGTCAGGAATATGAAGGTGTGAAACTAATTCGTGACCGAGTGAAGGAAGAGGTCAGGAAACTTAAAGAAGGGCAGATTCCTATGACACGGCGGATTGAGGAGATTGACCGGCAGCGTCACACTTTGGAAGTTCGAATCAAAGAAAAGTCAACCGATATTAAGGAAGCATCTCAGAAATGCAAGCAAAGGCAAGACTTGATTGAACGGAAGGACAGACAGATTAAGGAACTTCAGCAGGCATTAACAGTCAAGCAGAATGAAGAGCTGGACCGGCAGAAGAGAATAAGTAACACCCGCAAGATGATAGAGGATCTGCAGAGTGAGCTCAAGACTGCGGAAAACTGCGAGAACCTTCAGCCTCAGATCGACACCGTCACAAATGATCTGAGGCGTGTGCAGGAGGAGAAAGCCTTATGTGAAGGCGAGATCATTGATAAACAGCGAGAAAAGGAAATGCTGGAGAAGCAGAGACGGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AATGATCTGAGGCGTGTGCA
60.04
CACATCAATCTCGCGGGTGA
60.46
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AATGATCTGAGGCGTGTGCA
60.04
TCACATCAATCTCGCGGGTG
60.46
144
PCR template sequence:
ACAAATGATCTGAGGCGTGTGCAGGAGGAGAAAGCCTTATGTGAAGGCGAGATCATTGATAAACAGCGAGAAAAGGAAATGCTGGAGAAGCAGAGACGGAGTTCAGGACTTCTGGAAATCTTATAATCACCCGCGAGATTGATGTGATAAAAAATCAGTCCTTTTGGTTCATCAACAAAAAGCCTGTAACCCAGAAGATA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
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-370-3p(1), mmu-miR-3470b(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGCAGAGACGGAGTTCAGGACTTCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMC5_929_ORF_1
1.2551
0.356880801
0.974891108
714
ORF sequence:
ATGCACAGATACCACTGTGAACTCAAAAACTTCAGGGAGAAGGAGAAGCAGCTAGAGACCTCTTGCAAAGAGAAAACTGAATACCTAGAGAAAATGGTTCAGAGAAATGAAAGGTACAAACAAGATGTGGAAAGATTCTATGAACGAAAACGACATTTAGATTTAATTGAGATGCTTGAGGCCAAAAGACCATGGGTGGAATATGAGAATGTACGTCAGGAATATGAAGGTGTGAAACTAATTCGTGACCGAGTGAAGGAAGAGGTCAGGAAACTTAAAGAAGGGCAGATTCCTATGACACGGCGGATTGAGGAGATTGACCGGCAGCGTCACACTTTGGAAGTTCGAATCAAAGAAAAGTCAACCGATATTAAGGAAGCATCTCAGAAATGCAAGCAAAGGCAAGACTTGATTGAACGGAAGGACAGACAGATTAAGGAACTTCAGCAGGCATTAACAGTCAAGCAGAATGAAGAGCTGGACCGGCAGAAGAGAATAAGTAACACCCGCAAGATGATAGAGGATCTGCAGAGTGAGCTCAAGACTGCGGAAAACTGCGAGAACCTTCAGCCTCAGATCGACACCGTCACAAATGATCTGAGGCGTGTGCAGGAGGAGAAAGCCTTATGTGAAGGCGAGATCATTGATAAACAGCGAGAAAAGGAAATGCTGGAGAAGCAGAGACGGAGTTCAGGACTTCTGGAAATCTTATAA
Peptide sequence:
MHRYHCELKNFREKEKQLETSCKEKTEYLEKMVQRNERYKQDVERFYERKRHLDLIEMLEAKRPWVEYENVRQEYEGVKLIRDRVKEEVRKLKEGQIPMTRRIEEIDRQRHTLEVRIKEKSTDIKEASQKCKQRQDLIERKDRQIKELQQALTVKQNEELDRQKRISNTRKMIEDLQSELKTAENCENLQPQIDTVTNDLRRVQEEKALCEGEIIDKQREKEMLEKQRRSSGLLEIL
IRESfinder result
IRESfinder score
0.498082453
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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