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mmu_circSlc29a4_630
Basic information of circular RNA
PanCircBase ID:
mmu_circSlc29a4_630
mm39_Chr. Position ID:
chr5|142691110|142700875|+
Gene name:
Slc29a4
Transcript:
ENSMUST00000058418.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
2,3,4,5,6
Exon/intron offsets:
0,6607,7531,8655,9690
Genomic length:
9765
Exon/intron sizes in nt:
180,132,114,129,75
Flanking exon/introns:
chr5:142688046-142691110|chr5:142700875-142703346
Splice length:
630
Other database IDs:
CIRCpedia: MMU_CIRCpedia_9207
circBase: hsa_circ_0079246
Human Ortholog IDs:
Mature spliced Sequence:
TGTGAACTGCCATGGGCTCTATCGGAAGCCAGCGCCTCAAGGAGCCCTGCGTGGCAGCCACATCTGACCAGAGTGTGGTGACAAGCTTTAGCTTTGACAACTTCCAGCTGGAGACGACAGCAGAGGGGGCTCAGGATCCAGGCATCAGAGTCAGGGGTGTCCCCACTTTCACAGACTCTGCGGTAGAGGAGCCTGTGCCAGATGACCGCTACCATGCCATCTACTTTGCCATGCTGCTGGCTGGCGTGGGCTTCCTACTGCCATACAACAGCTTTATCACCGATGTCGACTATCTTCACCACAAGTACCCAGGGACCTCCATCGTATTTGACATGAGCCTCACCTATATCCTGGTGGCATTGGCGGCTGTGCTCCTAAACAACGTTGTGGTGGAGAGGTTGAACCTGCACACCAGGATCACCACAGGCTACCTCCTCGCCTTGGGTCCCTTGCTCTTTATCAGCATATGCGATGTGTGGCTGCAGCTCTTCTCTCACGACCAGGCTTACGCCATCAACCTGGCCGCCGTGGGCACTGTGGCCTTTGGTTGCACAGTGCAGCAATCTAGCTTCTATGGCTACACGGGATTACTGCCCAAGAGGTACACGCAGGGTGTGATGACTGGAGAGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCACAGTGCAGCAATCTAGC
59.9
ACACTCTGGTCAGATGTGGC
59.68
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCACAGTGCAGCAATCTAGC
59.9
ACTCTGGTCAGATGTGGCTG
59.39
155
PCR template sequence:
GGCACTGTGGCCTTTGGTTGCACAGTGCAGCAATCTAGCTTCTATGGCTACACGGGATTACTGCCCAAGAGGTACACGCAGGGTGTGATGACTGGAGAGATGTGAACTGCCATGGGCTCTATCGGAAGCCAGCGCCTCAAGGAGCCCTGCGTGGCAGCCACATCTGACCAGAGTGTGGTGACAAGCTTTAGCTTTGACAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-let-7a-5p(1), mmu-miR-16-5p(1), mmu-miR-103-3p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-382-5p(1), mmu-miR-107-3p(1), mmu-miR-98-5p(1), mmu-miR-3470b(1), mmu-miR-540-3p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGACTGGAGAGATGTGAACTGCCAT
siRNA sets
GTTCACATCTCTCCAGTCA, ATGGCAGTTCACATCTCTC, TGGCAGTTCACATCTCTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSLC29A4_630_ORF_1
1.3368
0.402729298
0.966527913
624
ORF sequence:
ATGGGCTCTATCGGAAGCCAGCGCCTCAAGGAGCCCTGCGTGGCAGCCACATCTGACCAGAGTGTGGTGACAAGCTTTAGCTTTGACAACTTCCAGCTGGAGACGACAGCAGAGGGGGCTCAGGATCCAGGCATCAGAGTCAGGGGTGTCCCCACTTTCACAGACTCTGCGGTAGAGGAGCCTGTGCCAGATGACCGCTACCATGCCATCTACTTTGCCATGCTGCTGGCTGGCGTGGGCTTCCTACTGCCATACAACAGCTTTATCACCGATGTCGACTATCTTCACCACAAGTACCCAGGGACCTCCATCGTATTTGACATGAGCCTCACCTATATCCTGGTGGCATTGGCGGCTGTGCTCCTAAACAACGTTGTGGTGGAGAGGTTGAACCTGCACACCAGGATCACCACAGGCTACCTCCTCGCCTTGGGTCCCTTGCTCTTTATCAGCATATGCGATGTGTGGCTGCAGCTCTTCTCTCACGACCAGGCTTACGCCATCAACCTGGCCGCCGTGGGCACTGTGGCCTTTGGTTGCACAGTGCAGCAATCTAGCTTCTATGGCTACACGGGATTACTGCCCAAGAGGTACACGCAGGGTGTGATGACTGGAGAGATGTGA
Peptide sequence:
MGSIGSQRLKEPCVAATSDQSVVTSFSFDNFQLETTAEGAQDPGIRVRGVPTFTDSAVEEPVPDDRYHAIYFAMLLAGVGFLLPYNSFITDVDYLHHKYPGTSIVFDMSLTYILVALAAVLLNNVVVERLNLHTRITTGYLLALGPLLFISICDVWLQLFSHDQAYAINLAAVGTVAFGCTVQQSSFYGYTGLLPKRYTQGVMTGEM
IRESfinder result
IRESfinder score
0.428192529
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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