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mmu_circHelz_1607
Basic information of circular RNA
PanCircBase ID:
mmu_circHelz_1607
mm39_Chr. Position ID:
chr11|107504676|107528753|+
Gene name:
Helz
Transcript:
ENSMUST00000100305.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
13,14,15,16,17,18,19,20,21
Exon/intron offsets:
0,5132,6233,12684,13502,18321,21129,22315,23929
Genomic length:
24077
Exon/intron sizes in nt:
26,83,34,13,11,80,10,20,00,00,00,00,000
Flanking exon/introns:
chr11:107495189-107504676|chr11:107528753-107536875
Splice length:
1607
Other database IDs:
circBase: mmu_circ_0002736, CIRCpedia: MMU_CIRCpedia_2130, circAtlas: mmu-Helz_0022
circBase: hsa_circ_0107523, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_120301
Human Ortholog IDs:
Mature spliced Sequence:
ATCTTGAATACCTGATGCATGCAAAGCGGCAGCTGGTAACCACAGCCAAGCGCTGGGACTCTTCTTCTAAGACTATTGTAGATTTTGAACCTAATGAAACTACTGATTTGGAGAAGAGCCTTTTGATCAGATACCAAATTCCTCTGTCTGCTGACCAGCTGTTTACACAGTCCGTCTTAGACAAATCATTGACCAAGACTAACTATCAGGCACGGCTGCACGACCTGCTTTATATTGAGGAGATAGCCCAGTATAAAGAAGTCAGCAGGTTCAACCTTAAAGTGCAATTGCAGATTTTAGCAAGCTTCATGCTCACTGGAGTTTCTGGGGGTGCAAAGTATGCTCAGAATGGACAACTTTTTGGTCGTTTCAAGCTTACTGAAACCCTCTCGGAAGACACTTTGGCTGGACGGCTGGTGATGACCAGGGTCAATGCTGTTTATTTATTACCAGTCCCTAAAGAGAAGCTCGTTCAGTCCCAGGGAACCAAAGAGAAGGTTTATGAAGCTACTATTGAAGAAAAAACAAAAGACTATGTATTTTTAAGGATATCCAGGGAATGCTGTGAAGAGCTTAGTCTGCGGCCTGACTGTGACATCCAGGTTGAGCTTCAGTTTCAGTTGAACCGATTACCCCTCTGTGAAATGCATTATGCACTAGACAGGATTAAGGACAATGCTGTTTTGTTTCCAGACATCAGTATGACTCCTACCATACCTTGGAGTCCCAACAGACAGTGGGACGAGCAGTTGGATCCTCGGCTAAATGCAAAGCAGAAAGAAGCTGTTCTGGCCATCACCACTCCACTCTCCATCCAGCTGCCGCCTGTCCTCATCATTGGACCCTACGGGACGGGCAAAACCTTCACTCTGGCTCAGGCGGCCAAGCACATACTGCAGCAGCAGGAGACCAGGATTCTCATTTGCACCCATTCTAATAGTGCTGCTGACCTCTACATAAAGGATTATTTACATCCATATGTAGAAGCAGGCAATCCCCAGGCAAGACCTCTCAGGGTGTATTTCCGGAATCGCTGGGTGAAGACTGTCCACCCAGTCGTGCATCAGTACTGCTTGATCTCGAGCACACAGTCCACCTTTCAGATGCCCCAGAAGGAAGATATTCTTAAACATCGAGTGGTGGTGGTCACACTGAGCACTTCCCAGTACCTCTGCCAGCTGGACCTGGAACCTGGGTTCTTCACGCACGTTCTCTTAGATGAAGCTGCCCAGGCCATGGAGTGTGAGACCATTATGCCTCTAGCCTTAGCTACTAAAAACACACGGATTGTTTTGGCTGGTGATCACATGCAGCTCAGCCCTTTTGTTTACAGCGAGTTTGCCAGGGAGAGAAACCTTCACGTTTCGTTACTTGACCGACTCTACGAGCATTACCCTGCTGAGTTTCCATGCAGGATCCTCCTCTGTGAGAACTATCGTTCCCATGAAGCTATCATCAACTACACCTCTGAGCTTTTCTATGAGGGGAAGCTGATGGCCAGTGGGAAGCAGCCGGCGCACAAGGACTTCTATCCACTCACGTTCTTTACGGCACGGGGGGAGGACGTCCAAGAGAAGAACAGCACGGCATTCTACAACAATGCAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGGCGCACAAGGACTTCTAT
60.46
GAAGAAGAGTCCCAGCGCTT
60.04
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGGCGCACAAGGACTTCTAT
60.46
AAGAAGAGTCCCAGCGCTTG
60.32
161
PCR template sequence:
GCAGCCGGCGCACAAGGACTTCTATCCACTCACGTTCTTTACGGCACGGGGGGAGGACGTCCAAGAGAAGAACAGCACGGCATTCTACAACAATGCAGAGATCTTGAATACCTGATGCATGCAAAGCGGCAGCTGGTAACCACAGCCAAGCGCTGGGACTCTTCTTCTAAGACTATTGTAGATTTTGAACCTAATGAAAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
27
