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mmu_circOphn1_410
Basic information of circular RNA
PanCircBase ID:
mmu_circOphn1_410
mm39_Chr. Position ID:
chrX|97670519|97688600|-
Gene name:
Ophn1
Transcript:
ENSMUST00000033560.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
19,18,17,16
Exon/intron offsets:
0,13994,14837,17996
Genomic length:
18081
Exon/intron sizes in nt:
160,106,59,85
Flanking exon/introns:
chrX:97640781-97670519|chrX:97688600-97739604
Splice length:
410
Other database IDs:
circBase: mmu_circ_0001888, CIRCpedia: MMU_CIRCpedia_35829, circAtlas: mmu-Ophn1_0001
circBase: hsa_circ_0090930, circAtlas: hsa-OPHN1_0001, CIRCpedia: HSA_CIRCpedia_118568
Human Ortholog IDs:
Mature spliced Sequence:
ATCCAAAATGTCCAGGGGATGTTGATTTCCATAACAGTGACTGGGACATTAAGACAATCACAAGCTCTTTAAAATTCTACCTCAGGAATCTCTCAGAACCTGTCATGACTTATAAGCTCCATAAAGAACTCGTCTCTGCTGCCAAATCTGACAACCTGGATTACCGTCTGGGGGCTATTCACTCCCTAGTATATAAGCTACCAGAAAAGAACCGGGAGATGCTGGAACTTCTAATCAAACACTTGGTAAATGTGTGTGAGCACAGCAAAGAGAATCTTATGACACCTTCCAATATGGGGGTGATCTTTGGGCCCACCCTGATGAGAGCTCAAGAGGACACTGTGGCTGCTATGATGAACATCAAATTCCAGAACATTGTGGTAGAAATCCTGATTGAACACTTTGGCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGACACTGTGGCTGCTATGA
59.75
GGTTCTGAGAGATTCCTGAGGT
58.9
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGACACTGTGGCTGCTATG
59.75
GGTTCTGAGAGATTCCTGAGGT
58.9
177
PCR template sequence:
GCCCACCCTGATGAGAGCTCAAGAGGACACTGTGGCTGCTATGATGAACATCAAATTCCAGAACATTGTGGTAGAAATCCTGATTGAACACTTTGGCAAGATCCAAAATGTCCAGGGGATGTTGATTTCCATAACAGTGACTGGGACATTAAGACAATCACAAGCTCTTTAAAATTCTACCTCAGGAATCTCTCAGAACC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7c-5p(1), mmu-miR-324-5p(1), mmu-let-7d-5p(1), mmu-miR-98-5p(1), mmu-miR-342-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACACTTTGGCAAGATCCAAAATGTCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCOPHN1_410_ORF_1
1.0793
0.164438545
0.536168224
378
ORF sequence:
ATGACTTATAAGCTCCATAAAGAACTCGTCTCTGCTGCCAAATCTGACAACCTGGATTACCGTCTGGGGGCTATTCACTCCCTAGTATATAAGCTACCAGAAAAGAACCGGGAGATGCTGGAACTTCTAATCAAACACTTGGTAAATGTGTGTGAGCACAGCAAAGAGAATCTTATGACACCTTCCAATATGGGGGTGATCTTTGGGCCCACCCTGATGAGAGCTCAAGAGGACACTGTGGCTGCTATGATGAACATCAAATTCCAGAACATTGTGGTAGAAATCCTGATTGAACACTTTGGCAAGATCCAAAATGTCCAGGGGATGTTGATTTCCATAACAGTGACTGGGACATTAAGACAATCACAAGCTCTTTAA
Peptide sequence:
MTYKLHKELVSAAKSDNLDYRLGAIHSLVYKLPEKNREMLELLIKHLVNVCEHSKENLMTPSNMGVIFGPTLMRAQEDTVAAMMNIKFQNIVVEILIEHFGKIQNVQGMLISITVTGTLRQSQAL
IRESfinder result
IRESfinder score
0.644873626
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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