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mmu_circPum3_311
Basic information of circular RNA
PanCircBase ID:
mmu_circPum3_311
mm39_Chr. Position ID:
chr19|27403195|27404528|-
Gene name:
Pum3
Transcript:
ENSMUST00000076219.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,1241
Genomic length:
1333
Exon/intron sizes in nt:
219,92
Flanking exon/introns:
chr19:27401744-27403195|chr19:27404528-27407191
Splice length:
311
Other database IDs:
CIRCpedia: MMU_CIRCpedia_39307, circAtlas: mmu-D19Bwg1357e_0010
circBase: hsa_circ_0009025, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_68069
Human Ortholog IDs:
Mature spliced Sequence:
AAGTACTATGATGGAAGTCAAAGGGAAGAAAAAGTTTACAGGAAAGAGTCCACAGACATCACAAGGAAAGAATAAATTTCATAAGAACAGTGAGTCTAGTTCTTCAAAGACATTCCCAAGGAAAGCTGTTAAGGAAGGCGGACCTAAAGTCACATCTAAGAACTTTGAGAAAGGTGCCACAAAACCTGGCAAGAAAGGTGTGAAGCAGTTCAAGAACAAGCCACAAGGGGGCAAAGGACCGAAGGACAAATTTCAGAAGGCAAATAAATTCAGCAAGAAGCGGAAATTCCAGCCAGATGGTGAAAGTGATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGAACAAGCCACAAGGGGG
60.47
TCCTTGTGATGTCTGTGGACTC
59.7
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGAACAAGCCACAAGGGGG
60.47
CCTTGTGATGTCTGTGGACTCT
59.7
166
PCR template sequence:
AAGAACAAGCCACAAGGGGGCAAAGGACCGAAGGACAAATTTCAGAAGGCAAATAAATTCAGCAAGAAGCGGAAATTCCAGCCAGATGGTGAAAGTGATGAAGTACTATGATGGAAGTCAAAGGGAAGAAAAAGTTTACAGGAAAGAGTCCACAGACATCACAAGGAAAGAATAAATTTCATAAGAACAGTGAGTCTAGT
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-211-5p(1), mmu-miR-204-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGTGAAAGTGATGAAGTACTATGATG
siRNA sets
ATAGTACTTCATCACTTTC, TAGTACTTCATCACTTTCA, AGTACTTCATCACTTTCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPUM3_311_ORF_1
0.7693
0.200616495
0.324387689
315
ORF sequence:
ATGATGGAAGTCAAAGGGAAGAAAAAGTTTACAGGAAAGAGTCCACAGACATCACAAGGAAAGAATAAATTTCATAAGAACAGTGAGTCTAGTTCTTCAAAGACATTCCCAAGGAAAGCTGTTAAGGAAGGCGGACCTAAAGTCACATCTAAGAACTTTGAGAAAGGTGCCACAAAACCTGGCAAGAAAGGTGTGAAGCAGTTCAAGAACAAGCCACAAGGGGGCAAAGGACCGAAGGACAAATTTCAGAAGGCAAATAAATTCAGCAAGAAGCGGAAATTCCAGCCAGATGGTGAAAGTGATGAAGTACTATGA
Peptide sequence:
MMEVKGKKKFTGKSPQTSQGKNKFHKNSESSSSKTFPRKAVKEGGPKVTSKNFEKGATKPGKKGVKQFKNKPQGGKGPKDKFQKANKFSKKRKFQPDGESDEVL
IRESfinder result
IRESfinder score
0.373781966
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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