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mmu_circFhod3_2711

Basic information of circular RNA
PanCircBase ID:

mmu_circFhod3_2711

mm39_Chr. Position ID:

chr18|25199273|25263751|+

Gene name:

Fhod3

Transcript:

ENSMUST00000037097.9

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

11

Exon/intron indexes:

16,17,18,19,20,21,22,23,24,25,26

Exon/intron offsets:

0,19117,23813,35309,43838,46329,47293,49482,53902,59526,64316

Genomic length:

64478

Exon/intron sizes in nt:

20,92,79,87,81,59,18,30,00,00,00,00,00,00,00,000

Flanking exon/introns:

chr18:25193433-25199273|chr18:25263751-25265967

Splice length:

2711

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

ATACAAATACTTGGAGCAGTTGGCAGCCGAGACGCAGGAGAAGGAGCCTAGAAGCCAGAGCGTGAGCCGGGGTAGAGCTGACCTCTCCTTGGACCTGAGCTTGCCTGCAGCCCCTGCTCCACCTTCCCCTTCAAGCCAGAGTCCCTCTGCTGACTCACAAGAGGCTCTCCCTGTGCCTTCATCCCCACCCACTCTGCAGTGCCCCCAAGTAAGTGGTAAGGACCACGAGCCTGAACTGGAGGCAGAAGCTGGGCAAGGTGCTGATGAAGCCAGCCAGGATATAGCATCTGCCCACAGGGGAGCAGAGAGCCAAGAAGAGCCGGTGCTGGAGCTAGAGCCAGAGGAAAGAGCTTCACTGAGTGAAAAAGAGAGGCAAAACGAAGAGGTGAATGAGAGGGACAACTGTTCTGCTTCCAGCATCTCGTCCTCCAGCAGCACCTTGGAGAGGGAAGAGAAGGAAGACAAACTGTCTGAAGACAGGGCGACCGGTTTGTGGTCCACCAGCCTTCAGGATGTGGGTGTGAATGGACAGTGTGGTGACATCCTTACCAGCAAAAGGTTCATGCTGGACATGCTGTATGCCCATAACAGAAAATCCACAGAAGATGAGGAAAAAGATGACGGCGAGCCTGGGAGGTCTGCGCAGGAGGTGGAGGCAGTGGCCAGCCTCGCCACCAGGATATCCACTCTGCAGGCCAACTCTCAGGCCCCAGAGGAGAGCATCAAGAGGGTGGACATTGGCTGTCTAGACAACCGGGGCAGTGTGAAGGCATTTGCTGAGAAATTCAACAGTGGAGAAGTAGGGAGGGGTGCCATCTCTCCTGATGTGGAGTCTCAGGACAAGGTCCCGGATACACCCCCAGCACAGCTGAAGACTGAGTCTGATTACATCTGGGACCAGCTCATGGCCAATCCGAGGGAGCTCAGAATCCAAGACATGGATTTCACAGACCTAGGGGAGGAGGACGATATCGATGTTTTGGATGTGGATCTTGGCCACCGGGAAGCCCCAGGGCCACCCCCTCCACCCCCTCCCACCTTCCTGGGTTTGCCACCCCCACCCCCTCCACCCCTGTTGGACAGCGTGCCTCCCCCACCAGTCCCCGGTAATTTATTGGCTTCTCCTGTGTTCAACACTCCTCAGGGCTTAGGGTGGTCCCAGGTACCCAGGGGTCAGCCAGCGTTCACCAAGAAAAAGAAGACGATCCGGCTGTTCTGGAACGAAGTCCGGCCCTTTGAGTGGCCAAGTAAGAACAATCGCCGGTGCAGGGAATTCCTGTGGTCAAAACTGGAACCCATTAAGGTGGACACTTCCAGACTCGAGCACCTGTTTGAGTCCAAGTCTAAGGAGCTGTCTGTCACCAAGAAAACGGCTGCAGATGGTAAACGGCAGGAGATCATTGTTCTGGATTCCAAGAGGAGCAATGCCATCAACATCGGCCTGACGGTGCTGCCCCCTCCAAGGACAATTAAGATAGCCATTTTGAACTTTGATGAGTATGCCTTAAACAAAGAAGGGATCGAGAAAATTCTGACCATGATTCCAACTGAAGAGGAGAAGCAGAAAATCCAGGAGGCTCAGCTGGCTAACCCGGAAGTGCCGTTGGGCAGTGCAGAGCAGTTCCTTCTCACACTCTCTTCCATCAGTGAGCTCTCGGCTCGGCTCCACCTGTGGGCATTCAAAATGGATTATGAAACCACAGAAAAGGAAGTGGCCGAACCACTTTTGGACCTGAAGGAAGGAATAGACCAGTTGGAGAACAATAAGACTCTGGGCTTCATCCTGTCTACTCTCCTTGCCATTGGGAACTTTCTAAATGGAACTAATGCCAAAGCATTTGAGTTAAGCTACCTCGAGAAGGTTCCAGAAGTCAAAGATACAGTGCACAAGCAGTCTCTTCTCCACCACGTGTGCACCATGGTAGTGGAAAACTTTCCGGACAGCTCGGATCTGTACTCAGAGATTGGGGCCATCACTAGGTCAGCCAAGGTTGACTTTGATCAACTTCAGGATAATTTATGTCAGATGGAGAGACGCTGCAAAGCTTCATGGGACCACCTCAAGGCGATTGCAAAACACGAGATGAAGCCTGTTTTGAAACAGCGGATGTCAGAGTTCCTAAAAGACTGTGCAGAGCGAATTATAATTTTAAAGATCGTCCATCGGAGGATAATTAACAGATTTCACTCATTTTTACTGTTTATGGGCCATCCCCCTTATGCAATTCGAGAGGTGAACATCAACAAGTTCTGCAGGATCATCAGTGAGTTTGCCCTGGAGTATCGCACGACCAGGGAAAGGGTTCTACAGCAGAAACAGAAGCGGGCCAACCACAGAGAGAGAAACAAGACCAGAGGGAAGATGATCACTGACTCTGGCAAGTTCTCTGGCAGTTCTCCAGCAGCACCGAGCCAGCCACAGGGTCTGAGCTATGCTGAGGATGCAGCCGAACATGAGAACATGAAGGCCGTGTTGAAAACCTCCTCCCCTGCGCTGGAGGACGCCACCCCAGTGCTTGGTGTCCGCACTCGCAGCCGGGCAAGCCGAGGATCCACTAGTTCATGGACTATGGGAACTGAGGAGTCACCTAGTGTCACTGATGATGCGGCTGATGAGATCATGGACCGCATTGTCAAATCAGCCACCCAAGTGCCCAGTCAGAGAGTGGTGCCACGGGAGAGAAAGCGTTCCAGGGCCAACCGCAAATCTT