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-32-5p(1), mmu-miR-30e-5p(1), mmu-miR-92a-3p(1), mmu-miR-15b-5p(1), mmu-miR-33-5p(1), mmu-miR-298-5p(1), mmu-miR-125b-5p(1), mmu-miR-25-3p(1), mmu-miR-351-5p(1), mmu-miR-125a-5p(1), mmu-miR-127-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-382-5p(1), mmu-miR-370-3p(1), mmu-miR-541-5p(1), mmu-miR-340-5p(1), mmu-miR-27a-5p(1), mmu-miR-690(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1), mmu-miR-673-5p(1), mmu-miR-490-3p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAACAATGCAGAGATCTTGAATACCT
siRNA sets
AGGTATTCAAGATCTCTGC, TTCAAGATCTCTGCATTGT, ATTCAAGATCTCTGCATTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHELZ_1607_ORF_1
1.1306
0.222231709
0.999908288
1608
ORF sequence:
ATGCATGCAAAGCGGCAGCTGGTAACCACAGCCAAGCGCTGGGACTCTTCTTCTAAGACTATTGTAGATTTTGAACCTAATGAAACTACTGATTTGGAGAAGAGCCTTTTGATCAGATACCAAATTCCTCTGTCTGCTGACCAGCTGTTTACACAGTCCGTCTTAGACAAATCATTGACCAAGACTAACTATCAGGCACGGCTGCACGACCTGCTTTATATTGAGGAGATAGCCCAGTATAAAGAAGTCAGCAGGTTCAACCTTAAAGTGCAATTGCAGATTTTAGCAAGCTTCATGCTCACTGGAGTTTCTGGGGGTGCAAAGTATGCTCAGAATGGACAACTTTTTGGTCGTTTCAAGCTTACTGAAACCCTCTCGGAAGACACTTTGGCTGGACGGCTGGTGATGACCAGGGTCAATGCTGTTTATTTATTACCAGTCCCTAAAGAGAAGCTCGTTCAGTCCCAGGGAACCAAAGAGAAGGTTTATGAAGCTACTATTGAAGAAAAAACAAAAGACTATGTATTTTTAAGGATATCCAGGGAATGCTGTGAAGAGCTTAGTCTGCGGCCTGACTGTGACATCCAGGTTGAGCTTCAGTTTCAGTTGAACCGATTACCCCTCTGTGAAATGCATTATGCACTAGACAGGATTAAGGACAATGCTGTTTTGTTTCCAGACATCAGTATGACTCCTACCATACCTTGGAGTCCCAACAGACAGTGGGACGAGCAGTTGGATCCTCGGCTAAATGCAAAGCAGAAAGAAGCTGTTCTGGCCATCACCACTCCACTCTCCATCCAGCTGCCGCCTGTCCTCATCATTGGACCCTACGGGACGGGCAAAACCTTCACTCTGGCTCAGGCGGCCAAGCACATACTGCAGCAGCAGGAGACCAGGATTCTCATTTGCACCCATTCTAATAGTGCTGCTGACCTCTACATAAAGGATTATTTACATCCATATGTAGAAGCAGGCAATCCCCAGGCAAGACCTCTCAGGGTGTATTTCCGGAATCGCTGGGTGAAGACTGTCCACCCAGTCGTGCATCAGTACTGCTTGATCTCGAGCACACAGTCCACCTTTCAGATGCCCCAGAAGGAAGATATTCTTAAACATCGAGTGGTGGTGGTCACACTGAGCACTTCCCAGTACCTCTGCCAGCTGGACCTGGAACCTGGGTTCTTCACGCACGTTCTCTTAGATGAAGCTGCCCAGGCCATGGAGTGTGAGACCATTATGCCTCTAGCCTTAGCTACTAAAAACACACGGATTGTTTTGGCTGGTGATCACATGCAGCTCAGCCCTTTTGTTTACAGCGAGTTTGCCAGGGAGAGAAACCTTCACGTTTCGTTACTTGACCGACTCTACGAGCATTACCCTGCTGAGTTTCCATGCAGGATCCTCCTCTGTGAGAACTATCGTTCCCATGAAGCTATCATCAACTACACCTCTGAGCTTTTCTATGAGGGGAAGCTGATGGCCAGTGGGAAGCAGCCGGCGCACAAGGACTTCTATCCACTCACGTTCTTTACGGCACGGGGGGAGGACGTCCAAGAGAAGAACAGCACGGCATTCTACAACAATGCAGAGATCTTGAATACCTGA
Peptide sequence:
MHAKRQLVTTAKRWDSSSKTIVDFEPNETTDLEKSLLIRYQIPLSADQLFTQSVLDKSLTKTNYQARLHDLLYIEEIAQYKEVSRFNLKVQLQILASFMLTGVSGGAKYAQNGQLFGRFKLTETLSEDTLAGRLVMTRVNAVYLLPVPKEKLVQSQGTKEKVYEATIEEKTKDYVFLRISRECCEELSLRPDCDIQVELQFQLNRLPLCEMHYALDRIKDNAVLFPDISMTPTIPWSPNRQWDEQLDPRLNAKQKEAVLAITTPLSIQLPPVLIIGPYGTGKTFTLAQAAKHILQQQETRILICTHSNSAADLYIKDYLHPYVEAGNPQARPLRVYFRNRWVKTVHPVVHQYCLISSTQSTFQMPQKEDILKHRVVVVTLSTSQYLCQLDLEPGFFTHVLLDEAAQAMECETIMPLALATKNTRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEHYPAEFPCRILLCENYRSHEAIINYTSELFYEGKLMASGKQPAHKDFYPLTFFTARGEDVQEKNSTAFYNNAEILNT
IRESfinder result
IRESfinder score
0.60605207
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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