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mmu_circEtfdh_981
Basic information of circular RNA
PanCircBase ID:
mmu_circEtfdh_981
mm39_Chr. Position ID:
chr3|79512936|79525732|-
Gene name:
Etfdh
Transcript:
ENSMUST00000029386.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
11,10,9,8,7,6,5
Exon/intron offsets:
0,4169,6282,7992,9370,10294,12677
Genomic length:
12796
Exon/intron sizes in nt:
1,83,16,91,44,14,11,47,00,000
Flanking exon/introns:
chr3:79512433-79512936|chr3:79525732-79526145
Splice length:
981
Other database IDs:
CIRCpedia: MMU_CIRCpedia_216615, circAtlas: mmu-Etfdh_0014
Human Ortholog IDs:
Mature spliced Sequence:
GTCTTCCGATGAACAATCATGGCAATTACATCGTACGCCTAGGACATCTGGTGAGCTGGATGGGAGAACAGGCAGAGGCTCTTGGAGTCGAAGTGTATCCTGGGTATGCTGCTGCTGAGGTCCTTTATCATGAAGATGGTAGTGTAAAAGGAATCGCCACTAATGATGTAGGCATACAAAAGGATGGTGCACCAAAGACAACATTTGAGAGAGGACTGGAACTGCATGCCAAAGTCACAGTCTTTGCAGAGGGTTGCCATGGACACCTAGCCAAGCAGCTTTATAAGAAATTTGATCTGAGGGCCAGCTGTGATGCACAGACTTACGGAATTGGTTTGAAGGAGTTATGGATTATTGATGAAAAGAAGTGGAAACCTGGAAGAGTAGATCACACTGTTGGTTGGCCCTTGGACAGACATACTTATGGAGGCTCTTTCCTTTACCACTTAAATGAAGGTGAACCTCTAGTAGCTGTTGGCTTTGTGGTTGGCCTCGACTATCAGAATCCGTACCTGAGTCCATTCCGAGAGTTCCAGAGGTGGAAGCATCATCCCAGCATCCAGCCAACCCTGGAAGGCGGGAAGAGGATAGCCTACGGAGCCCGAGCGCTCAATGAAGGCGGCTTGCAGTCCATACCAAAACTCACTTTTCCTGGTGGCTTACTAATTGGTTGTAGTCCTGGTTTCATGAATGTCCCCAAGATCAAAGGTACCCACACGGCAATGAAAAGTGGAAGTTTGGCAGCAGAATCAATTTTTAAGCAACTAACTAGTGAAAATCTCCAGTCAAAGACAACAGGACTCCATGTAACTGAATATGAGGACAATTTGAAGCAATCCTGGGTATGGAAAGAGCTACACGCTGTTCGAAATATAAGGCCATCTTGCCACGGGATACTGGGAGTATATGGAGGGATGATTTACACTGGGATATTTTACTGGATATTGAGAGGAATGGAGCCATGGACTCTAAAACATAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGGGATGATTTACACTGGG
59.49
CTGCCTGTTCTCCCATCCAG
60.11
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGGGATGATTTACACTGGG
59.49
GTTCTCCCATCCAGCTCACC
60.11
143
PCR template sequence:
TCTTGCCACGGGATACTGGGAGTATATGGAGGGATGATTTACACTGGGATATTTTACTGGATATTGAGAGGAATGGAGCCATGGACTCTAAAACATAAAGGTCTTCCGATGAACAATCATGGCAATTACATCGTACGCCTAGGACATCTGGTGAGCTGGATGGGAGAACAGGCAGAGGCTCTTGGAGTCGAAGTGTATCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-103-3p(1), mmu-miR-135a-5p(1), mmu-miR-31-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-320-3p(1), mmu-miR-136-5p(1), mmu-miR-433-3p(1), mmu-miR-107-3p(1), mmu-miR-673-5p(1), mmu-miR-335-3p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTAAAACATAAAGGTCTTCCGATGAA
siRNA sets
CATCGGAAGACCTTTATGT, ATCGGAAGACCTTTATGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCETFDH_981_ORF_1
0.8573
0.06030976
0.99997619
1953
ORF sequence:
ATGAACAATCATGGCAATTACATCGTACGCCTAGGACATCTGGTGAGCTGGATGGGAGAACAGGCAGAGGCTCTTGGAGTCGAAGTGTATCCTGGGTATGCTGCTGCTGAGGTCCTTTATCATGAAGATGGTAGTGTAAAAGGAATCGCCACTAATGATGTAGGCATACAAAAGGATGGTGCACCAAAGACAACATTTGAGAGAGGACTGGAACTGCATGCCAAAGTCACAGTCTTTGCAGAGGGTTGCCATGGACACCTAGCCAAGCAGCTTTATAAGAAATTTGATCTGAGGGCCAGCTGTGATGCACAGACTTACGGAATTGGTTTGAAGGAGTTATGGATTATTGATGAAAAGAAGTGGAAACCTGGAAGAGTAGATCACACTGTTGGTTGGCCCTTGGACAGACATACTTATGGAGGCTCTTTCCTTTACCACTTAAATGAAGGTGAACCTCTAGTAGCTGTTGGCTTTGTGGTTGGCCTCGACTATCAGAATCCGTACCTGAGTCCATTCCGAGAGTTCCAGAGGTGGAAGCATCATCCCAGCATCCAGCCAACCCTGGAAGGCGGGAAGAGGATAGCCTACGGAGCCCGAGCGCTCAATGAAGGCGGCTTGCAGTCCATACCAAAACTCACTTTTCCTGGTGGCTTACTAATTGGTTGTAGTCCTGGTTTCATGAATGTCCCCAAGATCAAAGGTACCCACACGGCAATGAAAAGTGGAAGTTTGGCAGCAGAATCAATTTTTAAGCAACTAACTAGTGAAAATCTCCAGTCAAAGACAACAGGACTCCATGTAACTGAATATGAGGACAATTTGAAGCAATCCTGGGTATGGAAAGAGCTACACGCTGTTCGAAATATAAGGCCATCTTGCCACGGGATACTGGGAGTATATGGAGGGATGATTTACACTGGGATATTTTACTGGATATTGAGAGGAATGGAGCCATGGACTCTAAAACATAAAGGTCTTCCGATGAACAATCATGGCAATTACATCGTACGCCTAGGACATCTGGTGAGCTGGATGGGAGAACAGGCAGAGGCTCTTGGAGTCGAAGTGTATCCTGGGTATGCTGCTGCTGAGGTCCTTTATCATGAAGATGGTAGTGTAAAAGGAATCGCCACTAATGATGTAGGCATACAAAAGGATGGTGCACCAAAGACAACATTTGAGAGAGGACTGGAACTGCATGCCAAAGTCACAGTCTTTGCAGAGGGTTGCCATGGACACCTAGCCAAGCAGCTTTATAAGAAATTTGATCTGAGGGCCAGCTGTGATGCACAGACTTACGGAATTGGTTTGAAGGAGTTATGGATTATTGATGAAAAGAAGTGGAAACCTGGAAGAGTAGATCACACTGTTGGTTGGCCCTTGGACAGACATACTTATGGAGGCTCTTTCCTTTACCACTTAAATGAAGGTGAACCTCTAGTAGCTGTTGGCTTTGTGGTTGGCCTCGACTATCAGAATCCGTACCTGAGTCCATTCCGAGAGTTCCAGAGGTGGAAGCATCATCCCAGCATCCAGCCAACCCTGGAAGGCGGGAAGAGGATAGCCTACGGAGCCCGAGCGCTCAATGAAGGCGGCTTGCAGTCCATACCAAAACTCACTTTTCCTGGTGGCTTACTAATTGGTTGTAGTCCTGGTTTCATGAATGTCCCCAAGATCAAAGGTACCCACACGGCAATGAAAAGTGGAAGTTTGGCAGCAGAATCAATTTTTAAGCAACTAACTAGTGAAAATCTCCAGTCAAAGACAACAGGACTCCATGTAACTGAATATGAGGACAATTTGAAGCAATCCTGGGTATGGAAAGAGCTACACGCTGTTCGAAATATAAGGCCATCTTGCCACGGGATACTGGGAGTATATGGAGGGATGATTTACACTGGGATATTTTACTGGATATTGAGAGGAATGGAGCCATGGACTCTAAAACATAAA
Peptide sequence:
MNNHGNYIVRLGHLVSWMGEQAEALGVEVYPGYAAAEVLYHEDGSVKGIATNDVGIQKDGAPKTTFERGLELHAKVTVFAEGCHGHLAKQLYKKFDLRASCDAQTYGIGLKELWIIDEKKWKPGRVDHTVGWPLDRHTYGGSFLYHLNEGEPLVAVGFVVGLDYQNPYLSPFREFQRWKHHPSIQPTLEGGKRIAYGARALNEGGLQSIPKLTFPGGLLIGCSPGFMNVPKIKGTHTAMKSGSLAAESIFKQLTSENLQSKTTGLHVTEYEDNLKQSWVWKELHAVRNIRPSCHGILGVYGGMIYTGIFYWILRGMEPWTLKHKGLPMNNHGNYIVRLGHLVSWMGEQAEALGVEVYPGYAAAEVLYHEDGSVKGIATNDVGIQKDGAPKTTFERGLELHAKVTVFAEGCHGHLAKQLYKKFDLRASCDAQTYGIGLKELWIIDEKKWKPGRVDHTVGWPLDRHTYGGSFLYHLNEGEPLVAVGFVVGLDYQNPYLSPFREFQRWKHHPSIQPTLEGGKRIAYGARALNEGGLQSIPKLTFPGGLLIGCSPGFMNVPKIKGTHTAMKSGSLAAESIFKQLTSENLQSKTTGLHVTEYEDNLKQSWVWKELHAVRNIRPSCHGILGVYGGMIYTGIFYWILRGMEPWTLKHK
IRESfinder result
IRESfinder score
0.488587508
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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