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CAAATCAGCCACCCAAGTGC

60.04

CTCACGCTCTGGCTTCTAGG

59.9

143

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CCAAGTGCCCAGTCAGAGAG

60.04

AGGAGAGGTCAGCTCTACCC

59.74

154

PCR template sequence:

GATGAGATCATGGACCGCATTGTCAAATCAGCCACCCAAGTGCCCAGTCAGAGAGTGGTGCCACGGGAGAGAAAGCGTTCCAGGGCCAACCGCAAATCTTATACAAATACTTGGAGCAGTTGGCAGCCGAGACGCAGGAGAAGGAGCCTAGAAGCCAGAGCGTGAGCCGGGGTAGAGCTGACCTCTCCTTGGACCTGAGC

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

26

Interacting miRNAs (#binding sites)

mmu-miR-324-3p(3), mmu-miR-149-5p(2), mmu-miR-1904(2), mmu-miR-124-3p(1), mmu-miR-103-3p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-18a-5p(1), mmu-miR-298-5p(1), mmu-miR-326-3p(1), mmu-miR-138-5p(1), mmu-miR-185-5p(1), mmu-miR-339-5p(1), mmu-miR-351-5p(1), mmu-miR-382-3p(1), mmu-miR-127-5p(1), mmu-miR-125b-1-3p(1), mmu-miR-215-5p(1), mmu-miR-107-3p(1), mmu-miR-98-5p(1), mmu-miR-705(1), mmu-miR-207(1), mmu-miR-3087-3p(1), mmu-miR-540-3p(1), mmu-miR-697(1), mmu-miR-338-3p(1)

siRNAs for circular RNA silencing
Junction sequence

AACCGCAAATCTTATACAAATACTTG

siRNA sets

TATTTGTATAAGATTTGCG, GTATTTGTATAAGATTTGC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCFHOD3_2711_ORF_1

1.1694

0.324183925

0.999999253

2214

ORF sequence:

ATGCTGGACATGCTGTATGCCCATAACAGAAAATCCACAGAAGATGAGGAAAAAGATGACGGCGAGCCTGGGAGGTCTGCGCAGGAGGTGGAGGCAGTGGCCAGCCTCGCCACCAGGATATCCACTCTGCAGGCCAACTCTCAGGCCCCAGAGGAGAGCATCAAGAGGGTGGACATTGGCTGTCTAGACAACCGGGGCAGTGTGAAGGCATTTGCTGAGAAATTCAACAGTGGAGAAGTAGGGAGGGGTGCCATCTCTCCTGATGTGGAGTCTCAGGACAAGGTCCCGGATACACCCCCAGCACAGCTGAAGACTGAGTCTGATTACATCTGGGACCAGCTCATGGCCAATCCGAGGGAGCTCAGAATCCAAGACATGGATTTCACAGACCTAGGGGAGGAGGACGATATCGATGTTTTGGATGTGGATCTTGGCCACCGGGAAGCCCCAGGGCCACCCCCTCCACCCCCTCCCACCTTCCTGGGTTTGCCACCCCCACCCCCTCCACCCCTGTTGGACAGCGTGCCTCCCCCACCAGTCCCCGGTAATTTATTGGCTTCTCCTGTGTTCAACACTCCTCAGGGCTTAGGGTGGTCCCAGGTACCCAGGGGTCAGCCAGCGTTCACCAAGAAAAAGAAGACGATCCGGCTGTTCTGGAACGAAGTCCGGCCCTTTGAGTGGCCAAGTAAGAACAATCGCCGGTGCAGGGAATTCCTGTGGTCAAAACTGGAACCCATTAAGGTGGACACTTCCAGACTCGAGCACCTGTTTGAGTCCAAGTCTAAGGAGCTGTCTGTCACCAAGAAAACGGCTGCAGATGGTAAACGGCAGGAGATCATTGTTCTGGATTCCAAGAGGAGCAATGCCATCAACATCGGCCTGACGGTGCTGCCCCCTCCAAGGACAATTAAGATAGCCATTTTGAACTTTGATGAGTATGCCTTAAACAAAGAAGGGATCGAGAAAATTCTGACCATGATTCCAACTGAAGAGGAGAAGCAGAAAATCCAGGAGGCTCAGCTGGCTAACCCGGAAGTGCCGTTGGGCAGTGCAGAGCAGTTCCTTCTCACACTCTCTTCCATCAGTGAGCTCTCGGCTCGGCTCCACCTGTGGGCATTCAAAATGGATTATGAAACCACAGAAAAGGAAGTGGCCGAACCACTTTTGGACCTGAAGGAAGGAATAGACCAGTTGGAGAACAATAAGACTCTGGGCTTCATCCTGTCTACTCTCCTTGCCATTGGGAACTTTCTAAATGGAACTAATGCCAAAGCATTTGAGTTAAGCTACCTCGAGAAGGTTCCAGAAGTCAAAGATACAGTGCACAAGCAGTCTCTTCTCCACCACGTGTGCACCATGGTAGTGGAAAACTTTCCGGACAGCTCGGATCTGTACTCAGAGATTGGGGCCATCACTAGGTCAGCCAAGGTTGACTTTGATCAACTTCAGGATAATTTATGTCAGATGGAGAGACGCTGCAAAGCTTCATGGGACCACCTCAAGGCGATTGCAAAACACGAGATGAAGCCTGTTTTGAAACAGCGGATGTCAGAGTTCCTAAAAGACTGTGCAGAGCGAATTATAATTTTAAAGATCGTCCATCGGAGGATAATTAACAGATTTCACTCATTTTTACTGTTTATGGGCCATCCCCCTTATGCAATTCGAGAGGTGAACATCAACAAGTTCTGCAGGATCATCAGTGAGTTTGCCCTGGAGTATCGCACGACCAGGGAAAGGGTTCTACAGCAGAAACAGAAGCGGGCCAACCACAGAGAGAGAAACAAGACCAGAGGGAAGATGATCACTGACTCTGGCAAGTTCTCTGGCAGTTCTCCAGCAGCACCGAGCCAGCCACAGGGTCTGAGCTATGCTGAGGATGCAGCCGAACATGAGAACATGAAGGCCGTGTTGAAAACCTCCTCCCCTGCGCTGGAGGACGCCACCCCAGTGCTTGGTGTCCGCACTCGCAGCCGGGCAAGCCGAGGATCCACTAGTTCATGGACTATGGGAACTGAGGAGTCACCTAGTGTCACTGATGATGCGGCTGATGAGATCATGGACCGCATTGTCAAATCAGCCACCCAAGTGCCCAGTCAGAGAGTGGTGCCACGGGAGAGAAAGCGTTCCAGGGCCAACCGCAAATCTTATACAAATACTTGGAGCAGTTGGCAGCCGAGACGCAGGAGAAGGAGCCTAGAAGCCAGAGCGTGA

