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mmu_circPrpf40a_558
Basic information of circular RNA
PanCircBase ID:
mmu_circPrpf40a_558
mm39_Chr. Position ID:
chr2|53034795|53036220|-
Gene name:
Prpf40a
Transcript:
ENSMUST00000076313.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
21,20,19,18,17
Exon/intron offsets:
0,449,836,1040,1310
Genomic length:
1425
Exon/intron sizes in nt:
96,13,81,17,92,115
Flanking exon/introns:
chr2:53032041-53034795|chr2:53036220-53040649
Splice length:
558
Other database IDs:
circAtlas: mmu-Prpf40a_0004
Human Ortholog IDs:
Mature spliced Sequence:
ATCTTTCTGGACGAGTTGCACGAGCATGGGCAGCTGCACTCTATGTCCTCTTGGATGGAGCTGTATCCCACCATCAGCTCTGACATTCGCTTCACTAACATGCTGGGTCAGCCGGGATCAACTGCACTTGATCTTTTCAAGTTTTATGTTGAAGATCTTAAAGCACGATATCATGATGAAAAGAAGATAATAAAAGACATTCTGAAGGATAAAGGATTTGTAGTTGAAGTAAACACTACTTTTGAAGATTTTGTGGCAATAATCAGTTCAACCAAAAGATCAACTACTTTGGATGCTGGAAATATCAAGTTGGCTTTCAATAGTTTACTAGAAAAGGCAGAAGCCCGTGAACGTGAGAGAGAAAAAGAAGAGGCTCGGAAAATGAAACGGAAAGAGTCTGCCTTTAAGAGTATGTTGAAACAGGCTACCCCTCCAATAGAACTGGATGCTGTCTGGGAAGATATCCGGGAAAGATTTGTAAAGGAACCAGCGTTTGAGGATATAACTCTAGAATCTGAAAGAAAAAGAATATTTAAAGATTTCATGCATGTGCTTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGAACCAGCGTTTGAGGA
59.53
GGTGGGATACAGCTCCATCC
59.6
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGAACCAGCGTTTGAGGA
59.53
TGTCAGAGCTGATGGTGGGA
60.55
163
PCR template sequence:
AGATATCCGGGAAAGATTTGTAAAGGAACCAGCGTTTGAGGATATAACTCTAGAATCTGAAAGAAAAAGAATATTTAAAGATTTCATGCATGTGCTTGAGATCTTTCTGGACGAGTTGCACGAGCATGGGCAGCTGCACTCTATGTCCTCTTGGATGGAGCTGTATCCCACCATCAGCTCTGACATTCGCTTCACTAACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-335-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCATGTGCTTGAGATCTTTCTGGACG
siRNA sets
AAAGATCTCAAGCACATGC, GAAAGATCTCAAGCACATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRPF40A_558_ORF_1
0.9536
0.166289816
0.992856453
1074
ORF sequence:
ATGTCCTCTTGGATGGAGCTGTATCCCACCATCAGCTCTGACATTCGCTTCACTAACATGCTGGGTCAGCCGGGATCAACTGCACTTGATCTTTTCAAGTTTTATGTTGAAGATCTTAAAGCACGATATCATGATGAAAAGAAGATAATAAAAGACATTCTGAAGGATAAAGGATTTGTAGTTGAAGTAAACACTACTTTTGAAGATTTTGTGGCAATAATCAGTTCAACCAAAAGATCAACTACTTTGGATGCTGGAAATATCAAGTTGGCTTTCAATAGTTTACTAGAAAAGGCAGAAGCCCGTGAACGTGAGAGAGAAAAAGAAGAGGCTCGGAAAATGAAACGGAAAGAGTCTGCCTTTAAGAGTATGTTGAAACAGGCTACCCCTCCAATAGAACTGGATGCTGTCTGGGAAGATATCCGGGAAAGATTTGTAAAGGAACCAGCGTTTGAGGATATAACTCTAGAATCTGAAAGAAAAAGAATATTTAAAGATTTCATGCATGTGCTTGAGATCTTTCTGGACGAGTTGCACGAGCATGGGCAGCTGCACTCTATGTCCTCTTGGATGGAGCTGTATCCCACCATCAGCTCTGACATTCGCTTCACTAACATGCTGGGTCAGCCGGGATCAACTGCACTTGATCTTTTCAAGTTTTATGTTGAAGATCTTAAAGCACGATATCATGATGAAAAGAAGATAATAAAAGACATTCTGAAGGATAAAGGATTTGTAGTTGAAGTAAACACTACTTTTGAAGATTTTGTGGCAATAATCAGTTCAACCAAAAGATCAACTACTTTGGATGCTGGAAATATCAAGTTGGCTTTCAATAGTTTACTAGAAAAGGCAGAAGCCCGTGAACGTGAGAGAGAAAAAGAAGAGGCTCGGAAAATGAAACGGAAAGAGTCTGCCTTTAAGAGTATGTTGAAACAGGCTACCCCTCCAATAGAACTGGATGCTGTCTGGGAAGATATCCGGGAAAGATTTGTAAAGGAACCAGCGTTTGAGGATATAACTCTAGAATCTGAAAGAAAAAGAATATTTAAAGATTTCATGCATGTGCTTGAG
Peptide sequence:
MSSWMELYPTISSDIRFTNMLGQPGSTALDLFKFYVEDLKARYHDEKKIIKDILKDKGFVVEVNTTFEDFVAIISSTKRSTTLDAGNIKLAFNSLLEKAEAREREREKEEARKMKRKESAFKSMLKQATPPIELDAVWEDIRERFVKEPAFEDITLESERKRIFKDFMHVLEIFLDELHEHGQLHSMSSWMELYPTISSDIRFTNMLGQPGSTALDLFKFYVEDLKARYHDEKKIIKDILKDKGFVVEVNTTFEDFVAIISSTKRSTTLDAGNIKLAFNSLLEKAEAREREREKEEARKMKRKESAFKSMLKQATPPIELDAVWEDIRERFVKEPAFEDITLESERKRIFKDFMHVLE
IRESfinder result
IRESfinder score
0.686982915
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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