top of page
mmu_circAtp9b_304_2
Basic information of circular RNA
PanCircBase ID:
mmu_circAtp9b_304_2
mm39_Chr. Position ID:
chr18|80887741|80913008|-
Gene name:
Atp9b
Transcript:
ENSMUST00000091790.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
10,9,8,7
Exon/intron offsets:
0,2645,14017,25215
Genomic length:
25267
Exon/intron sizes in nt:
76,81,95,52
Flanking exon/introns:
chr18:80879646-80887741|chr18:80913008-80920529
Splice length:
304
Other database IDs:
CIRCpedia: MMU_CIRCpedia_30633, circAtlas: mmu-Atp9b_0029
circBase: hsa_circ_0108910, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_88618
Human Ortholog IDs:
Mature spliced Sequence:
AACCAAAGAATTCCATCAGATATGGTATTTCTTAGAACTTCAGAGAAAGCAGGTTCATGTTTTATCCGCACGGACCAGCTAGATGGTGAGACTGACTGGAAGCTGAAGGTGGCGGTGAGCTGCACACAACGGCTGCCAGCCCTCGGGGACCTTTTTTCTATCAGTGCCTATGTTTATGCTCAGAAGCCACAACTGGATATTCATAGCTTTGAAGGAACATTTACCAGGGAAGACAGTGATCCTCCCATTCATGAGAGTCTCAGCATAGAGAACACTCTGTGGGCAAGCACTATTGTTGCATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGAAGACAGTGATCCTCCC
59.17
CACCATCTAGCTGGTCCGTG
60.18
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGAAGACAGTGATCCTCCC
59.17
TCACCATCTAGCTGGTCCGT
60.32
167
PCR template sequence:
AGCTTTGAAGGAACATTTACCAGGGAAGACAGTGATCCTCCCATTCATGAGAGTCTCAGCATAGAGAACACTCTGTGGGCAAGCACTATTGTTGCATCAGAACCAAAGAATTCCATCAGATATGGTATTTCTTAGAACTTCAGAGAAAGCAGGTTCATGTTTTATCCGCACGGACCAGCTAGATGGTGAGACTGACTGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTGTTGCATCAGAACCAAAGAATTC
siRNA sets
AATTCTTTGGTTCTGATGC, ATTCTTTGGTTCTGATGCA, CTTTGGTTCTGATGCAACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATP9B_304_2_ORF_1
0.9983
0.044909298
0.284461927
318
ORF sequence:
ATGGTATTTCTTAGAACTTCAGAGAAAGCAGGTTCATGTTTTATCCGCACGGACCAGCTAGATGGTGAGACTGACTGGAAGCTGAAGGTGGCGGTGAGCTGCACACAACGGCTGCCAGCCCTCGGGGACCTTTTTTCTATCAGTGCCTATGTTTATGCTCAGAAGCCACAACTGGATATTCATAGCTTTGAAGGAACATTTACCAGGGAAGACAGTGATCCTCCCATTCATGAGAGTCTCAGCATAGAGAACACTCTGTGGGCAAGCACTATTGTTGCATCAGAACCAAAGAATTCCATCAGATATGGTATTTCTTAG
Peptide sequence:
MVFLRTSEKAGSCFIRTDQLDGETDWKLKVAVSCTQRLPALGDLFSISAYVYAQKPQLDIHSFEGTFTREDSDPPIHESLSIENTLWASTIVASEPKNSIRYGIS
IRESfinder result
IRESfinder score
0.721682693
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page