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mmu_circUbe4b_1109
Basic information of circular RNA
PanCircBase ID:
mmu_circUbe4b_1109
mm39_Chr. Position ID:
chr4|149421841|149440013|-
Gene name:
Ube4b
Transcript:
ENSMUST00000103212.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
23,22,21,20,19,18,17,16
Exon/intron offsets:
0,5494,7130,10542,13273,14073,15543,18033
Genomic length:
18172
Exon/intron sizes in nt:
135,145,127,236,99,128,100,139
Flanking exon/introns:
chr4:149419760-149421841|chr4:149440013-149442081
Splice length:
1109
Other database IDs:
circAtlas: mmu-Ube4b_0023
Human Ortholog IDs:
Mature spliced Sequence:
ATGGTGATCAGCCTCCATTTTCTGAGCCAAAATTCCCTACGGAATGTTTCTTTCTCACCCTGCATGCTCATCACCTCTCTATTCTGCCTAGTTGTCGTCGCTACATTCGCCGACTTCGAGCCATCCGCGAGCTCAATAGAACCGTGGAAGATTTGAAAAATAATGAAAGCCAGTGGAAAGATTCCCCACTGGCCACCAGACACCGTGAAATGCTGAAGCGCTGTAAAACTCAGCTTAAGAAACTGGTACGGTGCAAGGCCTGTGCTGACGCTGGCTTACTTGACGAGAGCTTCCTAAGAAGATGCCTGAATTTTTATGGCCTTCTCATTCAGCTGATGCTGCGCATCCTGGACCCTGCATATCCTGACGTAACACTGCCTTTGAATTCAGAAGTCCCCAAGGTATTTGCAGCATTGCCTGAGTTTTATGTCGAAGATGTTGCTGAATTTTTATTTTTTATTGTACAATACTCTCCTCAGGTGCTTTATGAGCCCTGCACTCAGGACATTGTCATGTTCCTCGTTGTGATGCTGTGCAACCAGAACTACATCCGAAACCCTTACCTAGTGGCCAAGCTGGTGGAGGTCATGTTCATGACCAACCCTTCTGTCCAGCCGAGAACTCAGAAGTTCTTTGAGATGATTGAGAACCATCCTCTCTCTACCAAACTGCTGGTGCCGTCCCTCATGAAGTTCTATACAGATGTCGAGCATACTGGAGCCACCAGCGAGTTCTATGACAAGTTCACAATTCGCTATCACATTAGCACTATTTTTAAAAGCCTTTGGCAAAACATAGCTCACCATGGCACCTTCATGGAGGAGTTCAATTCTGGAAAGCAGTTCGTTCGGTATATCAATATGCTAATAAATGACACGACCTTTTTACTGGACGAAAGTCTGGAGTCTCTGAAGCGGATCCATGAAGTGCAAGAAGAGATGAAGAACAAAGAACAGTGGGACCAGCTGCCTCGGGATCAGCAGCAGGCCCGGCAGTCTCAGCTTGCTCAGGACGAGCGTGTTTCCCGTTCTTATCTTGCCCTGGCAACTGAAACCGTGGACATGTTCCATCTCCTCACCAAGCAAGTCCAGAAGCCGTTCCTGAGGCCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGCAACTGAAACCGTGGA
60.82
TGATGAGCATGCAGGGTGAG
60.11
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGCAACTGAAACCGTGGA
60.82
GATGAGCATGCAGGGTGAGA
59.82
141
PCR template sequence:
GGACGAGCGTGTTTCCCGTTCTTATCTTGCCCTGGCAACTGAAACCGTGGACATGTTCCATCTCCTCACCAAGCAAGTCCAGAAGCCGTTCCTGAGGCCAATGGTGATCAGCCTCCATTTTCTGAGCCAAAATTCCCTACGGAATGTTTCTTTCTCACCCTGCATGCTCATCACCTCTCTATTCTGCCTAGTTGTCGTCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-155-5p(1), mmu-miR-34c-5p(1), mmu-miR-26a-5p(1), mmu-miR-26b-5p(1), mmu-miR-676-3p(1), mmu-miR-34b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTTCCTGAGGCCAATGGTGATCAGCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUBE4B_1109_ORF_1
1.1523
0.24392831
0.995788389
1056
ORF sequence:
ATGCTGAAGCGCTGTAAAACTCAGCTTAAGAAACTGGTACGGTGCAAGGCCTGTGCTGACGCTGGCTTACTTGACGAGAGCTTCCTAAGAAGATGCCTGAATTTTTATGGCCTTCTCATTCAGCTGATGCTGCGCATCCTGGACCCTGCATATCCTGACGTAACACTGCCTTTGAATTCAGAAGTCCCCAAGGTATTTGCAGCATTGCCTGAGTTTTATGTCGAAGATGTTGCTGAATTTTTATTTTTTATTGTACAATACTCTCCTCAGGTGCTTTATGAGCCCTGCACTCAGGACATTGTCATGTTCCTCGTTGTGATGCTGTGCAACCAGAACTACATCCGAAACCCTTACCTAGTGGCCAAGCTGGTGGAGGTCATGTTCATGACCAACCCTTCTGTCCAGCCGAGAACTCAGAAGTTCTTTGAGATGATTGAGAACCATCCTCTCTCTACCAAACTGCTGGTGCCGTCCCTCATGAAGTTCTATACAGATGTCGAGCATACTGGAGCCACCAGCGAGTTCTATGACAAGTTCACAATTCGCTATCACATTAGCACTATTTTTAAAAGCCTTTGGCAAAACATAGCTCACCATGGCACCTTCATGGAGGAGTTCAATTCTGGAAAGCAGTTCGTTCGGTATATCAATATGCTAATAAATGACACGACCTTTTTACTGGACGAAAGTCTGGAGTCTCTGAAGCGGATCCATGAAGTGCAAGAAGAGATGAAGAACAAAGAACAGTGGGACCAGCTGCCTCGGGATCAGCAGCAGGCCCGGCAGTCTCAGCTTGCTCAGGACGAGCGTGTTTCCCGTTCTTATCTTGCCCTGGCAACTGAAACCGTGGACATGTTCCATCTCCTCACCAAGCAAGTCCAGAAGCCGTTCCTGAGGCCAATGGTGATCAGCCTCCATTTTCTGAGCCAAAATTCCCTACGGAATGTTTCTTTCTCACCCTGCATGCTCATCACCTCTCTATTCTGCCTAGTTGTCGTCGCTACATTCGCCGACTTCGAGCCATCCGCGAGCTCAATAGAACCGTGGAAGATTTGA
Peptide sequence:
MLKRCKTQLKKLVRCKACADAGLLDESFLRRCLNFYGLLIQLMLRILDPAYPDVTLPLNSEVPKVFAALPEFYVEDVAEFLFFIVQYSPQVLYEPCTQDIVMFLVVMLCNQNYIRNPYLVAKLVEVMFMTNPSVQPRTQKFFEMIENHPLSTKLLVPSLMKFYTDVEHTGATSEFYDKFTIRYHISTIFKSLWQNIAHHGTFMEEFNSGKQFVRYINMLINDTTFLLDESLESLKRIHEVQEEMKNKEQWDQLPRDQQQARQSQLAQDERVSRSYLALATETVDMFHLLTKQVQKPFLRPMVISLHFLSQNSLRNVSFSPCMLITSLFCLVVVATFADFEPSASSIEPWKI
IRESfinder result
IRESfinder score
0.562270931
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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