Peptide sequence:

MLDMLYAHNRKSTEDEEKDDGEPGRSAQEVEAVASLATRISTLQANSQAPEESIKRVDIGCLDNRGSVKAFAEKFNSGEVGRGAISPDVESQDKVPDTPPAQLKTESDYIWDQLMANPRELRIQDMDFTDLGEEDDIDVLDVDLGHREAPGPPPPPPPTFLGLPPPPPPPLLDSVPPPPVPGNLLASPVFNTPQGLGWSQVPRGQPAFTKKKKTIRLFWNEVRPFEWPSKNNRRCREFLWSKLEPIKVDTSRLEHLFESKSKELSVTKKTAADGKRQEIIVLDSKRSNAINIGLTVLPPPRTIKIAILNFDEYALNKEGIEKILTMIPTEEEKQKIQEAQLANPEVPLGSAEQFLLTLSSISELSARLHLWAFKMDYETTEKEVAEPLLDLKEGIDQLENNKTLGFILSTLLAIGNFLNGTNAKAFELSYLEKVPEVKDTVHKQSLLHHVCTMVVENFPDSSDLYSEIGAITRSAKVDFDQLQDNLCQMERRCKASWDHLKAIAKHEMKPVLKQRMSEFLKDCAERIIILKIVHRRIINRFHSFLLFMGHPPYAIREVNINKFCRIISEFALEYRTTRERVLQQKQKRANHRERNKTRGKMITDSGKFSGSSPAAPSQPQGLSYAEDAAEHENMKAVLKTSSPALEDATPVLGVRTRSRASRGSTSSWTMGTEESPSVTDDAADEIMDRIVKSATQVPSQRVVPRERKRSRANRKSYTNTWSSWQPRRRRRSLEARA

IRESfinder result

IRESfinder score

0.445922953

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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Institute of Life sciences, Bhubaneswar, India

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